diff --git a/Makefile b/Makefile index fbfe0db..9531ea6 100644 --- a/Makefile +++ b/Makefile @@ -16,13 +16,11 @@ test-cov: all install: all bash install-sra-tools.sh - maturin build --release -m fastq_writer/Cargo.toml $(PYTHON) setup.py install - $(PYTHON) -m pip install --no-deps fastq_writer --find-links fastq_writer/target/wheels/ dev: all bash install-sra-tools.sh - pip install coverage parameterized maturin==0.10.3 + pip install coverage parameterized pip install -e . clean: distclean diff --git a/ci/recipe/meta.yaml b/ci/recipe/meta.yaml index 3c3c259..e748515 100644 --- a/ci/recipe/meta.yaml +++ b/ci/recipe/meta.yaml @@ -14,29 +14,24 @@ build: make install requirements: - build: - - maturin ==0.10.3 - - rust ==1.58.1 - host: - python {{ python }} - setuptools run: - - python {{ python }} + - entrezpy >=2.1.2 - xmltodict - - pyzotero + - python {{ python }} - python-dotenv - - tqdm >=4.62.3 - - entrezpy >=2.1.2 + - pyzotero - q2-types {{ qiime2_epoch }}.* - qiime2 {{ qiime2_epoch }}.* + - tqdm >=4.62.3 test: imports: - q2_fondue - qiime2.plugins.fondue - - fastq_writer requires: - parameterized - coverage diff --git a/fastq_writer/Cargo.lock b/fastq_writer/Cargo.lock deleted file mode 100644 index 01a0015..0000000 --- a/fastq_writer/Cargo.lock +++ /dev/null @@ -1,327 +0,0 @@ -# This file is automatically @generated by Cargo. -# It is not intended for manual editing. -version = 3 - -[[package]] -name = "adler" -version = "1.0.2" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "f26201604c87b1e01bd3d98f8d5d9a8fcbb815e8cedb41ffccbeb4bf593a35fe" - -[[package]] -name = "autocfg" -version = "1.1.0" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "d468802bab17cbc0cc575e9b053f41e72aa36bfa6b7f55e3529ffa43161b97fa" - -[[package]] -name = "bitflags" -version = "1.3.2" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "bef38d45163c2f1dde094a7dfd33ccf595c92905c8f8f4fdc18d06fb1037718a" - -[[package]] -name = "cfg-if" -version = "1.0.0" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "baf1de4339761588bc0619e3cbc0120ee582ebb74b53b4efbf79117bd2da40fd" - -[[package]] -name = "crc32fast" -version = "1.3.2" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "b540bd8bc810d3885c6ea91e2018302f68baba2129ab3e88f32389ee9370880d" -dependencies = [ - "cfg-if", -] - -[[package]] -name = "ctor" -version = "0.1.23" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "cdffe87e1d521a10f9696f833fe502293ea446d7f256c06128293a4119bdf4cb" -dependencies = [ - "quote", - "syn", -] - -[[package]] -name = "fastq_writer" -version = "0.1.0" -dependencies = [ - "flate2", - "pyo3", -] - -[[package]] -name = "flate2" -version = "1.0.24" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "f82b0f4c27ad9f8bfd1f3208d882da2b09c301bc1c828fd3a00d0216d2fbbff6" -dependencies = [ - "crc32fast", - "miniz_oxide", -] - -[[package]] -name = "ghost" -version = "0.1.6" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "eb19fe8de3ea0920d282f7b77dd4227aea6b8b999b42cdf0ca41b2472b14443a" -dependencies = [ - "proc-macro2", - "quote", - "syn", -] - -[[package]] -name = "indoc" -version = "0.3.6" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "47741a8bc60fb26eb8d6e0238bbb26d8575ff623fdc97b1a2c00c050b9684ed8" -dependencies = [ - "indoc-impl", - "proc-macro-hack", -] - -[[package]] -name = "indoc-impl" -version = "0.3.6" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "ce046d161f000fffde5f432a0d034d0341dc152643b2598ed5bfce44c4f3a8f0" -dependencies = [ - "proc-macro-hack", - "proc-macro2", - "quote", - "syn", - "unindent", -] - -[[package]] -name = "instant" -version = "0.1.12" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "7a5bbe824c507c5da5956355e86a746d82e0e1464f65d862cc5e71da70e94b2c" -dependencies = [ - "cfg-if", -] - -[[package]] -name = "inventory" -version = "0.1.11" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "f0eb5160c60ba1e809707918ee329adb99d222888155835c6feedba19f6c3fd4" -dependencies = [ - "ctor", - "ghost", - "inventory-impl", -] - -[[package]] -name = "inventory-impl" -version = "0.1.11" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "7e41b53715c6f0c4be49510bb82dee2c1e51c8586d885abe65396e82ed518548" -dependencies = [ - "proc-macro2", - "quote", - "syn", -] - -[[package]] -name = "libc" -version = "0.2.132" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "8371e4e5341c3a96db127eb2465ac681ced4c433e01dd0e938adbef26ba93ba5" - -[[package]] -name = "lock_api" -version = "0.4.7" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "327fa5b6a6940e4699ec49a9beae1ea4845c6bab9314e4f84ac68742139d8c53" -dependencies = [ - "autocfg", - "scopeguard", -] - -[[package]] -name = "miniz_oxide" -version = "0.5.3" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "6f5c75688da582b8ffc1f1799e9db273f32133c49e048f614d22ec3256773ccc" -dependencies = [ - "adler", -] - -[[package]] -name = "parking_lot" -version = "0.11.2" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "7d17b78036a60663b797adeaee46f5c9dfebb86948d1255007a1d6be0271ff99" -dependencies = [ - "instant", - "lock_api", - "parking_lot_core", -] - -[[package]] -name = "parking_lot_core" -version = "0.8.5" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "d76e8e1493bcac0d2766c42737f34458f1c8c50c0d23bcb24ea953affb273216" -dependencies = [ - "cfg-if", - "instant", - "libc", - "redox_syscall", - "smallvec", - "winapi", -] - -[[package]] -name = "paste" -version = "0.1.18" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "45ca20c77d80be666aef2b45486da86238fabe33e38306bd3118fe4af33fa880" -dependencies = [ - "paste-impl", - "proc-macro-hack", -] - -[[package]] -name = "paste-impl" -version = "0.1.18" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "d95a7db200b97ef370c8e6de0088252f7e0dfff7d047a28528e47456c0fc98b6" -dependencies = [ - "proc-macro-hack", -] - -[[package]] -name = "proc-macro-hack" -version = "0.5.19" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "dbf0c48bc1d91375ae5c3cd81e3722dff1abcf81a30960240640d223f59fe0e5" - -[[package]] -name = "proc-macro2" -version = "1.0.43" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "0a2ca2c61bc9f3d74d2886294ab7b9853abd9c1ad903a3ac7815c58989bb7bab" -dependencies = [ - "unicode-ident", -] - -[[package]] -name = "pyo3" -version = "0.13.2" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "4837b8e8e18a102c23f79d1e9a110b597ea3b684c95e874eb1ad88f8683109c3" -dependencies = [ - "cfg-if", - "ctor", - "indoc", - "inventory", - "libc", - "parking_lot", - "paste", - "pyo3-macros", - "unindent", -] - -[[package]] -name = "pyo3-macros" -version = "0.13.2" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "a47f2c300ceec3e58064fd5f8f5b61230f2ffd64bde4970c81fdd0563a2db1bb" -dependencies = [ - "pyo3-macros-backend", - "quote", - "syn", -] - -[[package]] -name = "pyo3-macros-backend" -version = "0.13.2" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "87b097e5d84fcbe3e167f400fbedd657820a375b034c78bd852050749a575d66" -dependencies = [ - "proc-macro2", - "quote", - "syn", -] - -[[package]] -name = "quote" -version = "1.0.21" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "bbe448f377a7d6961e30f5955f9b8d106c3f5e449d493ee1b125c1d43c2b5179" -dependencies = [ - "proc-macro2", -] - -[[package]] -name = "redox_syscall" -version = "0.2.16" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "fb5a58c1855b4b6819d59012155603f0b22ad30cad752600aadfcb695265519a" -dependencies = [ - "bitflags", -] - -[[package]] -name = "scopeguard" -version = "1.1.0" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "d29ab0c6d3fc0ee92fe66e2d99f700eab17a8d57d1c1d3b748380fb20baa78cd" - -[[package]] -name = "smallvec" -version = "1.9.0" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "2fd0db749597d91ff862fd1d55ea87f7855a744a8425a64695b6fca237d1dad1" - -[[package]] -name = "syn" -version = "1.0.99" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "58dbef6ec655055e20b86b15a8cc6d439cca19b667537ac6a1369572d151ab13" -dependencies = [ - "proc-macro2", - "quote", - "unicode-ident", -] - -[[package]] -name = "unicode-ident" -version = "1.0.3" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "c4f5b37a154999a8f3f98cc23a628d850e154479cd94decf3414696e12e31aaf" - -[[package]] -name = "unindent" -version = "0.1.10" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "58ee9362deb4a96cef4d437d1ad49cffc9b9e92d202b6995674e928ce684f112" - -[[package]] -name = "winapi" -version = "0.3.9" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "5c839a674fcd7a98952e593242ea400abe93992746761e38641405d28b00f419" -dependencies = [ - "winapi-i686-pc-windows-gnu", - "winapi-x86_64-pc-windows-gnu", -] - -[[package]] -name = "winapi-i686-pc-windows-gnu" -version = "0.4.0" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "ac3b87c63620426dd9b991e5ce0329eff545bccbbb34f3be09ff6fb6ab51b7b6" - -[[package]] -name = "winapi-x86_64-pc-windows-gnu" -version = "0.4.0" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "712e227841d057c1ee1cd2fb22fa7e5a5461ae8e48fa2ca79ec42cfc1931183f" diff --git a/fastq_writer/Cargo.toml b/fastq_writer/Cargo.toml deleted file mode 100644 index cf63ae8..0000000 --- a/fastq_writer/Cargo.toml +++ /dev/null @@ -1,13 +0,0 @@ -[package] -name = "fastq_writer" -version = "0.1.0" -authors = ["Michal Ziemski "] -edition = "2021" - -[dependencies] -pyo3 = { version = "0.13", features = ["extension-module"] } -flate2 = "1.0.24" - -[lib] -name = "fastq_writer" -crate-type = ["cdylib"] diff --git a/fastq_writer/data/test_input.fastq b/fastq_writer/data/test_input.fastq deleted file mode 100644 index 8f86019..0000000 --- a/fastq_writer/data/test_input.fastq +++ /dev/null @@ -1,8 +0,0 @@ -@SRR20363956.1 1 length=245 -ACTCCTACGGGAGGCAGCAGTGGGGAATATTGGACAATGGGCCACAAGCCTGATCCAGCAATTCTGTGTGCACGATGAAGGTCTTCGGATTGTAAAGTGCTTTCAGTTGGGAAGAAGAAAGTGACGGTACCAACAGAAGAAGCGACGGCTAAATACGTGCCAGCAGCCGCGGTAATACGTATGTCGCAAGCGTTATCCGGATTTATTGGGCGTAAAGCGCGTCTAGGCGGAAAAATAAGTCTGAT -+SRR20363956.1 1 length=245 -FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFF:F,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFF:FFFF,FFFFFFFFFF:FFFFF,FFFFFFFFFFFFF -@SRR20363956.2 