From ed501be0af8a7483f3f94f24a21ecce967531cdf Mon Sep 17 00:00:00 2001 From: Ravi Bandaru <80599578+ravibandaru-lab@users.noreply.github.com> Date: Fri, 31 Jan 2025 13:50:25 -0600 Subject: [PATCH 1/5] Update _filter_file.py --- src/finaletoolkit/utils/_filter_file.py | 332 +++++++++++------------- 1 file changed, 147 insertions(+), 185 deletions(-) diff --git a/src/finaletoolkit/utils/_filter_file.py b/src/finaletoolkit/utils/_filter_file.py index c174394..c59f89a 100644 --- a/src/finaletoolkit/utils/_filter_file.py +++ b/src/finaletoolkit/utils/_filter_file.py @@ -1,11 +1,63 @@ from __future__ import annotations import tempfile as tf import subprocess -import traceback +import logging import warnings import gzip import pysam +def validate_deprecated_args(old_arg, new_arg, old_name, new_name): + if old_arg is not None: + warnings.warn(f"{old_name} is deprecated. Use {new_name} instead.", + category=DeprecationWarning, + stacklevel=2) + if new_arg is None: + return old_arg + raise ValueError(f'{old_name} and {new_name} cannot both be specified.') + return new_arg + +def validate_input_file(input_file): + valid_suffixes = {".gz", ".bam", ".cram"} + if not any(input_file.endswith(suffix) for suffix in valid_suffixes): + raise ValueError(f"Input file should have one of the following suffixes: {', '.join(valid_suffixes)}") + return next(suffix for suffix in valid_suffixes if input_file.endswith(suffix)) + +def run_subprocess(cmd: str, error_msg: str = "Command failed", verbose: bool = False, logger=None): + try: + if verbose: + logger.info(f"Running: {cmd}") + subprocess.run(cmd, shell=True, check=True) + except subprocess.CalledProcessError as e: + logger.error(f"{error_msg}: {str(e)}") + raise + +def filter_bed_entries(infile, min_length=None, max_length=None, quality_threshold=30): + def get_mapq_col(length): + if len(parts) < 5: + raise ValueError("There are not enough columns in the BED file to determine the MAPQ column") + return 3 if length==5 else 4 + + for line in infile: + if line.startswith('#'): + continue + + parts = line.strip().split('\t') + mapq_column = get_mapq_col(len(parts)) + + try: + start = int(parts[1]) + end = int(parts[2]) + length = end - start + score = float(parts[mapq_column]) + + if ((min_length is None or length >= min_length) and + (max_length is None or length <= max_length) and + score >= quality_threshold): + yield line + + except (ValueError, IndexError): + continue + def filter_file( input_file: str, whitelist_file: str | None = None, @@ -43,7 +95,7 @@ def filter_file( Maximum length for reads/intervals intersect_policy: str, optional Specifies how to determine whether fragments are in interval for - whitelisting and blacklisting functionality.'midpoint' (default) + whitelisting and blacklisting functionality. 'midpoint' (default) calculates the central coordinate of each fragment and only selects the fragment if the midpoint is in the interval. 'any' includes fragments with any overlap with the interval. @@ -63,7 +115,7 @@ def filter_file( output_file : str Path to the filtered output file. """ - + logger = logging.getLogger(__name__) if verbose: print( f""" @@ -79,50 +131,21 @@ def filter_file( verbose: {verbose} """ ) - - # Pass aliases and check for conflicts - if fraction_low is not None and min_length is None: - min_length = fraction_low - warnings.warn("fraction_low is deprecated. Use min_length instead.", - category=DeprecationWarning, - stacklevel=2) - elif fraction_low is not None and min_length is not None: - warnings.warn("fraction_low is deprecated. Use min_length instead.", - category=DeprecationWarning, - stacklevel=2) - raise ValueError( - 'fraction_low and min_length cannot both be specified') - - if fraction_high is not None and max_length is None: - max_length = fraction_high - warnings.warn("fraction_high is deprecated. Use max_length instead.", - category=DeprecationWarning, - stacklevel=2) - elif fraction_high is not None and max_length is not None: - warnings.warn("fraction_high is deprecated. Use max_length instead.", - category=DeprecationWarning, - stacklevel=2) - raise ValueError( - 'fraction_high and max_length cannot both be specified.') + logging.basicConfig(level=logging.INFO) - if input_file.endswith(".gz"): - suffix = ".gz" - elif input_file.endswith(".bgz"): - suffix = ".bgz" - elif input_file.endswith(".bam"): - suffix = ".bam" - elif input_file.endswith(".cram"): - suffix = ".cram" + # Pass aliases and check for conflicts + min_length = validate_deprecated_args(fraction_low, min_length, "fraction_low", "min_length") + max_length = validate_deprecated_args(fraction_high, max_length, "fraction_high", "max_length") + + suffix = validate_input_file(input_file) + + if intersect_policy == "midpoint": + intersect_param = "-f 0.500" + elif intersect_policy == "any": + intersect_param = "" else: - raise ValueError('Input file should have suffix .bam, .cram, .bgz, or .gz') - - # create tempfile to contain filtered output - if output_file is None: - _, output_file = tf.mkstemp(suffix=suffix) - elif not output_file.endswith(suffix) and output_file != '-': - raise ValueError('Output file should share same suffix as input file.') - - intersect = "-f 0.500" if intersect_policy == "midpoint" else "" + raise ValueError("intersect_policy must be 'midpoint' or 'any'") + pysam.set_verbosity(pysam.set_verbosity(0)) with tf.TemporaryDirectory() as temp_dir: @@ -130,156 +153,95 @@ def filter_file( temp_2 = f"{temp_dir}/output2{suffix}" temp_3 = f"{temp_dir}/output3{suffix}" if input_file.endswith(('.bam', '.cram')): - # create temp dir to store intermediate sorted file - if whitelist_file is not None: - try: - subprocess.run( - f"bedtools intersect -abam {input_file} -b {whitelist_file} {intersect} > {temp_1} && samtools index {temp_1}", - shell=True, - check=True) - except Exception as e: - print(e) - traceback.print_exc() - exit(1) + if whitelist_file: + run_subprocess( + f"bedtools intersect -abam {input_file} -b {whitelist_file} {intersect_param} > {temp_1} && " + f"samtools index {temp_1}", + error_msg="Whitelist filtering failed", + verbose=verbose, + logger=logger + ) else: - subprocess.run( - f"cp {input_file} {temp_1}", shell=True, check=True) - if blacklist_file is not None: - try: - subprocess.run( - f"bedtools intersect -abam {temp_1} -b {blacklist_file} -v {intersect} > {temp_2} && samtools index {temp_2}", - shell=True, - check=True) - except Exception: - traceback.print_exc() - exit(1) + run_subprocess(f"cp {input_file} {temp_1}", verbose=verbose, logger=logger) + if blacklist_file: + intersect_param = "-f 0.500" if intersect_policy == "midpoint" else "" + run_subprocess( + f"bedtools intersect -abam {temp_1} -b {blacklist_file} -v {intersect_param} > {temp_2} && " + f"samtools index {temp_2}", + error_msg="Blacklist filtering failed", + verbose=verbose, + logger=logger + ) else: - subprocess.run( - f"mv {temp_1} {temp_2}", shell=True, check=True) - - try: - subprocess.run( - f"samtools view {temp_2} -F 3852 -f 3 -b -h -o {temp_3} -q {quality_threshold} -@ {workers}", - shell=True, - check=True) - except Exception: - traceback.print_exc() - exit(1) + run_subprocess(f"mv {temp_1} {temp_2}", verbose=verbose, logger=logger) + + run_subprocess( + f"samtools view {temp_2} -F 3852 -f 3 -b -h -o {temp_3} -q {quality_threshold} -@ {workers}", + error_msg="Quality filtering failed", + verbose=verbose, + logger=logger + ) - # filter for reads on different reference and length - with pysam.AlignmentFile(temp_3, 'rb',threads=workers//3) as in_file: - with pysam.AlignmentFile( - output_file, 'wb', template=in_file, threads=workers-workers//3) as out_file: + # Length filtering and final output + pysam.set_verbosity(0) + with pysam.AlignmentFile(temp_3, 'rb', threads=workers//3) as in_file: + with pysam.AlignmentFile(output_file, 'wb', template=in_file, threads=workers-workers//3) as out_file: for read in in_file: - if ( - read.reference_name == read.next_reference_name - and (max_length is None - or read.template_length <= max_length) - and (min_length is None - or read.template_length >= min_length) - ): + if (read.reference_name == read.next_reference_name and + (max_length is None or read.template_length <= max_length) and + (min_length is None or read.template_length >= min_length)): out_file.write(read) + out_file.flush() if output_file != '-': - # generate index for output_file - try: - subprocess.run( - f'samtools index {output_file} {output_file}.bai', - shell=True, - check=True + run_subprocess( + f'samtools index {output_file}', + error_msg="Index creation failed", + verbose=verbose, + logger=logger + ) + + elif input_file.endswith('.gz'): + with gzip.open(input_file, 'rt') as infile, open(temp_1, 'w') as outfile: + for line in filter_bed_entries(infile, min_length, max_length, quality_threshold): + outfile.write(line) + outfile.flush() + + if whitelist_file: + intersect_param = "-f 0.500" if intersect_policy == "midpoint" else "" + run_subprocess( + f"bedtools intersect -a {temp_1} -b {whitelist_file} {intersect_param} > {temp_2}", + error_msg="Whitelist filtering failed", + verbose=verbose, + logger=logger ) - except Exception: - traceback.print_exc() - exit(1) - - elif input_file.endswith('.gz') or input_file.endswith('.bgz'): - with gzip.open(input_file, 'r') as infile, open(temp_1, 'w') as outfile: - mapq_column = 0 # 1-index for sanity when comparing with len() - for line in infile: - line = line.decode('utf-8') - parts = line.strip().split('\t') - if len(parts) < max(mapq_column,4) or line.startswith('#'): - continue - - if mapq_column == 0: - if parts[4-1].isnumeric(): - mapq_column = 4 - elif len(parts) >= 5 and parts[5-1].isnumeric(): - mapq_column = 5 - else: - continue - try: - start = int(parts[1]) - end = int(parts[2]) - length = end - start - score = None - try: - score = float(parts[mapq_column-1]) - except ValueError: - pass - - passes_length_restriction = True - - if min_length is not None and length < min_length: - passes_length_restriction = False - - if max_length is not None and length > max_length: - passes_length_restriction = False - - passes_quality_restriction = True - if score is None or score < quality_threshold: - passes_quality_restriction = False - - if passes_length_restriction and passes_quality_restriction: - outfile.write(line) - except ValueError: - continue - if whitelist_file is not None: - try: - subprocess.run( - f"bedtools intersect -a {temp_1} -b {whitelist_file} {intersect} > {temp_2}", - shell=True, - check=True - ) - except Exception: - traceback.print_exc() - exit(1) else: - subprocess.run(f"mv {temp_1} {temp_2}", shell=True, check=True) - - if blacklist_file is not None: - try: - subprocess.run( - f"bedtools intersect -v -a {temp_2} -b {blacklist_file} {intersect} > {temp_3}", - shell=True, - check=True - ) - except Exception: - traceback.print_exc() - exit(1) + run_subprocess(f"mv {temp_1} {temp_2}", verbose=verbose, logger=logger) + + if blacklist_file: + intersect_param = "-f 0.500" if intersect_policy == "midpoint" else "" + run_subprocess( + f"bedtools intersect -v -a {temp_2} -b {blacklist_file} {intersect_param} > {temp_3}", + error_msg="Blacklist filtering failed", + verbose=verbose, + logger=logger + ) else: - subprocess.run(f"mv {temp_2} {temp_3}", shell=True, check=True) - try: - subprocess.run( - f"bgzip -@ {workers} -c {temp_3} > {output_file}", - shell=True, - check=True - ) - except Exception: - traceback.print_exc() - exit(1) + run_subprocess(f"mv {temp_2} {temp_3}", verbose=verbose, logger=logger) + + # Compression and indexing + run_subprocess( + f"bgzip -@ {workers} -c {temp_3} > {output_file}", + error_msg="Compression failed", + verbose=verbose, + logger=logger + ) if output_file != '-': - # generate index for output_file - try: - subprocess.run( - f'tabix -p bed {output_file}', - shell=True, - check=True - ) - except Exception: - traceback.print_exc() - exit(1) - else: - raise ValueError("Input file must be a BAM, CRAM, or bgzipped BED file.") + run_subprocess( + f'tabix -p bed {output_file}', + error_msg="Index creation failed", + verbose=verbose, + logger=logger + ) return output_file From c0041c02beb41aa7a1a9acabbcfb98ec9af8dfd2 Mon Sep 17 00:00:00 2001 From: James Li <58196853+jamesli124@users.noreply.github.com> Date: Sun, 2 Feb 2025 17:18:13 -0500 Subject: [PATCH 2/5] Update _filter_file.py add support for `.bgz` file endings sometimes used by FinaleDB --- src/finaletoolkit/utils/_filter_file.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/finaletoolkit/utils/_filter_file.py b/src/finaletoolkit/utils/_filter_file.py index c59f89a..805fcdd 100644 --- a/src/finaletoolkit/utils/_filter_file.py +++ b/src/finaletoolkit/utils/_filter_file.py @@ -17,7 +17,7 @@ def validate_deprecated_args(old_arg, new_arg, old_name, new_name): return new_arg def validate_input_file(input_file): - valid_suffixes = {".gz", ".bam", ".cram"} + valid_suffixes = {".gz", ".bam", ".cram", ".bgz"} if not any(input_file.endswith(suffix) for suffix in valid_suffixes): raise ValueError(f"Input file should have one of the following suffixes: {', '.join(valid_suffixes)}") return next(suffix for suffix in valid_suffixes if input_file.endswith(suffix)) @@ -201,7 +201,7 @@ def filter_file( logger=logger ) - elif input_file.endswith('.gz'): + elif input_file.endswith('.gz') or input_file.endswith('.bgz'): with gzip.open(input_file, 'rt') as infile, open(temp_1, 'w') as outfile: for line in filter_bed_entries(infile, min_length, max_length, quality_threshold): outfile.write(line) From 23129884a4f3495a58f9d832dba4a9b9692fd4cd Mon Sep 17 00:00:00 2001 From: jamesli124 <58196853+jamesli124@users.noreply.github.com> Date: Sun, 2 Feb 2025 17:27:27 -0500 Subject: [PATCH 3/5] update changelog and version number --- CHANGELOG.md | 4 ++++ src/finaletoolkit/version.py | 2 +- 2 files changed, 5 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 4e9b6e6..122c478 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -12,6 +12,10 @@ and this project adheres to ### Added - Snakemake workflow included in FinaleToolkit documentation. +### Fixed +- Issue with `filter-file` where the lack of `output_file.flush()` would +create incorrect outputs. + ## [0.10.6] - 2025-1-14 ### Fixed diff --git a/src/finaletoolkit/version.py b/src/finaletoolkit/version.py index ab71ebd..63e65a0 100644 --- a/src/finaletoolkit/version.py +++ b/src/finaletoolkit/version.py @@ -2,4 +2,4 @@ Single-source module for the package version number. """ -__version__ = "0.10.6" +__version__ = "0.10.7" From e2feba7891e04757c7088337b26318833322ac2e Mon Sep 17 00:00:00 2001 From: jamesli124 <58196853+jamesli124@users.noreply.github.com> Date: Sun, 2 Feb 2025 17:28:08 -0500 Subject: [PATCH 4/5] update docs --- .../api_reference/basicfeatures.doctree | Bin 91172 -> 90956 bytes .../api_reference/cleavageprofile.doctree | Bin 32089 -> 30431 bytes .../documentation/api_reference/delfi.doctree | Bin 43524 -> 44920 bytes .../api_reference/endmotifs.doctree | Bin 183122 -> 182193 bytes .../api_reference/fragfile.doctree | Bin 137225 -> 136820 bytes .../api_reference/genomeutils.doctree | Bin 80502 -> 80099 bytes .../documentation/api_reference/index.doctree | Bin 3094 -> 3094 bytes .../documentation/api_reference/wps.doctree | Bin 101598 -> 98876 bytes .../documentation/cli_reference/index.doctree | Bin 255822 -> 248580 bytes .../doctrees/documentation/index.doctree | Bin 3184 -> 3184 bytes .../documentation/user_guide/features.doctree | Bin 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.../documentation/api_reference/index.html | 6 +- .../html/documentation/api_reference/wps.html | 10 +- .../documentation/cli_reference/index.html | 306 +++++++++--------- docs/_build/html/documentation/index.html | 6 +- .../documentation/user_guide/features.html | 6 +- .../html/documentation/user_guide/help.html | 6 +- .../html/documentation/user_guide/index.html | 6 +- .../documentation/user_guide/inputdata.html | 6 +- .../user_guide/installation.html | 6 +- .../user_guide/intersectpolicy.html | 6 +- .../documentation/user_guide/quickstart.html | 10 +- .../documentation/user_guide/structure.html | 6 +- .../html/documentation/user_guide/what.html | 6 +- .../workflow_reference/dependencies.html | 6 +- .../workflow_reference/filter_file.html | 7 +- .../finaletoolkit_commands.html | 7 +- .../workflow_reference/index.html | 6 +- .../workflow_reference/installation.html | 6 +- .../workflow_reference/key_features.html | 13 +- .../mappability_filtering.html | 7 +- 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const [docname, title, anchor, descr, score, filename, kind] = result + const [docname, title, anchor, descr, score, filename] = result return score }, */ @@ -40,14 +47,6 @@ if (typeof Scorer === "undefined") { }; } -// Global search result kind enum, used by themes to style search results. -class SearchResultKind { - static get index() { return "index"; } - static get object() { return "object"; } - static get text() { return "text"; } - static get title() { return "title"; } -} - const _removeChildren = (element) => { while (element && element.lastChild) element.removeChild(element.lastChild); }; @@ -65,13 +64,9 @@ const _displayItem = (item, searchTerms, highlightTerms) => { const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY; const contentRoot = document.documentElement.dataset.content_root; - const [docName, title, anchor, descr, score, _filename, kind] = item; + const [docName, title, anchor, descr, score, _filename] = item; let listItem = document.createElement("li"); - // Add a class representing the item's type: - // can be used by a theme's CSS selector for styling - // See SearchResultKind for the class names. - listItem.classList.add(`kind-${kind}`); let requestUrl; let linkUrl; if (docBuilder === "dirhtml") { @@ -120,10 +115,8 @@ const _finishSearch = (resultCount) => { "Your search did not match any documents. Please make sure that all words are spelled correctly and that you've selected enough categories." ); else - Search.status.innerText = Documentation.ngettext( - "Search finished, found one page matching the search query.", - "Search finished, found ${resultCount} pages matching the search query.", - resultCount, + Search.status.innerText = _( + "Search finished, found ${resultCount} page(s) matching the search query." ).replace('${resultCount}', resultCount); }; const _displayNextItem = ( @@ -145,7 +138,7 @@ const _displayNextItem = ( else _finishSearch(resultCount); }; // Helper function used by query() to order search results. -// Each input is an array of [docname, title, anchor, descr, score, filename, kind]. +// Each input is an array of [docname, title, anchor, descr, score, filename]. // Order the results by score (in opposite order of appearance, since the // `_displayNextItem` function uses pop() to retrieve items) and then alphabetically. const _orderResultsByScoreThenName = (a, b) => { @@ -255,7 +248,6 @@ const Search = { searchSummary.classList.add("search-summary"); searchSummary.innerText = ""; const searchList = document.createElement("ul"); - searchList.setAttribute("role", "list"); searchList.classList.add("search"); const out = document.getElementById("search-results"); @@ -326,7 +318,7 @@ const Search = { const indexEntries = Search._index.indexentries; // Collect multiple result groups to be sorted separately and then ordered. - // Each is an array of [docname, title, anchor, descr, score, filename, kind]. + // Each is an array of [docname, title, anchor, descr, score, filename]. const normalResults = []; const nonMainIndexResults = []; @@ -345,7 +337,6 @@ const Search = { null, score + boost, filenames[file], - SearchResultKind.title, ]); } } @@ -363,7 +354,6 @@ const Search = { null, score, filenames[file], - SearchResultKind.index, ]; if (isMain) { normalResults.push(result); @@ -485,7 +475,6 @@ const Search = { descr, score, filenames[match[0]], - SearchResultKind.object, ]); }; Object.keys(objects).forEach((prefix) => @@ -596,7 +585,6 @@ const Search = { null, score, filenames[file], - SearchResultKind.text, ]); } return results; diff --git a/docs/_build/html/documentation/api_reference/basicfeatures.html b/docs/_build/html/documentation/api_reference/basicfeatures.html index 90834a6..41bcd39 100644 --- a/docs/_build/html/documentation/api_reference/basicfeatures.html +++ b/docs/_build/html/documentation/api_reference/basicfeatures.html @@ -30,7 +30,7 @@ - + @@ -39,7 +39,7 @@ - + @@ -376,7 +376,7 @@

