EndMotifFreqs.to_tsv()EndMotifsIntervals
+region_end_motifs()end_motifs()interval_end_motifs()Return estimated fragment coverage over intervals specified in -intervals. Fragments are read from input_file which may be
---a SAM, BAM, CRAM, or Frag.gz file. Uses an algorithm where the midpoints of
-
fragments are calculated and coverage is tabulated from the +intervals. Fragments are read from input_file which may be +a SAM, BAM, CRAM, or Frag.gz file. Uses an algorithm where the midpoints of +fragments are calculated and coverage is tabulated from the midpoints that fall into the specified region. Not suitable for fragments of size approaching interval size.
Helper function that takes window data and performs GC adjustment.
Class that stores frequencies of end-motif k-mers over +user-specified intervals and contains methods to manipulate this +data.
+intervals (Iterable) – A collection of tuples, each containing a tuple representing +a genomic interval (chrom, 0-based start, 1-based stop) and a +dict that maps kmers to frequencies in the interval.
k (int) – Size of k-mers
quality_threshold (int, optional) – Minimum mapping quality used. Default is 30.
Returns a list of intervals and associated frquency for given +kmer. Results are in the form (chrom, 0-based start, 1-based +stop, frequency).
+Reads kmer frequency from a tab-delimited file
+file_path (str) – Path string containing path to file.
sep (str, optional) – Delimiter used in file.
kmer_freqs
+Writes MDS for each interval to a bed/bedgraph file.
+Calculates a motif diversity score (MDS) for each interval using +normalized Shannon entropy as described by Jiang et al (2020). This +function is generalized for any k instead of just 4-mers.
+Take frequency of specified kmer and writes to BED.
+output_file (str) – File to write frequencies to.
calc_freq (bool, optional) – Calculates frequency of motifs if true. Otherwise, writes counts +for each motif. Default is true.
sep (str, optional) – Separator for table. Tab-separated by default.
Take frequency of specified kmer and writes to bedgraph.
+output_file (str) – File to write frequencies to.
calc_freq (bool, optional) – Calculates frequency of motifs if true. Otherwise, writes counts +for each motif. Default is true.
sep (str, optional) – Separator for table. Tab-separated by default.
Writes all intervals and associated frquencies to file.
+output_file (str) – File to write frequencies to.
calc_freq (bool, optional) – Calculates frequency of motifs if true. Otherwise, writes counts +for each motif. Default is true.
sep (str, optional) – Separator for table. Tab-separated by default.
Function that reads fragments in the specified region from a BAM, SAM, or tabix indexed file and returns the 5’ k-mer (default is -4-mer) end motif counts as a structured array. This function +4-mer) end motif counts as a dictionary. This function reproduces the methodology of Zhou et al (2023).
input_file (str) –
contig (str) –
start (int) –
stop (int) –
refseq_file (str) –
k (int, optional) –
input_file (str) – Path of SAM, BAM, CRAM, or Frag.gz containing pair-end reads.
contig (str) – Name of contig or chromosome for region.
start (int) – 0-based start coordinate.
stop (int) – 1-based end coordinate.
refseq_file (str) – 2bit file with reference sequence input_file was aligned to.
k (int, optional) – Length of end motif kmer. Default is 4.
fraction_low (int, optional) – Minimum fragment length.
fraction_high (int, optional) – Maximum fragment length.
both_strands (bool, optional) – Choose whether to use forward 5’ ends only or use 5’ ends for +both ends of PE reads.
output_file (None or str, optional) –
quality_threshold (int, optional) –
verbose (bool or int, optional) –
Function that reads fragments from a BAM, SAM, 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 @@ -517,12 +647,42 @@
input_file (str) –
refseq_file (str) –
k (int, optional) –
output_file (None or str, optional) –
quality_threshold (int, optional) –
workers (int, optional) –
input_file (str) – SAM, BAM, CRAM, or Frag.gz file with paired-end reads.
refseq_file (str) – 2bit file with sequence of reference genome input_file is +aligned to.
k (int, optional) – Length of end motif kmer. Default is 4.
output_file (None or str, optional) – File path to write results to. Either tsv or csv.
quality_threshold (int, optional) – Minimum MAPQ to filter.
workers (int, optional) – Number of worker processes.
verbose (bool or int, optional) –
end_motif_freq
+Function that reads fragments from a BAM, SAM, 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.
+input_file (str) – Path of SAM, BAM, CRAM, or Frag.gz containing pair-end reads.
refseq_file (str) – Path of 2bit file for reference genome that reads are aligned to.
intervals (str or tuple) – Path of BED file containing intervals or list of tuples +(chrom, start, stop).
k (int, optional) – Length of end motif kmer. Default is 4.
output_file (None or str, optional) – File path to write results to. Either tsv or csv.
quality_threshold (int, optional) – Minimum MAPQ to filter.
workers (int, optional) – Number of worker processes.
verbose (bool or int, optional) –
end_motif_freq
list
+EndMotifIntervals