Basic Features#

-finaletoolkit.frag.coverage(input_file: str | TabixFile | AlignmentFile | Path, interval_file: str, output_file: str, scale_factor: float = 1.0, min_length: int | None = None, max_length: int | None = None, normalize: bool = False, intersect_policy: str = 'midpoint', quality_threshold: int = 30, workers: int = 1, verbose: bool | int = False) → list[tuple[str, int, int, str, float]]#
+finaletoolkit.frag.coverage(input_file: str | pysam.TabixFile | pysam.AlignmentFile | Path, interval_file: str, output_file: str, scale_factor: float = 1.0, min_length: int | None = None, max_length: int | None = None, normalize: bool = False, intersect_policy: str = 'midpoint', quality_threshold: int = 30, workers: int = 1, verbose: bool | int = False) → list[tuple[str, int, int, str, float]]#

Return estimated fragment coverage over intervals specified in intervals. Fragments are read from input_file which may be a BAM, CRAM, or fragment file. Uses an algorithm where the @@ -418,7 +418,7 @@

Basic Features
-finaletoolkit.frag.frag_length(input_file: str | AlignmentFile | TabixFile, contig: str | None = None, start: int | None = None, stop: int | None = None, intersect_policy: str = 'midpoint', output_file: str | None = None, quality_threshold: int = 30, verbose: bool = False) → ndarray#
+finaletoolkit.frag.frag_length(input_file: str | pysam.AlignmentFile | pysam.TabixFile, contig: str | None = None, start: int | None = None, stop: int | None = None, intersect_policy: str = 'midpoint', output_file: str | None = None, quality_threshold: int = 30, verbose: bool = False) → np.ndarray#

Return np.ndarray containing lengths of fragments in input_file that are above the quality threshold and are proper-paired reads.

@@ -451,7 +451,7 @@

Basic Features
-finaletoolkit.frag.frag_length_bins(input_file: str | AlignmentFile, contig: str | None = None, start: int | None = None, stop: int | None = None, min_length: int | None = 0, max_length: int | None = None, bin_size: int = 1, output_file: str | None = None, intersect_policy: str = 'midpoint', quality_threshold: int = 30, histogram_path: str | None = None, verbose: bool | int = False) → tuple[ndarray, ndarray]#
+finaletoolkit.frag.frag_length_bins(input_file: str | pysam.AlignmentFile, contig: str | None = None, start: int | None = None, stop: int | None = None, min_length: int | None = 0, max_length: int | None = None, bin_size: int = 1, output_file: str | None = None, intersect_policy: str = 'midpoint', quality_threshold: int = 30, histogram_path: str | None = None, verbose: bool | int = False) → tuple[np.ndarray, np.ndarray]#

Takes input_file, computes frag lengths of fragments and returns two arrays containing bins and counts by size. Optionally prints data to output as a tab delimited table or histogram.

@@ -580,7 +580,7 @@

This Page

- Created using Sphinx 8.1.3. + Created using Sphinx 7.4.7.

diff --git a/docs/_build/html/documentation/api_reference/cleavageprofile.html b/docs/_build/html/documentation/api_reference/cleavageprofile.html index 2f35145..59def8d 100644 --- a/docs/_build/html/documentation/api_reference/cleavageprofile.html +++ b/docs/_build/html/documentation/api_reference/cleavageprofile.html @@ -30,7 +30,7 @@ - + @@ -39,7 +39,7 @@ - + @@ -376,7 +376,7 @@

Cleavage Profile#

-finaletoolkit.frag.cleavage_profile(input_file: str | PathLike | AlignmentFile | TabixFile, chrom_size: int, contig: str, start: int, stop: int, left: int = 0, right: int = 0, min_length: int | None = None, max_length: int | None = None, quality_threshold: int = 30, verbose: bool | int = 0, fraction_low: int | None = None, fraction_high: int | None = None) → ndarray#
+finaletoolkit.frag.cleavage_profile(input_file: FragFile, chrom_size: int, contig: str, start: int, stop: int, left: int = 0, right: int = 0, min_length: int | None = None, max_length: int | None = None, quality_threshold: int = 30, verbose: bool | int = 0, fraction_low: int | None = None, fraction_high: int | None = None) → np.ndarray#

Cleavage profile calculated over a single interval.

Parameters:
@@ -502,7 +502,7 @@

This Page

- Created using Sphinx 8.1.3. + Created using Sphinx 7.4.7.

diff --git a/docs/_build/html/documentation/api_reference/delfi.html b/docs/_build/html/documentation/api_reference/delfi.html index 1266d7a..a35469b 100644 --- a/docs/_build/html/documentation/api_reference/delfi.html +++ b/docs/_build/html/documentation/api_reference/delfi.html @@ -30,7 +30,7 @@ - + @@ -39,7 +39,7 @@ - + @@ -376,7 +376,7 @@

DELFI#

-finaletoolkit.frag.delfi(input_file: str, chrom_sizes: str, bins_file: str, reference_file: str, blacklist_file: str = None, gap_file: str | GenomeGaps = None, output_file: str = None, gc_correct: bool = True, remove_nocov: bool = True, merge_bins: bool = True, window_size: int = 5000000, quality_threshold: int = 30, workers: int = 1, verbose: int | bool = False) → DataFrame#
+finaletoolkit.frag.delfi(input_file: str, chrom_sizes: str, bins_file: str, reference_file: str, blacklist_file: str | None = None, gap_file: str | GenomeGaps | None = None, output_file: str | None = None, gc_correct: bool = True, remove_nocov: bool = True, merge_bins: bool = True, window_size: int = 5000000, quality_threshold: int = 30, workers: int = 1, verbose: int | bool = False) → DataFrame#

A function that replicates the methodology of Christiano et al (2019).

@@ -533,7 +533,7 @@

This Page

- Created using Sphinx 8.1.3. + Created using Sphinx 7.4.7.

diff --git a/docs/_build/html/documentation/api_reference/endmotifs.html b/docs/_build/html/documentation/api_reference/endmotifs.html index cc520b9..4798449 100644 --- a/docs/_build/html/documentation/api_reference/endmotifs.html +++ b/docs/_build/html/documentation/api_reference/endmotifs.html @@ -30,7 +30,7 @@ - + @@ -39,7 +39,7 @@ - + @@ -391,7 +391,7 @@

End-Motifs
-classmethod from_file(file_path: str | Path, quality_threshold: int, sep: str = '\t', header: int = 0) → EndMotifFreqs#
+classmethod from_file(file_path: str | Path, quality_threshold: int, sep: str = '\t', header: int = 0) → EndMotifFreqs#

Reads kmer frequency from a two-column tab-delimited file.

Parameters:
@@ -579,7 +579,7 @@

End-Motifs
-finaletoolkit.frag.end_motifs(input_file: str, refseq_file: str | Path, k: int = 4, min_length: int = 10, max_length: int = 600, both_strands: bool = True, negative_strand: bool = False, output_file: None | str = None, quality_threshold: int = 30, workers: int = 1, verbose: bool | int = False, fraction_low: int | None = None, fraction_high: int | None = None) → EndMotifFreqs#
+finaletoolkit.frag.end_motifs(input_file: str, refseq_file: str | Path, k: int = 4, min_length: int = 10, max_length: int = 600, both_strands: bool = True, negative_strand: bool = False, output_file: None | str = None, quality_threshold: int = 30, workers: int = 1, verbose: bool | int = False, fraction_low: int | None = None, fraction_high: int | None = None) → EndMotifFreqs#

Function that reads fragments from a BAM, CRAM, or tabix indexed file and returns the 5’ k-mer (default is 4-mer) end motif frequencies as a dictionary. Optionally writes data to a tsv. This @@ -619,7 +619,7 @@

End-Motifs
-finaletoolkit.frag.interval_end_motifs(input_file: str, refseq_file: str | Path, intervals: str | Iterable[tuple[str, int, int, str]], k: int = 4, min_length: int | None = 10, max_length: int | None = 600, both_strands: bool = True, negative_strand: bool = False, output_file: str | None = None, quality_threshold: int = 30, workers: int = 1, verbose: bool | int = False, fraction_low: int | None = None, fraction_high: int | None = None) → EndMotifsIntervals#
+finaletoolkit.frag.interval_end_motifs(input_file: str, refseq_file: str | Path, intervals: str | Iterable[tuple[str, int, int, str]], k: int = 4, min_length: int | None = 10, max_length: int | None = 600, both_strands: bool = True, negative_strand: bool = False, output_file: str | None = None, quality_threshold: int = 30, workers: int = 1, verbose: bool | int = False, fraction_low: int | None = None, fraction_high: int | None = None) → EndMotifsIntervals#

Function that reads fragments from a BAM, CRAM, or tabix indexed file and user-specified intervals and returns the 5’ k-mer (default is 4-mer) end motif. Optionally writes data to a tsv.

@@ -766,7 +766,7 @@

This Page

- Created using Sphinx 8.1.3. + Created using Sphinx 7.4.7.

diff --git a/docs/_build/html/documentation/api_reference/fragfile.html b/docs/_build/html/documentation/api_reference/fragfile.html index b1aa998..0114b63 100644 --- a/docs/_build/html/documentation/api_reference/fragfile.html +++ b/docs/_build/html/documentation/api_reference/fragfile.html @@ -30,7 +30,7 @@ - + @@ -39,7 +39,7 @@ - + @@ -376,7 +376,7 @@

Frag File Utilities#

-finaletoolkit.utils.filter_file(input_file: str, whitelist_file: str | None = None, blacklist_file: str | None = None, output_file: str | None = None, min_length: int | None = None, max_length: int | None = None, quality_threshold: int = 30, workers: int = 1, verbose: bool = False, fraction_low: int | None = None, fraction_high: int | None = None)#
+finaletoolkit.utils.filter_file(input_file: str, whitelist_file: str | None = None, blacklist_file: str | None = None, output_file: str | None = None, min_length: int | None = None, max_length: int | None = None, intersect_policy: str = 'midpoint', quality_threshold: int = 30, workers: int = 1, verbose: bool = False, fraction_low: int | None = None, fraction_high: int | None = None)#

Accepts the path to a BAM, CRAM, or BED file and creates a filtered version.

Filter reads/intervals based on exceeding the specified quality threshold, intersections with a region in the region bed (if provided), and read length.

@@ -390,6 +390,11 @@

Frag File Utilities
-finaletoolkit.utils.frag_array(input_file: str | PathLike | AlignmentFile | TabixFile, contig: str, quality_threshold: int = 30, start: int | None = None, stop: int | None = None, min_length: int | None = None, max_length: int | None = None, intersect_policy: str = 'midpoint', verbose: bool = False) → ndarray[Any, dtype[_ScalarType_co]]#
+finaletoolkit.utils.frag_array(input_file: FragFile, contig: str, quality_threshold: int = 30, start: int | None = None, stop: int | None = None, min_length: int | None = None, max_length: int | None = None, intersect_policy: str = 'midpoint', verbose: bool = False) → NDArray#

Reads from BAM, CRAM, or fragment file and returns a three column matrix with fragment start and stop positions and strand.

@@ -693,7 +698,7 @@

This Page

- Created using Sphinx 8.1.3. + Created using Sphinx 7.4.7.

diff --git a/docs/_build/html/documentation/api_reference/genomeutils.html b/docs/_build/html/documentation/api_reference/genomeutils.html index 63ac15c..5adfe72 100644 --- a/docs/_build/html/documentation/api_reference/genomeutils.html +++ b/docs/_build/html/documentation/api_reference/genomeutils.html @@ -30,7 +30,7 @@ - + @@ -39,7 +39,7 @@ - + @@ -750,7 +750,7 @@

This Page

- Created using Sphinx 8.1.3. + Created using Sphinx 7.4.7.

diff --git a/docs/_build/html/documentation/api_reference/index.html b/docs/_build/html/documentation/api_reference/index.html index 00d42f2..bbaec29 100644 --- a/docs/_build/html/documentation/api_reference/index.html +++ b/docs/_build/html/documentation/api_reference/index.html @@ -30,7 +30,7 @@ - + @@ -39,7 +39,7 @@ - + @@ -508,7 +508,7 @@

This Page

- Created using Sphinx 8.1.3. + Created using Sphinx 7.4.7.

diff --git a/docs/_build/html/documentation/api_reference/wps.html b/docs/_build/html/documentation/api_reference/wps.html index 78f8933..d362640 100644 --- a/docs/_build/html/documentation/api_reference/wps.html +++ b/docs/_build/html/documentation/api_reference/wps.html @@ -30,7 +30,7 @@ - + @@ -39,7 +39,7 @@ - + @@ -376,7 +376,7 @@

Window Protection Score (WPS)#

-finaletoolkit.frag.wps(input_file: str | AlignmentFile, chrom: str, start: int, stop: int, chrom_size: int, output_file: str | None = None, window_size: int = 120, min_length: int = 120, max_length: int = 180, quality_threshold: int = 30, verbose: bool | int = 0, fraction_low: int | None = None, fraction_high: int | None = None) → ndarray#
+finaletoolkit.frag.wps(input_file: str | pysam.AlignmentFile, chrom: str, start: int, stop: int, chrom_size: int, output_file: str | None = None, window_size: int = 120, min_length: int = 120, max_length: int = 180, quality_threshold: int = 30, verbose: bool | int = 0, fraction_low: int | None = None, fraction_high: int | None = None) → np.ndarray#

Return (raw) Windowed Protection Scores as specified in Snyder et al (2016) over a region [start,stop).

@@ -413,7 +413,7 @@

Window Protection Score (WPS)
-finaletoolkit.frag.multi_wps(input_file: str | PathLike | AlignmentFile | TabixFile, site_bed: str | PathLike, chrom_sizes: str | PathLike | None = None, output_file: str | None = None, window_size: int = 120, interval_size: int = 5000, min_length: int = 120, max_length: int = 180, quality_threshold: int = 30, workers: int = 1, verbose: bool | int = 0, fraction_low: int | None = None, fraction_high: int | None = None)#
+finaletoolkit.frag.multi_wps(input_file: FragFile, site_bed: Intervals, chrom_sizes: ChromSizes | None = None, output_file: str | None = None, window_size: int = 120, interval_size: int = 5000, min_length: int = 120, max_length: int = 180, quality_threshold: int = 30, workers: int = 1, verbose: bool | int = 0, fraction_low: int | None = None, fraction_high: int | None = None)#

Function that aggregates WPS over sites in BED file according to the method described by Snyder et al (2016).

@@ -586,7 +586,7 @@

This Page

- Created using Sphinx 8.1.3. + Created using Sphinx 7.4.7.

diff --git a/docs/_build/html/documentation/cli_reference/index.html b/docs/_build/html/documentation/cli_reference/index.html index da0d4c1..5a22516 100644 --- a/docs/_build/html/documentation/cli_reference/index.html +++ b/docs/_build/html/documentation/cli_reference/index.html @@ -30,7 +30,7 @@ - + @@ -39,7 +39,7 @@ - + @@ -369,8 +369,8 @@

CLI#

... -
-

Named Arguments#

+
+

Named Arguments#

-v, --version

show program’s version number and exit

@@ -382,7 +382,8 @@

Sub-commands

coverage#

Calculates fragmentation coverage over intervals defined in a BED file based on alignment data from a BAM/CRAM/Fragment file.

-
finaletoolkit coverage [-h] [-o OUTPUT_FILE] [-n] [-s SCALE_FACTOR] [-min MIN_LENGTH] [-max MAX_LENGTH] [-p {midpoint,any}] [-q QUALITY_THRESHOLD] [-w WORKERS] [-v]
+
finaletoolkit coverage [-h] [-o OUTPUT_FILE] [-n] [-s SCALE_FACTOR] [-min MIN_LENGTH] [-max MAX_LENGTH] [-p {midpoint,any}]
+                       [-q QUALITY_THRESHOLD] [-w WORKERS] [-v]
                        input_file interval_file
 

 

@@ -397,24 +398,24 @@ 
Positional Arguments

-
-

Named Arguments#

+
+

Named Arguments#

-o, --output-file

A BED file containing coverage values over the intervals specified in interval file.

-

Default: '-'

+

Default: “-”

-n, --normalize

If flag set, multiplies by user inputed scale factor if given and normalizes output by total coverage. May lead to longer execution time for high-throughput data.

-

Default: False

+

Default: False

-s, --scale-factor

Scale factor for coverage values. Default is 1.

-

Default: 1.0

+

Default: 1.0

-min, --min-length

Minimum length for a fragment to be included in coverage.

-

Default: 0

+

Default: 0

-max, --max-length

Maximum length for a fragment to be included in coverage.

@@ -422,19 +423,19 @@

Named Arguments'midpoint'

+

Default: “midpoint”

-q, --quality-threshold

Minimum mapping quality threshold.

-

Default: 30

+

Default: 30

-w, --workers

Number of worker processes.

-

Default: 1

+

Default: 1

-v, --verbose

Enable verbose mode to display detailed processing information.

-

Default: False

+

Default: False

@@ -442,8 +443,9 @@

Named Arguments

frag-length-bins#

Retrieves fragment lengths grouped in bins given a BAM/CRAM/Fragment file.

-
finaletoolkit frag-length-bins [-h] [-c CONTIG] [-S START] [-E STOP] [-min MIN_LENGTH] [-max MAX_LENGTH] [-p {midpoint,any}] [--bin-size BIN_SIZE] [-o OUTPUT_FILE]
-                               [--histogram-path HISTOGRAM_PATH] [-q QUALITY_THRESHOLD] [-v]
+
finaletoolkit frag-length-bins [-h] [-c CONTIG] [-S START] [-E STOP] [-min MIN_LENGTH] [-max MAX_LENGTH] [-p {midpoint,any}]
+                               [--bin-size BIN_SIZE] [-o OUTPUT_FILE] [--histogram-path HISTOGRAM_PATH] [-q QUALITY_THRESHOLD]
+                               [-v]
                                input_file
 

 

@@ -455,8 +457,8 @@ 
Positional Arguments
-
Named Arguments#

+

+
Named Arguments#

 

 
-c, --contig

 
Specify the contig or chromosome to select fragments from. (Required if using –start or –stop.)

@@ -469,7 +471,7 @@ 
Named Arguments0

+
Default: 0

 

 
-max, --max-length

 
Maximum length for a fragment to be included in fragment length.

@@ -477,26 +479,26 @@ 
Named Arguments'midpoint'

+
Default: “midpoint”

 

 
--bin-size

 
Specify the size of the bins to group fragment lengths into.

-
Default: 1

+
Default: 1

 

 
-o, --output-file

 
A .TSV file containing containing fragment lengths binned according to the specified bin size.

-
Default: '-'

+
Default: “-”

 

 
--histogram-path

 
Path to store histogram.

 

 
-q, --quality-threshold

 
Minimum mapping quality threshold.

-
Default: 30

+
Default: 30

 

 
-v, --verbose

 
Enable verbose mode to display detailed processing information.

-
Default: 0

+
Default: 0

 

 

 

@@ -504,7 +506,9 @@ 
Named Arguments
 
frag-length-intervals#

 
Retrieves fragment length summary statistics over intervals defined in a BED file based on alignment data from a BAM/CRAM/Fragment file.

-
finaletoolkit frag-length-intervals [-h] [-min MIN_LENGTH] [-max MAX_LENGTH] [-p {midpoint,any}] [-o OUTPUT_FILE] [-q QUALITY_THRESHOLD] [-w WORKERS] [-v] input_file interval_file
+
finaletoolkit frag-length-intervals [-h] [-min MIN_LENGTH] [-max MAX_LENGTH] [-p {midpoint,any}] [-o OUTPUT_FILE]
+                                    [-q QUALITY_THRESHOLD] [-w WORKERS] [-v]
+                                    input_file interval_file
 

 

 

@@ -518,12 +522,12 @@ 
Positional Arguments
-
Named Arguments#

+

+
Named Arguments#

 

 
-min, --min-length

 
Minimum length for a fragment to be included in fragment length.

-
Default: 0

+
Default: 0

 

 
-max, --max-length

 
Maximum length for a fragment to be included in fragment length.

@@ -531,23 +535,23 @@ 
Named Arguments'midpoint'

+
Default: “midpoint”

 

 
-o, --output-file

 
A BED file containing fragment length summary statistics (mean, median, st. dev, min, max) over the intervals specified in the interval file.

-
Default: '-'

+
Default: “-”

 

 
-q, --quality-threshold

 
Minimum mapping quality threshold.

-
Default: 30

+
Default: 30

 

 
-w, --workers

 
Number of worker processes.

-
Default: 1

+
Default: 1

 

 
-v, --verbose

 
Enable verbose mode to display detailed processing information.

-
Default: 0

+
Default: 0

 

 

 

@@ -555,8 +559,8 @@ 
Named Arguments
 
cleavage-profile#

 
Calculates cleavage proportion over intervals defined in a BED file based on alignment data from a BAM/CRAM/Fragment file.

-
finaletoolkit cleavage-profile [-h] [-c CHROM_SIZES] [-o OUTPUT_FILE] [-min MIN_LENGTH] [-max MAX_LENGTH] [-lo MIN_LENGTH] [-hi MAX_LENGTH] [-q QUALITY_THRESHOLD] [-l LEFT] [-r RIGHT]
-                               [-w WORKERS] [-v]
+
finaletoolkit cleavage-profile [-h] [-c CHROM_SIZES] [-o OUTPUT_FILE] [-min MIN_LENGTH] [-max MAX_LENGTH] [-lo MIN_LENGTH]
+                               [-hi MAX_LENGTH] [-q QUALITY_THRESHOLD] [-l LEFT] [-r RIGHT] [-w WORKERS] [-v]
                                input_file interval_file
 

 

@@ -571,19 +575,19 @@ 
Positional Arguments
-
Named Arguments#

+

+
Named Arguments#

 

 
-c, --chrom-sizes

 
A .chrom.sizes file containing chromosome names and sizes.

 

 
-o, --output-file

 
A bigWig file containing the cleavage proportion results over the intervals specified in interval file.

-
Default: '-'

+
Default: “-”

 

 
-min, --min-length

 
Minimum length for a fragment to be included.

-
Default: 0

+
Default: 0

 

 
-max, --max-length

 
Maximum length for a fragment to be included.

@@ -596,23 +600,23 @@ 
Named Arguments20

+
Default: 20

 

 
-l, --left

 
Number of base pairs to subtract from start coordinate to create interval. Useful when dealing with BED files with only CpG coordinates. Default is 0.

-
Default: 0

+
Default: 0

 

 
-r, --right

 
Number of base pairs to add to stop coordinate to create interval. Useful when dealing with BED files with only CpG coordinates. Default is 0.

-
Default: 0

+
Default: 0

 

 
-w, --workers

 
Number of worker processes.

-
Default: 1

+
Default: 1

 

 
-v, --verbose

 
Enable verbose mode to display detailed processing information.

-
Default: 0

+
Default: 0

 

 

 

@@ -620,8 +624,8 @@ 
Named Arguments
 
wps#

 
Calculates Windowed Protection Score (WPS) over intervals defined in a BED file based on alignment data from a BAM/CRAM/Fragment file.

-
finaletoolkit wps [-h] [-c CHROM_SIZES] [-o OUTPUT_FILE] [-i INTERVAL_SIZE] [-W WINDOW_SIZE] [-min MIN_LENGTH] [-max MAX_LENGTH] [-lo MIN_LENGTH] [-hi MAX_LENGTH] [-q QUALITY_THRESHOLD]
-                  [-w WORKERS] [-v]
+
finaletoolkit wps [-h] [-c CHROM_SIZES] [-o OUTPUT_FILE] [-i INTERVAL_SIZE] [-W WINDOW_SIZE] [-min MIN_LENGTH]
+                  [-max MAX_LENGTH] [-lo MIN_LENGTH] [-hi MAX_LENGTH] [-q QUALITY_THRESHOLD] [-w WORKERS] [-v]
                   input_file site_bed
 

 

@@ -636,31 +640,31 @@ 
Positional Arguments
-
Named Arguments#

+

+
Named Arguments#

 

 
-c, --chrom-sizes

 
A .chrom.sizes file containing chromosome names and sizes.

 

 
-o, --output-file

 
A bigWig file containing the WPS results over the intervals specified in interval file.

-
Default: '-'

+
Default: “-”

 

 
-i, --interval-size

 
Size in bp of the intervals to calculate WPS over. Thesenew intervals are centered over those specified in the site_bed.Default is 5000

-
Default: 5000

+
Default: 5000

 

 
-W, --window-size

 
Size of the sliding window used to calculate WPS scores. Default is 120

-
Default: 120

+
Default: 120

 

 
-min, --min-length

 
Minimum length for a fragment to be included. Default is 120, corresponding to L-WPS.

-
Default: 120

+
Default: 120

 

 
-max, --max-length

 
Maximum length for a fragment to be included. Default is 180, corresponding to L-WPS.

-
Default: 180

+
Default: 180

 

 
-lo, --fraction_low

 
Minimum length for a fragment to be included in WPS calculation. Deprecated. Use –min-length instead.

@@ -670,15 +674,15 @@ 
Named Arguments30

+
Default: 30

 

 
-w, --workers

 
Number of worker processes.

-
Default: 1

+
Default: 1

 

 
-v, --verbose

 
Enable verbose mode to display detailed processing information.

-
Default: 0

+
Default: 0

 

 

 

@@ -686,8 +690,8 @@ 
Named Arguments
 
adjust-wps#

 
Adjusts raw Windowed Protection Score (WPS) by applying a median filter and Savitsky-Golay filter.

-
finaletoolkit adjust-wps [-h] [-o OUTPUT_FILE] [-i INTERVAL_SIZE] [-m MEDIAN_WINDOW_SIZE] [-s SAVGOL_WINDOW_SIZE] [-p SAVGOL_POLY_DEG] [-S] [-w WORKERS] [--mean] [--subtract-edges]
-                         [--edge-size EDGE_SIZE] [-v]
+
finaletoolkit adjust-wps [-h] [-o OUTPUT_FILE] [-i INTERVAL_SIZE] [-m MEDIAN_WINDOW_SIZE] [-s SAVGOL_WINDOW_SIZE]
+                         [-p SAVGOL_POLY_DEG] [-S] [-w WORKERS] [--mean] [--subtract-edges] [--edge-size EDGE_SIZE] [-v]
                          input_file interval_file chrom_sizes
 

 

@@ -705,48 +709,48 @@ 
Positional Arguments
-
Named Arguments#

+

+
Named Arguments#

 

 
-o, --output-file

 
A bigWig file containing the adjusted WPS results over the intervals specified in interval file.

-
Default: '-'

+
Default: “-”

 

 
-i, --interval_size

 
Size in bp of each interval in the interval file.

-
Default: 5000

+
Default: 5000

 

 
-m, --median-window-size

 
Size of the median filter or mean filter window used to adjust WPS scores.

-
Default: 1000

+
Default: 1000

 

 
-s, --savgol-window-size

 
Size of the Savitsky-Golay filter window used to adjust WPS scores.

-
Default: 21

+
Default: 21

 

 
-p, --savgol-poly-deg

 
Degree polynomial for Savitsky-Golay filter.

-
Default: 2

+
Default: 2

 

 
-S, --exclude-savgol

 
Do not perform Savitsky-Golay filteringscores.

-
Default: True

+
Default: True

 

 
-w, --workers

 
Number of worker processes.

-
Default: 1

+
Default: 1

 

 
--mean

 
A mean filter is used instead of median.

-
Default: False

+
Default: False

 

 
--subtract-edges

 
Take the median of the first and last 500 bases in a window and subtract from the whole interval.

-
Default: False

+
Default: False

 

 
--edge-size

 
size of the edge subtracted from ends of window when –subtract-edges is set. Default is 500.

-
Default: 500

+
Default: 500

 

 
-v, --verbose

 
Enable verbose mode to display detailed processing information.

@@ -757,7 +761,8 @@ 
Named Arguments
 
delfi#

 
Calculates DELFI features over genome, returning information about (GC-corrected) short fragments, long fragments, DELFI ratio, and total fragments.

-
finaletoolkit delfi [-h] [-b BLACKLIST_FILE] [-g GAP_FILE] [-o OUTPUT_FILE] [-G] [-R] [-M] [-s WINDOW_SIZE] [-q QUALITY_THRESHOLD] [-w WORKERS] [-v]
+
finaletoolkit delfi [-h] [-b BLACKLIST_FILE] [-g GAP_FILE] [-o OUTPUT_FILE] [-G] [-R] [-M] [-s WINDOW_SIZE]
+                    [-q QUALITY_THRESHOLD] [-w WORKERS] [-v]
                     input_file chrom_sizes reference_file bins_file
 

 

@@ -778,8 +783,8 @@ 
Positional Arguments
-
Named Arguments#

+

+
Named Arguments#

 

 
-b, --blacklist-file

 
BED file containing regions to ignore when calculating DELFI.

@@ -789,35 +794,35 @@ 
Named Arguments'-'

+
Default: “-”

 

 
-G, --no-gc-correct

 
Skip GC correction.

-
Default: True

+
Default: True

 

 
-R, --keep-nocov

 
Skip removal two regions in hg19 with no coverage. Use this flag when not using hg19 human reference genome.

-
Default: True

+
Default: True

 

 
-M, --no-merge-bins

 
Keep 100kb bins and do not merge to 5Mb size.

-
Default: True

+
Default: True

 

 
-s, --window-size

 
Specify size of large genomic intervals to merge smaller 100kb intervals (or whatever the user specified in bins_file) into. Defaultis 5000000

-
Default: 5000000

+
Default: 5000000

 

 
-q, --quality-threshold

 
Minimum mapping quality threshold.

-
Default: 30

+
Default: 30

 

 
-w, --workers

 
Number of worker processes.

-
Default: 1

+
Default: 1

 

 
-v, --verbose

 
Enable verbose mode to display detailed processing information.

-
Default: 0

+
Default: 0

 

 

 

@@ -836,16 +841,16 @@ 
Positional Arguments
-
Named Arguments#

+

+
Named Arguments#

 

 
-o, --output-file

 
BED to print GC-corrected DELFI fractions. If “-”, will write to stdout.

-
Default: '-'

+
Default: “-”

 

 
--header-lines

 
Number of header lines in BED.

-
Default: 1

+
Default: 1

 

 
-v, --verbose

 
Enable verbose mode to display detailed processing information.

@@ -856,7 +861,9 @@ 
Named Arguments
 
end-motifs#

 
Measures frequency of k-mer 5’ end motifs.

-
finaletoolkit end-motifs [-h] [-k K] [-min MIN_LENGTH] [-max MAX_LENGTH] [-B] [-n] [-o OUTPUT_FILE] [-q QUALITY_THRESHOLD] [-w WORKERS] [-v] input_file refseq_file
+
finaletoolkit end-motifs [-h] [-k K] [-min MIN_LENGTH] [-max MAX_LENGTH] [-B] [-n] [-o OUTPUT_FILE] [-q QUALITY_THRESHOLD]
+                         [-w WORKERS] [-v]
+                         input_file refseq_file
 

 

 

@@ -870,43 +877,43 @@ 
Positional Arguments
-
Named Arguments#

+

+
Named Arguments#

 

 
-k

 
Length of k-mer.

-
Default: 4

+
Default: 4

 

 
-min, --min-length

 
Minimum length for a fragment to be included.

-
Default: 0

+
Default: 0

 

 
-max, --max-length

 
Maximum length for a fragment to be included.

 

 
-B, --no-both-strands

 
Set flag to only consider one strand for end-motifs.

-
Default: True

+
Default: True

 

 
-n, --negative-strand

 
Set flag in conjunction with -B to only consider 5’ end motifs on the negative strand.

-
Default: False

+
Default: False

 

 
-o, --output-file

 
TSV to print k-mer frequencies. If “-”, will write to stdout.

-
Default: '-'

+
Default: “-”

 

 
-q, --quality-threshold

 
Minimum mapping quality threshold.

-
Default: 20

+
Default: 20

 

 
-w, --workers

 
Number of worker processes.

-
Default: 1

+
Default: 1

 

 
-v, --verbose

 
Enable verbose mode to display detailed processing information.

-
Default: 0

+
Default: 0

 

 

 

@@ -914,7 +921,8 @@ 
Named Arguments
 
interval-end-motifs#

 
Measures frequency of k-mer 5’ end motifs in each region specified in a BED file and writes data into a table.

-
finaletoolkit interval-end-motifs [-h] [-k K] [-min MIN_LENGTH] [-max MAX_LENGTH] [-lo MIN_LENGTH] [-hi MAX_LENGTH] [-B] [-n] [-o OUTPUT_FILE] [-q QUALITY_THRESHOLD] [-w WORKERS] [-v]
+
finaletoolkit interval-end-motifs [-h] [-k K] [-min MIN_LENGTH] [-max MAX_LENGTH] [-lo MIN_LENGTH] [-hi MAX_LENGTH] [-B] [-n]
+                                  [-o OUTPUT_FILE] [-q QUALITY_THRESHOLD] [-w WORKERS] [-v]
                                   input_file refseq_file intervals
 

 

@@ -932,16 +940,16 @@ 
Positional Arguments
-
Named Arguments#

+

+
Named Arguments#

 

 
-k

 
Length of k-mer.

-
Default: 4

+
Default: 4

 

 
-min, --min-length

 
Minimum length for a fragment to be included.

-
Default: 0

+
Default: 0

 

 
-max, --max-length

 
Maximum length for a fragment to be included.

@@ -954,27 +962,27 @@ 
Named ArgumentsTrue

+
Default: True

 

 
-n, --negative-strand

 
Set flag in conjunction with -B to only consider 5’ end motifs on the negative strand.

-
Default: False

+
Default: False

 

 
-o, --output-file

 
Path to TSV or CSV file to write end motif frequencies to.

-
Default: '-'

+
Default: “-”

 

 
-q, --quality-threshold

 
Minimum mapping quality threshold.

-
Default: 20

+
Default: 20

 

 
-w, --workers

 
Number of worker processes.

-
Default: 1

+
Default: 1

 

 
-v, --verbose

 
Enable verbose mode to display detailed processing information.

-
Default: 0

+
Default: 0

 

 

 

@@ -990,20 +998,20 @@ 
Positional Arguments
 
file_path

 
Tab-delimited or similar file containing one column for all k-mers a one column for frequency. Reads from stdin by default.

-
Default: '-'

+
Default: “-”

 

 

 

-

-
Named Arguments#

+

+
Named Arguments#

 

 
-s, --sep

 
Separator used in tabular file.

-
Default: '    '

+
Default: “      “

 

 
--header

 
Number of header rows to ignore. Default is 0

-
Default: 0

+
Default: 0

 

 

 

@@ -1019,24 +1027,24 @@ 
Positional Arguments
 
file_path

 
Tab-delimited or similar file containing one column for all k-mers a one column for frequency. Reads from stdin by default.

-
Default: '-'

+
Default: “-”

 

 
file_out

 
Path to the output BED/BEDGraph file containing MDS for each interval.

-
Default: '-'

+
Default: “-”

 

 

 

-

-
Named Arguments#

+

+
Named Arguments#

 

 
-s, --sep

 
Separator used in tabular file.

-
Default: '    '

+
Default: “      “

 

 
--header

 
Number of header rows to ignore. Default is 0

-
Default: 0

+
Default: 0

 

 

 

@@ -1044,7 +1052,8 @@ 
Named Arguments
 
filter-file#

 
Filters a BED/BAM/CRAM file so that all reads/intervals, when applicable,are in mapped pairs, exceed a certain MAPQ, are not flagged for quality, are read1, are not secondary or supplementary alignments, are within/excluding specified intervals, and are on the same reference sequence as the mate.

-
finaletoolkit filter-file [-h] [-W WHITELIST_FILE] [-B BLACKLIST_FILE] [-o OUTPUT_FILE] [-q QUALITY_THRESHOLD] [-min MIN_LENGTH] [-max MAX_LENGTH] [-lo MIN_LENGTH] [-hi MAX_LENGTH]
+
finaletoolkit filter-file [-h] [-W WHITELIST_FILE] [-B BLACKLIST_FILE] [-o OUTPUT_FILE] [-q QUALITY_THRESHOLD]
+                          [-min MIN_LENGTH] [-max MAX_LENGTH] [-p {midpoint,any}] [-lo MIN_LENGTH] [-hi MAX_LENGTH]
                           [-w WORKERS] [-v]
                           input_file
 

@@ -1057,8 +1066,8 @@ 
Positional Arguments
-
Named Arguments#

+

+
Named Arguments#

 

 
-W, --whitelist-file

 
Only output alignments overlapping the intervals in this BED file will be included.

@@ -1068,11 +1077,11 @@ 
Named Arguments
 
-o, --output-file

 
Output BED/BAM/CRAM file path.

-
Default: '-'

+
Default: “-”

 

 
-q, --quality-threshold

 
Minimum mapping quality threshold.

-
Default: 30

+
Default: 30

 

 
-min, --min-length

 
Minimum length for a fragment to be included.

@@ -1080,6 +1089,11 @@ 
Named Arguments-max, --max-length
 
Maximum length for a fragment to be included.

 

+
-p, --intersect-policy

+
Possible choices: midpoint, any

+
Specifies what policy is used to include/exclude fragments in the given interval. See User Guide for more information.

+
Default: “midpoint”

+

 
-lo, --fraction-low

 
Deprecated alias for –min-length

 

@@ -1088,7 +1102,7 @@ 
Named Arguments
 
-w, --workers

 
Number of worker processes.

-
Default: 1

+
Default: 1

 

 
-v, --verbose

 
Enable verbose mode to display detailed processing information.

@@ -1115,20 +1129,20 @@ 
Positional Arguments
-
Named Arguments#

+

+
Named Arguments#

 

 
-o, --output-file

 
A wiggle file containing the aggregate signal over the intervals specified in interval file.

-
Default: '-'

+
Default: “-”

 

 
-m, --median-window-size

 
Size of the median filter window used to aggregate scores. Set to 120 if aggregating WPS signals.

-
Default: 1

+
Default: 1

 

 
-a, --mean

 
use mean instead

-
Default: False

+
Default: False

 

 
-v, --verbose

 
Enable verbose mode to display detailed processing information.

@@ -1206,76 +1220,76 @@ 
Positional Arguments
     
    
-
  • Named Arguments
    • 
+
  • Named Arguments
    • 
 
  • Sub-commands
      
 
    • coverage
 
      • 
 
    • frag-length-bins
 
      • 
 
    • frag-length-intervals
 
      • 
 
    • cleavage-profile
 
      • 
 
    • wps
 
      • 
 
    • adjust-wps
 
      • 
 
    • delfi
 
      • 
 
    • delfi-gc-correct
 
      • 
 
    • end-motifs
 
      • 
 
    • interval-end-motifs
 
      • 
 
    • mds
 
      • 
 
    • interval-mds
 
      • 
 
    • filter-file
 
      • 
 
    • agg-bw
 
      • 
 
    • gap-bed
        
@@ -1330,7 +1344,7 @@ 
        This Page
        
         
        
 
   
        
-    Created using Sphinx 8.1.3.
+    Created using Sphinx 7.4.7.
     
        
   
        
 
        
diff --git a/docs/_build/html/documentation/index.html b/docs/_build/html/documentation/index.html
index d0f15d0..754c017 100644
--- a/docs/_build/html/documentation/index.html
+++ b/docs/_build/html/documentation/index.html
@@ -30,7 +30,7 @@
   
 
 
-    
+    
   
   
   
@@ -39,7 +39,7 @@
 
 
     
-    
+    
     
     
     
@@ -490,7 +490,7 @@ 
        This Page
        
         
        
 
   
        
-    Created using Sphinx 8.1.3.
+    Created using Sphinx 7.4.7.
     
        
   
        
 
        
diff --git a/docs/_build/html/documentation/user_guide/features.html b/docs/_build/html/documentation/user_guide/features.html
index 9ee9641..61c3583 100644
--- a/docs/_build/html/documentation/user_guide/features.html
+++ b/docs/_build/html/documentation/user_guide/features.html
@@ -30,7 +30,7 @@
   
 
 
-    
+    
   
   
   
@@ -39,7 +39,7 @@
 
 
     
-    
+    
     
     
     
@@ -510,7 +510,7 @@ 
        This Page
        
         
        
 
   
        
-    Created using Sphinx 8.1.3.
+    Created using Sphinx 7.4.7.
     
        
   
        
 
        
diff --git a/docs/_build/html/documentation/user_guide/help.html b/docs/_build/html/documentation/user_guide/help.html
index 01ec7b5..aea8747 100644
--- a/docs/_build/html/documentation/user_guide/help.html
+++ b/docs/_build/html/documentation/user_guide/help.html
@@ -30,7 +30,7 @@
   
 
 
-    
+    
   
   
   
@@ -39,7 +39,7 @@
 
 
     
-    
+    
     
     
     
@@ -467,7 +467,7 @@ 
        This Page
        
         
        
 
   
        
-    Created using Sphinx 8.1.3.
+    Created using Sphinx 7.4.7.
     
        
   
        
 
        
diff --git a/docs/_build/html/documentation/user_guide/index.html b/docs/_build/html/documentation/user_guide/index.html
index a6e026b..46dda9a 100644
--- a/docs/_build/html/documentation/user_guide/index.html
+++ b/docs/_build/html/documentation/user_guide/index.html
@@ -30,7 +30,7 @@
   
 
 
-    
+    
   
   
   
@@ -39,7 +39,7 @@
 
 
     
-    
+    
     
     
     
@@ -495,7 +495,7 @@ 
        This Page
        
         
        
 
   
        
-    Created using Sphinx 8.1.3.
+    Created using Sphinx 7.4.7.
     
        
   
        
 
        
diff --git a/docs/_build/html/documentation/user_guide/inputdata.html b/docs/_build/html/documentation/user_guide/inputdata.html
index de17b88..0923bcb 100644
--- a/docs/_build/html/documentation/user_guide/inputdata.html
+++ b/docs/_build/html/documentation/user_guide/inputdata.html
@@ -30,7 +30,7 @@
   
 
 
-    
+    
   
   
   
@@ -39,7 +39,7 @@
 
 
     
-    
+    
     
     
     
@@ -523,7 +523,7 @@ 
        This Page
        
         
        
 
   
        
-    Created using Sphinx 8.1.3.
+    Created using Sphinx 7.4.7.
     
        
   
        
 
        
diff --git a/docs/_build/html/documentation/user_guide/installation.html b/docs/_build/html/documentation/user_guide/installation.html
index af87112..45475ca 100644
--- a/docs/_build/html/documentation/user_guide/installation.html
+++ b/docs/_build/html/documentation/user_guide/installation.html
@@ -30,7 +30,7 @@
   
 
 
-    
+    
   
   
   
@@ -39,7 +39,7 @@
 
 
     
-    
+    
     
     
     
@@ -494,7 +494,7 @@ 
        This Page
        
         
        
 
   
        
-    Created using Sphinx 8.1.3.
+    Created using Sphinx 7.4.7.
     
        
   
        
 
        
diff --git a/docs/_build/html/documentation/user_guide/intersectpolicy.html b/docs/_build/html/documentation/user_guide/intersectpolicy.html
index 85c07b9..cddefd7 100644
--- a/docs/_build/html/documentation/user_guide/intersectpolicy.html
+++ b/docs/_build/html/documentation/user_guide/intersectpolicy.html
@@ -30,7 +30,7 @@
   
 
 
-    
+    
   
   
   
@@ -39,7 +39,7 @@
 
 
     
-    
+    
     
     
     
@@ -484,7 +484,7 @@ 
        This Page
        
         
        
 
   
        
-    Created using Sphinx 8.1.3.
+    Created using Sphinx 7.4.7.
     
        
   
        
 
        
diff --git a/docs/_build/html/documentation/user_guide/quickstart.html b/docs/_build/html/documentation/user_guide/quickstart.html
index 6ce775c..05d2754 100644
--- a/docs/_build/html/documentation/user_guide/quickstart.html
+++ b/docs/_build/html/documentation/user_guide/quickstart.html
@@ -30,7 +30,7 @@
   
 
 
-    
+    
   
   
   
@@ -39,7 +39,7 @@
 
 
     
-    
+    
     
     
     
@@ -394,12 +394,12 @@ 
        Importing Modules
        >>> import finaletoolkit.frag as ft
+
        >>> import finaletoolkit.frag as ft
 
        
 
        
 
        If you want to load a specific function, you can do so by using the following:
        
 
        Assuming we wanted to load the DELFI function:
        
-
        >>> from finaletoolkit.frag import delfi
+
        >>> from finaletoolkit.frag import delfi
 
        
 
        
 
        For more detailed tutorials, please check out our [wiki](epifluidlab/FinaleToolkit).
        
@@ -501,7 +501,7 @@ 
        This Page
        
         
        
 
   
        
-    Created using Sphinx 8.1.3.
+    Created using Sphinx 7.4.7.
     
        
   
        
 
        
diff --git a/docs/_build/html/documentation/user_guide/structure.html b/docs/_build/html/documentation/user_guide/structure.html
index a11aee9..144527b 100644
--- a/docs/_build/html/documentation/user_guide/structure.html
+++ b/docs/_build/html/documentation/user_guide/structure.html
@@ -30,7 +30,7 @@
   
 
 
-    
+    
   
   
   
@@ -39,7 +39,7 @@
 
 
     
-    
+    
     
     
     
@@ -472,7 +472,7 @@ 
        This Page
        
         
        
 
   
        
-    Created using Sphinx 8.1.3.
+    Created using Sphinx 7.4.7.
     
        
   
        
 
        
diff --git a/docs/_build/html/documentation/user_guide/what.html b/docs/_build/html/documentation/user_guide/what.html
index 56ea10e..6492afa 100644
--- a/docs/_build/html/documentation/user_guide/what.html
+++ b/docs/_build/html/documentation/user_guide/what.html
@@ -30,7 +30,7 @@
   
 
 
-    
+    
   
   
   
@@ -39,7 +39,7 @@
 
 
     
-    
+    
     
     
     
@@ -463,7 +463,7 @@ 
        This Page
        
         
        
 
   
        
-    Created using Sphinx 8.1.3.
+    Created using Sphinx 7.4.7.
     
        
   
        
 
        
diff --git a/docs/_build/html/documentation/workflow_reference/dependencies.html b/docs/_build/html/documentation/workflow_reference/dependencies.html
index dc14c0b..1c15f01 100644
--- a/docs/_build/html/documentation/workflow_reference/dependencies.html
+++ b/docs/_build/html/documentation/workflow_reference/dependencies.html
@@ -30,7 +30,7 @@
   
 
 
-    
+    
   
   
   
@@ -39,7 +39,7 @@
 
 
     
-    
+    
     
     
     
@@ -471,7 +471,7 @@ 
        This Page
        
         
        
 
   
        
-    Created using Sphinx 8.1.3.
+    Created using Sphinx 7.4.7.
     
        
   
        
 
        
diff --git a/docs/_build/html/documentation/workflow_reference/filter_file.html b/docs/_build/html/documentation/workflow_reference/filter_file.html
index 13f4497..3e604f8 100644
--- a/docs/_build/html/documentation/workflow_reference/filter_file.html
+++ b/docs/_build/html/documentation/workflow_reference/filter_file.html
@@ -30,7 +30,7 @@
   
 
 
-    
+    
   
   
   
@@ -39,7 +39,7 @@
 
 
     
-    
+    
     
     
     
@@ -304,6 +304,7 @@
   
        Contents:
        
 
          
 
        • Key Features
          • 
+
        • Installation
          • 
 
        • Dependencies
          • 
 
        • Quick Start
          • 
 
        • Workflow Structure
          • 
@@ -466,7 +467,7 @@ 
          This Page
          
         
          
 
   
          
-    Created using Sphinx 8.1.3.
+    Created using Sphinx 7.4.7.
     
          
   
          
 
          
diff --git a/docs/_build/html/documentation/workflow_reference/finaletoolkit_commands.html b/docs/_build/html/documentation/workflow_reference/finaletoolkit_commands.html
index 8c835bc..d86b648 100644
--- a/docs/_build/html/documentation/workflow_reference/finaletoolkit_commands.html
+++ b/docs/_build/html/documentation/workflow_reference/finaletoolkit_commands.html
@@ -30,7 +30,7 @@
   
 
 
-    
+    
   
   
   
@@ -39,7 +39,7 @@
 
 
     
-    
+    
     
     
     
@@ -304,6 +304,7 @@
   
          Contents:
          
 
            
 
          • Key Features
            • 
+
          • Installation
            • 
 
          • Dependencies
            • 
 
          • Quick Start
            • 
 
          • Workflow Structure
            • 
@@ -467,7 +468,7 @@ 
            This Page
            
         
            
 
   
            
-    Created using Sphinx 8.1.3.
+    Created using Sphinx 7.4.7.
     
            
   
            
 
            
diff --git a/docs/_build/html/documentation/workflow_reference/index.html b/docs/_build/html/documentation/workflow_reference/index.html
index 445862f..eff718b 100644
--- a/docs/_build/html/documentation/workflow_reference/index.html
+++ b/docs/_build/html/documentation/workflow_reference/index.html
@@ -30,7 +30,7 @@
   
 
 
-    
+    
   
   
   
@@ -39,7 +39,7 @@
 
 
     
-    
+    
     
     
     
@@ -477,7 +477,7 @@ 
            This Page
            
         
            
 
   
            
-    Created using Sphinx 8.1.3.
+    Created using Sphinx 7.4.7.
     
            
   
            
 
            
diff --git a/docs/_build/html/documentation/workflow_reference/installation.html b/docs/_build/html/documentation/workflow_reference/installation.html
index dcfcd55..04d3365 100644
--- a/docs/_build/html/documentation/workflow_reference/installation.html
+++ b/docs/_build/html/documentation/workflow_reference/installation.html
@@ -30,7 +30,7 @@
   
 
 
-    
+    
   
   
   
@@ -39,7 +39,7 @@
 
 
     
-    
+    
     
     
     
@@ -472,7 +472,7 @@ 
            This Page
            
         
            
 
   
            
-    Created using Sphinx 8.1.3.
+    Created using Sphinx 7.4.7.
     
            
   
            
 
            
diff --git a/docs/_build/html/documentation/workflow_reference/key_features.html b/docs/_build/html/documentation/workflow_reference/key_features.html
index 3647e10..5b38dd4 100644
--- a/docs/_build/html/documentation/workflow_reference/key_features.html
+++ b/docs/_build/html/documentation/workflow_reference/key_features.html
@@ -30,7 +30,7 @@
   
 
 
-    
+    
   
   
   
@@ -39,13 +39,13 @@
 
 
     
-    
+    
     
     
     
     
     
-    
+    
     
   
   
@@ -304,6 +304,7 @@
   
            Contents:
            
 
              
 
            • Key Features
              • 
+
            • Installation
              • 
 
            • Dependencies
              • 
 
            • Quick Start
              • 
 
            • Workflow Structure
              • 
@@ -407,11 +408,11 @@ 
              Key Features
       
              
         
              next
              
-        
              Dependencies
              
+        
              Installation
              
       
              
       
                   
@@ -469,7 +470,7 @@ 
              This Page
              
         
              
 
   
              
-    Created using Sphinx 8.1.3.
+    Created using Sphinx 7.4.7.
     
              
   
              
 
              
diff --git a/docs/_build/html/documentation/workflow_reference/mappability_filtering.html b/docs/_build/html/documentation/workflow_reference/mappability_filtering.html
index 2fa7698..f4807ed 100644
--- a/docs/_build/html/documentation/workflow_reference/mappability_filtering.html
+++ b/docs/_build/html/documentation/workflow_reference/mappability_filtering.html
@@ -30,7 +30,7 @@
   
 
 
-    
+    
   
   
   
@@ -39,7 +39,7 @@
 
 
     
-    
+    
     
     
     
@@ -304,6 +304,7 @@
   
              Contents:
              
 
                
 
              • Key Features
                • 
+
              • Installation
                • 
 
              • Dependencies
                • 
 
              • Quick Start
                • 
 
              • Workflow Structure
                • 
@@ -466,7 +467,7 @@ 
                This Page
                
         
                
 
   
                
-    Created using Sphinx 8.1.3.
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diff --git a/docs/_build/html/documentation/workflow_reference/notes.html b/docs/_build/html/documentation/workflow_reference/notes.html
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                  Contents:
                  
 
                    
 
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                    Contents:
                    
 
                      
 
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                      Contents:
                      
 
                        
 
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                        DocumentationCLI
 
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                        Citationsyear = {2024},
     doi = {10.1101/2024.05.29.596414},
     publisher = {Cold Spring Harbor Laboratory},
-    abstract = {Cell-free DNA (cfDNA) fragmentation pattern represents a promising non-invasive biomarker for disease diagnosis and prognosis. Numerous fragmentation features, such as end motif and window protection score (WPS), have been characterized in cfDNA genomic sequencing. However, the analytical tools developed in these studies are often not released to the liquid biopsy community or are inefficient for genome-wide analysis in large datasets. To address this gap, we have developed FinaleToolkit, a fast and memory efficient Python package designed to generate comprehensive fragmentation features from large cfDNA genomic sequencing data. For instance, FinaleToolkit can generate genome-wide WPS features from a \~{}100X cfDNA whole-genome sequencing (WGS) dataset in 1.2 hours using 16 CPU cores, offering up to a \~{}50-fold increase in processing speed compared to original implementations in the same dataset. We have benchmarked FinaleToolkit against original studies or implementations where possible, confirming its efficacy. Furthermore, FinaleToolkit enabled the genome-wide analysis of fragmentation patterns over arbitrary genomic intervals, significantly boosting the performance for cancer early detection. FinaleToolkit is open source and thoroughly documented with both command line interface and Python application programming interface (API) to facilitate its widespread adoption and use within the research community: https://github.com/epifluidlab/FinaleToolkitCompeting Interest StatementY.L. owns stocks from Freenome Inc. The remaining authors declare no competing interests.},
+    abstract = {Cell-free DNA (cfDNA) fragmentation pattern represents a promising non-invasive biomarker for disease diagnosis and prognosis. Numerous fragmentation features, such as end motif and window protection score (WPS), have been characterized in cfDNA genomic sequencing. However, the analytical tools developed in these studies are often not released to the liquid biopsy community or are inefficient for genome-wide analysis in large datasets. To address this gap, we have developed FinaleToolkit, a fast and memory efficient Python package designed to generate comprehensive fragmentation features from large cfDNA genomic sequencing data. For instance, FinaleToolkit can generate genome-wide WPS features from a \~{}100X cfDNA whole-genome sequencing (WGS) dataset in 1.2 hours using 16 CPU cores, offering up to a \~{}50-fold increase in processing speed compared to original implementations in the same dataset. We have benchmarked FinaleToolkit against original studies or implementations where possible, confirming its efficacy. Furthermore, FinaleToolkit enabled the genome-wide analysis of fragmentation patterns over arbitrary genomic intervals, significantly boosting the performance for cancer early detection. FinaleToolkit is open source and thoroughly documented with both command line interface and Python application programming interface (API) to facilitate its widespread adoption and use within the research community: https://github.com/epifluidlab/FinaleToolkitCompeting Interest StatementY.L. owns stocks from Freenome Inc. The remaining authors declare no competing interests.},
     URL = {https://www.biorxiv.org/content/early/2024/06/02/2024.05.29.596414},
     eprint = {https://www.biorxiv.org/content/early/2024/06/02/2024.05.29.596414.full.pdf},
     journal = {bioRxiv}
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"py:function"}, "terms": {"": [2, 8, 10, 14], "0": [0, 1, 2, 3, 4, 7, 8, 25, 30], "02": 31, "05": 31, "06": 31, "1": [0, 1, 2, 3, 4, 7, 8, 25, 28, 30, 31], "10": [3, 31], "1000": [5, 7, 8], "10000": 13, "10050": 13, "100kb": [2, 8], "100x": 31, "10100": 13, "10150": 13, "10200": 13, "10250": 13, "10300": 13, "10350": 13, "10400": 13, "10450": 13, "10500": 13, "1101": 31, "120": [4, 7, 8, 10], "16": 31, "180": [7, 8], "1964": 7, "1bp": 15, "1kb": 4, "2": [4, 7, 8, 13, 23, 28, 31], "20": [3, 8], "2002": 8, "2016": [7, 10], "2019": [2, 10], "2020": [3, 8, 10], "2022": 10, "2023": 3, "2024": 31, "21": [7, 8], "250": 30, "29": 31, "2bit": [2, 3, 8], "3": [4, 14], "30": [0, 1, 2, 3, 4, 7, 8], "3852": 4, "4": [3, 8, 23], "4kb": 4, "5": [3, 8], "50": 31, "500": [7, 8], "5000": [7, 8], "5000000": [2, 8], "596414": 31, "5kb": 4, "5mb": [2, 8], "60": 13, "600": 3, "6th": 4, "75": 2, "8": [2, 14], "A": [2, 3, 7, 8, 11, 13, 17, 19, 31], "As": 15, "At": 17, "By": 8, "For": [4, 13, 16, 21, 31], "If": [0, 3, 4, 5, 7, 8, 11, 14, 15, 16, 20, 31], "In": [10, 18], "It": [10, 13, 17, 18], "Not": 0, "The": [7, 8, 10, 11, 13, 14, 15, 16, 17, 21, 31], "There": [2, 4], "These": [2, 15], "To": [8, 11, 31], "_": 21, "_scalartype_co": 4, "abnorm": 10, "about": [8, 13], "abov": 0, "absenc": 5, "absent": 18, "abstract": 31, "acceler": 31, "accept": 4, "access": [13, 19, 22], "accord": [7, 8, 10], "acrocentr": 5, "across": 10, "activ": 23, "ad": [5, 18], "add": [1, 8], "addit": 18, "address": 31, "adjust": [2, 4, 7, 21, 30], "adjust_wp": [6, 7, 30], "adjust_wps_max_length": 30, "adopt": 31, "against": 31, "agg_bw": [4, 6], "agg_scor": 4, "aggreg": [4, 7, 8], "al": [2, 3, 4, 7, 8, 10], "algorithm": 0, "alia": [1, 3, 4, 7, 8], "align": [3, 5, 7, 8, 13], "alignedseg": 4, "alignmentfil": [0, 4, 7], "all": [3, 8, 10, 13, 16, 28], "almost": 13, "along": 4, "alpha": 2, "also": [4, 5, 8, 14, 15], "altern": 2, "alwai": 27, "among": 17, "amount": [0, 1], "an": [0, 3, 4, 5, 7, 10, 11, 13, 14, 15], "analysi": [2, 31], "analyt": 31, "analyz": 19, "ani": [0, 3, 4, 8, 12, 13, 14, 20], "annot": 8, "anoth": 13, "answer": 15, "api": [9, 15, 16, 31], "apoptosi": 18, "appear": 2, "append": 21, "appli": [2, 7, 8], "applic": [8, 31], "approach": [0, 4, 18], "ar": [0, 2, 3, 4, 5, 7, 8, 10, 11, 14, 15, 17, 18, 20, 21, 25, 26, 27, 29, 31], "arbitrari": 31, "argument": [15, 17, 31], "aris": 14, "arm": [5, 8], "around": [7, 10], "arrai": [0, 1, 4, 7], "articl": 31, "assess": 10, "associ": [2, 3, 8, 10, 13, 18], "assum": 16, "author": [2, 10, 31], "autom": 22, "autosom": [2, 8], "averag": [0, 4, 30], "avoid": 11, "b": 8, "b37": [2, 5, 8], "b37_gap_b": [5, 6], "background": 28, "bai": 13, "bam": [0, 1, 2, 3, 4, 7, 8, 12, 17, 19, 24, 30], "bandaru": 31, "bar": 2, "base": [0, 1, 2, 3, 4, 5, 7, 8, 10, 24], "basic": [6, 28, 31], "becaus": [3, 5], "becom": 30, "bed": [0, 2, 3, 4, 5, 7, 19, 24, 27, 30], "bed3": 13, "bed4": [0, 2, 5, 8], "bedgraph": [3, 8], "bedtool": 19, "been": [18, 31], "befor": [11, 27], "being": [4, 19], "below": 28, "benchmark": 31, "between": [5, 10, 15], "bgz": 13, "bgzip": 19, "bibtex": 31, "bigwig": [4, 7, 8, 30], "bin": [0, 2], "bin_siz": [0, 8], "binari": 13, "bins_fil": [2, 8], "bioconda": 19, "biomark": [18, 31], "biopsi": 31, "biorxiv": 31, "blacklist": [2, 4, 8, 29], "blacklist_fil": [2, 4, 8], "block": 13, "blood": 18, "bool": [0, 1, 2, 3, 4, 5, 7], "boolean": 4, "boost": 31, "both": [3, 4, 8, 31], "both_strand": 3, "bp": 8, "brew": 14, "broad": 5, "browser": 8, "bug": [11, 31], "c": 8, "calc_freq": 3, "calcul": [0, 1, 3, 4, 7, 8, 10], "can": [2, 4, 10, 11, 13, 14, 15, 16, 18, 22, 31], "cancer": [10, 18, 31], "capac": 15, "carri": 19, "case": 8, "categor": 10, "categori": 8, "cd": [23, 28], "cell": [8, 10, 18, 31], "center": [7, 8, 10], "central": [0, 4], "centromer": [2, 5, 8], "certain": [8, 10], "cfdna": [10, 18, 31], "chang": 18, "changelog": 31, "channel": 19, "character": 31, "check": [4, 5, 16], "choic": [2, 8], "choos": 3, "chr": 5, "chr1": 13, "christiano": 2, "chrom": [2, 3, 4, 7, 8, 13], "chrom_siz": [1, 2, 7, 8], "chrom_sizes_fil": 4, "chrom_sizes_to_dict": [4, 6], "chrom_sizes_to_list": [4, 6], "chromosom": [0, 1, 2, 3, 4, 5, 7, 8], "chromsiz": [4, 7], "circul": 18, "cite": 31, "class": [3, 5], "classmethod": [3, 5], "clear": 11, "cleavag": [6, 12, 31], "cleavage_profil": [1, 6], "cleavage_proport": 1, "cli": [9, 15, 16, 24, 31], "clone": 23, "cluster": 24, "code": [11, 18, 31], "cofragr": 4, "cold": 31, "column": [2, 3, 4, 7, 8, 13], "column3": 4, "com": [23, 31], "command": [14, 15, 16, 19, 22, 23, 24, 25, 26, 27, 28, 30, 31], "common": 22, "commun": 31, "compar": [13, 31], "compat": [13, 24], "compet": 31, "comprehens": [13, 18, 31], "compress": 13, "comput": [0, 4, 18, 31], "concurr": 28, "conda": [14, 19, 23], "condit": [10, 18], "config": 28, "configfil": [23, 28], "configur": [28, 29], "confirm": 31, "conjunct": 8, "consid": [3, 8], "constant": 8, "contain": [0, 2, 3, 4, 5, 7, 8, 13, 23], "content": 31, "contig": [0, 1, 3, 4, 5, 7, 8], "contig_1": 4, "contiggap": [5, 6], "contigs_1": 4, "contigs_2": 4, "convert": 21, "coordin": [0, 1, 3, 4, 5, 8, 10], "core": [23, 24, 28, 31], "correct": [2, 10, 24], "correl": 10, "correspond": [2, 3, 8], "count": [0, 3, 10], "counterpart": 13, "cover": 2, "coverag": [0, 2, 6, 12], "coverage_mapping_qu": 30, "coverage_mapq": 30, "cpg": [1, 8, 10], "cpu": [28, 31], "crai": 13, "cram": [0, 1, 3, 4, 7, 8, 12, 17, 19, 24, 30], "creat": [4, 5, 7, 8, 23, 28], "cristiano": [2, 8, 10], "csv": [3, 8], "curl": 14, "current": 8, "data": [0, 2, 3, 4, 7, 8, 12, 18, 19, 29, 31], "databas": 13, "datafram": 2, "dataset": 31, "deal": 8, "declar": 31, "default": [0, 2, 3, 4, 7, 8, 26, 28, 30], "defaulti": 8, "defin": [4, 8, 10, 28], "definit": 10, "deg": 8, "degre": [7, 8], "delfi": [6, 12, 16, 18, 24, 31], "delfi_gc_correct": [2, 6], "delfi_merge_bin": [2, 6], "delimit": [0, 3, 4, 7, 8], "demonstr": 11, "denot": 8, "depend": [21, 22, 31], "deprec": [1, 3, 4, 7, 8, 26], "deriv": 13, "describ": [2, 3, 4, 7, 8, 31], "design": [10, 17, 18, 31], "detail": [8, 14, 16], "detect": [10, 18, 31], "determin": [0, 2, 4, 15, 19], "dev": 8, "develop": 31, "dhss": 10, "diagnosi": 31, "dict": [3, 4], "dictat": 29, "dictionari": 3, "differ": [5, 18], "directli": 16, "directori": [13, 27, 29, 30], "diseas": [10, 18, 31], "displai": 8, "distribut": 10, "divers": [3, 8, 12, 18], "divid": [0, 16], "dna": [8, 10, 18, 31], "dnase": 10, "do": [4, 8, 16, 30], "document": 18, "doe": 15, "doesn": 3, "doi": 31, "download": 23, "drop": 5, "dtype": 4, "duplic": 11, "dure": [8, 14], "e": [4, 5, 7, 8, 17, 18, 27, 30], "each": [0, 2, 3, 4, 7, 8, 13, 27], "earli": 31, "easi": 18, "edg": [7, 8, 15], "edge_s": [7, 8], "edu": 31, "efficaci": 31, "effici": [13, 31], "either": [3, 13, 15], "eloc": 31, "els": 15, "email": 31, "empti": 5, "enabl": [8, 24, 27, 30, 31], "encount": 11, "encourag": 13, "end": [0, 1, 4, 5, 6, 7, 12, 13, 15, 21, 31], "end_motif": [3, 6], "end_motif_freq": 3, "endmotiffreq": [3, 6], "endmotifinterv": 3, "endmotifsinterv": [3, 6], "endpoint": 10, "engin": 19, "enter": [23, 28], "entri": [2, 8, 13, 31], "entropi": [3, 8, 10], "env": 23, "environ": [14, 23], "epifluidlab": [4, 16, 23, 31], "epigenom": [19, 22], "eprint": 31, "equival": [4, 7], "error": [11, 12], "especi": 7, "establish": 18, "estim": 0, "et": [2, 3, 4, 7, 8, 10], "etc": 17, "ex": [11, 18], "exampl": [11, 13, 21], "exce": 8, "exceed": 4, "exclud": [4, 8, 24], "execut": [8, 23, 28], "exist": [4, 30], "exit": 8, "expect": 3, "expens": 0, "explan": 11, "export": 3, "extens": 27, "extract": [8, 18, 19, 22, 31], "f": [4, 23], "facilit": 31, "factor": 8, "fall": [0, 8, 10, 15], "fals": [0, 2, 3, 4, 5, 7, 8, 30], "fast": [18, 31], "featur": [6, 7, 8, 12, 16, 18, 19, 22, 31], "fetch": 4, "few": 5, "field": 2, "file": [0, 1, 2, 3, 5, 6, 7, 12, 17, 19, 22, 24, 25, 28, 29, 30, 31], "file_format": 30, "file_out": 8, "file_path": [3, 8], "fill": 14, "filter": [3, 4, 7, 17, 22, 24, 27, 30, 31], "filter_fil": [4, 6, 20], "filteringscor": 8, "finaledb": [4, 13], "finaletoolkit": [0, 1, 2, 3, 4, 5, 7, 8, 10, 11, 13, 14, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 30], "finaletoolkit_command": 30, "finaletoolkit_command_flag": 30, "finaletoolkit_workflow": [23, 28], "finaletoolkitcompet": 31, "find": [7, 22], "first": [7, 8], "flag": [8, 21, 26, 30], "flag_nam": 21, "flexibl": 17, "float": [0, 2, 3, 25], "fold": 31, "folder": [23, 28], "follow": [9, 10, 11, 13, 14, 16, 17, 19, 23, 28], "form": 3, "format": [7, 8, 13, 22, 27, 30], "forward": 3, "found": [8, 10], "fourth": 2, "fraction": [3, 4, 7, 8], "fraction_high": [1, 3, 4, 7, 8], "fraction_low": [1, 3, 4, 7, 8], "frag": [0, 1, 2, 3, 6, 7, 13, 16, 31], "frag_arrai": [4, 6], "frag_end": 4, "frag_gener": [4, 6], "frag_length": [0, 6], "frag_length_bin": [0, 6, 27], "fragfil": [1, 4, 7], "fragment": [0, 1, 2, 3, 4, 7, 8, 12, 15, 17, 18, 31], "fragmentom": [10, 16], "free": [8, 10, 18, 31], "freenom": 31, "freq": 3, "frequenc": [3, 8, 10], "friendli": 18, "from": [0, 1, 2, 3, 4, 5, 7, 8, 10, 13, 15, 16, 18, 25, 31], "from_fil": 3, "frquenci": 3, "ft": 16, "full": 31, "fulli": 10, "function": [2, 3, 4, 7, 16, 17], "furthermor": 31, "futur": 8, "g": [4, 7, 8, 18, 27, 30], "gap": [2, 5, 24, 31], "gap_fil": [2, 8], "gaps_b": 5, "gc": [2, 10, 24], "gc_correct": 2, "gener": [0, 2, 3, 4, 5, 15, 16, 17, 31], "genom": [2, 3, 4, 6, 7, 8, 10, 13, 16, 18, 19, 22, 29, 31], "genomegap": [2, 5, 6], "get": [0, 12, 14], "get_arm": 5, "get_contig_gap": 5, "git": 23, "github": [11, 14, 23, 31], "give": [15, 17], "given": [0, 1, 3, 4, 5, 8, 27], "go": 17, "golai": [7, 8], "good": 14, "grch37": 5, "grch38": [2, 5, 8], "greater": 14, "group": 8, "guid": [8, 9, 31], "gz": [0, 3, 8, 13, 27, 30], "gzip": [5, 13, 19], "h": 8, "ha": [8, 10, 15, 16, 18, 31], "half": 4, "harbor": 31, "has_short_arm": 5, "have": [4, 8, 13, 18, 27, 31], "head": 3, "header": [3, 8], "header_lin": 8, "healthi": 18, "heart": 17, "help": [7, 12, 31], "helper": 2, "hematopoiet": 18, "here": [13, 22, 30, 31], "hg19": [2, 5, 8], "hg38": [2, 5, 7, 8], "hi": 8, "high": [8, 31], "highest": [4, 7], "highli": 18, "histogram": [0, 8], "histogram_path": [0, 8], "hoc": [5, 18], "hood": 17, "hour": 31, "how": [0, 2, 4], "howev": [18, 31], "htslib": 19, "http": [23, 31], "human": [8, 13], "human_g1k_v37": [5, 8], "hundred_kb_bin": 2, "hypersensit": 10, "hyphen": [21, 30], "i": [0, 2, 3, 4, 5, 7, 8, 10, 11, 13, 14, 16, 17, 18, 20, 30, 31], "id": 31, "identifi": 10, "ifyou": 8, "ignor": [3, 8], "implement": [24, 31], "import": 12, "importerror": 14, "in_gap": 5, "in_tcmer": 5, "in_telomere_or_centromer": 5, "inaccess": 18, "inc": 31, "includ": [0, 1, 3, 4, 5, 7, 8, 10, 11, 17, 19], "increas": [0, 31], "index": [3, 4, 7, 13], "indic": [3, 30], "ineffici": 31, "info": 2, "inform": [1, 8, 11, 13], "input": [4, 8, 12, 20, 27, 28, 29, 30, 31], "input_dir": [29, 30], "input_fil": [0, 1, 2, 3, 4, 7, 8], "insert": 27, "instal": [12, 19, 22, 31], "instanc": 31, "instead": [3, 4, 7, 8, 21], "institut": 5, "int": [0, 1, 2, 3, 4, 5, 7], "integ": 8, "integr": [16, 24, 31], "intend": 16, "interest": [17, 31], "interfac": [16, 18, 31], "intersect": [4, 5, 8, 12, 31], "intersect_polici": [0, 4, 15], "interv": [0, 1, 2, 3, 4, 5, 7, 15, 19, 24, 25, 29, 30, 31], "interval_end_motif": [3, 6], "interval_fil": [0, 4, 7, 8, 25, 30], "interval_s": [7, 8], "introduc": 10, "introduct": [12, 31], "invalid": 5, "invas": [18, 31], "io": 31, "is_low_qu": 4, "issu": [11, 14, 31], "iter": [0, 3, 5], "its": [0, 3, 7, 13, 16, 31], "itself": [13, 16], "jame": 31, "jiang": [3, 8, 10], "job": [23, 24, 28], "journal": 31, "just": [3, 15], "k": [3, 7, 8, 10], "keep": 8, "kei": [4, 22, 31], "kent": 8, "kmer": 3, "kmer_freq": 3, "kmer_frequ": 3, "l": [7, 8, 31], "labl": 2, "laboratori": 31, "larg": [8, 31], "last": [7, 8], "lead": 8, "learn": 13, "least": 25, "left": [0, 1, 4, 8], "length": [0, 1, 3, 4, 7, 12], "level": 10, "li": [0, 4, 31], "li2024": 31, "liber": 8, "librari": 19, "lijw21": 31, "like": [7, 14], "limit": 28, "line": [3, 8, 16, 19, 31], "liquid": 31, "list": [0, 3, 4], "liu": 31, "lo": 8, "load": [2, 16], "locat": [2, 7, 10, 29], "log": 28, "long": [4, 7, 8, 10, 15], "longer": 8, "low": [2, 4, 8, 17], "low_quality_read_pair": [4, 6], "lowest": [4, 7], "m": 8, "mac": 14, "made": 31, "mai": [0, 2, 4, 8], "mainli": 18, "maintain": 18, "make": [5, 11, 17], "mani": [2, 15], "manipul": [3, 19], "map": [3, 4, 8, 10, 13, 17], "mappability_fil": [25, 30], "mappability_threshold": [25, 30], "mappabl": [22, 24, 29, 30, 31], "mapping_qu": 30, "mapq": [0, 1, 3, 4, 8, 13, 30], "mate": 8, "matrix": 4, "max": 8, "max_length": [0, 1, 3, 4, 7, 8], "maximum": [0, 1, 3, 4, 8, 28], "md": [3, 12, 18, 21], "mds_bed": 3, "mean": [4, 7, 8], "measur": 8, "median": [4, 7, 8], "median_window_s": [4, 7, 8], "memori": [0, 31], "mer": [3, 8, 10], "merg": [2, 8], "merge_bin": 2, "messag": 11, "method": [3, 5, 7], "methodologi": [2, 3, 8], "methyl": 10, 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\ No newline at end of file

From c5cedd23582a40cd07996f5523002be9362e8a1c Mon Sep 17 00:00:00 2001
From: jamesli124 <58196853+jamesli124@users.noreply.github.com>
Date: Sun, 2 Feb 2025 18:02:57 -0500
Subject: [PATCH 5/5] remove erroneous flush statement

---
 src/finaletoolkit/utils/_filter_file.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/src/finaletoolkit/utils/_filter_file.py b/src/finaletoolkit/utils/_filter_file.py
index 805fcdd..9f4ba5c 100644
--- a/src/finaletoolkit/utils/_filter_file.py
+++ b/src/finaletoolkit/utils/_filter_file.py
@@ -191,7 +191,6 @@ def filter_file(
                             (max_length is None or read.template_length <= max_length) and
                             (min_length is None or read.template_length >= min_length)):
                             out_file.write(read)
-                            out_file.flush()
 
             if output_file != '-':
                 run_subprocess(