2 length=245 -ACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGGGAAACCCTGATGCAGCCATGCCTCGTGTGTGAAGAAGGCCTTCGGGTTGTAAAGCACTTTCAGTAGGGAGGAAAGGGTGAGTCTTAATACGGCTCATCTGTGACGTTACCTACAGAAGAAGGACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTCCGAGCGTTAATCGGACTTACTGGGCGTAAAGCGTGCGC -+SRR20363956.2 2 length=245 -FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,F,FFFF:FFFFFFFFFFFFFFFFFFFFFFFFF:FFFF::FFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFF diff --git a/fastq_writer/src/lib.rs b/fastq_writer/src/lib.rs deleted file mode 100644 index 27ee842..0000000 --- a/fastq_writer/src/lib.rs +++ /dev/null @@ -1,81 +0,0 @@ -use flate2::write::GzEncoder; -use flate2::Compression; -use pyo3::prelude::{pymodule, PyModule, PyResult, Python}; -use std::fs::File; -use std::io::{BufRead, BufReader, Write}; - -#[pymodule] -fn fastq_writer(_py: Python<'_>, m: &PyModule) -> PyResult<()> { - fn rewrite_fastq(fin: &str, fout: &str) { - _rewrite(fin, fout) - } - - #[pyfn(m, "rewrite_fastq")] - fn rewrite_fastq_py<'py>(_py: Python<'py>, fin: &str, fout: &str) { - rewrite_fastq(fin, fout) - } - - Ok(()) -} - -fn _rewrite(fin: &str, fout: &str) { - let buff_in = BufReader::new(File::open(fin).expect("Could not open file for reading.")); - let mut buff_out = GzEncoder::new( - File::create(fout).expect("Could not open file for writing."), - Compression::default(), - ); - - for line in buff_in.lines() { - let l = line.expect("Unable to read line."); - buff_out - .write_all(l.trim().as_bytes()) - .expect("Unable to write sequence to file."); - buff_out - .write_all("\n".as_bytes()) - .expect("Unable to write to file."); - } - buff_out.try_finish().expect("Could not close the stream."); -} - -mod tests { - use super::*; - use flate2::read::GzDecoder; - use std::env::temp_dir; - use std::io::{BufRead, BufReader}; - - #[allow(dead_code)] - fn create_tmp_file(name: &str) -> String { - let mut dir = temp_dir(); - dir.push(name); - let _fexp = File::create(&dir).expect("Could not create file"); - let a = format!("{}", &dir.as_path().display()); - a - } - - #[allow(dead_code)] - fn assert_file_content(f1: &str, f2: &str) { - let buff1 = BufReader::new(File::open(f1).expect("Could not open file for reading.")); - let buff2 = BufReader::new(GzDecoder::new( - File::open(f2).expect("Could not open gz file."), - )); - - let it = buff1.lines().zip(buff2.lines()); - for (l1, l2) in it { - assert_eq!( - l1.expect("Unable to read line from file 1."), - l2.expect("Unable to read line from file 2.") - ) - } - } - - #[test] - fn test_rewrite_ok() { - let fin = "./data/test_input.fastq"; - let _fout = create_tmp_file("test_seq.fastq.gz"); - let fout = _fout.as_str(); - - _rewrite(fin, fout); - - assert_file_content(fin, fout); - } -} diff --git a/q2_fondue/sequences.py b/q2_fondue/sequences.py index eef644e..88502f1 100644 --- a/q2_fondue/sequences.py +++ b/q2_fondue/sequences.py @@ -20,7 +20,6 @@ import threading import time -from fastq_writer import rewrite_fastq from qiime2 import Metadata from warnings import warn @@ -33,7 +32,7 @@ from q2_fondue.entrezpy_clients._utils import set_up_logger from q2_fondue.utils import ( _determine_id_type, handle_threaded_exception, DownloadError, - _has_enough_space, _find_next_id + _has_enough_space, _find_next_id, _rewrite_fastq ) threading.excepthook = handle_threaded_exception @@ -248,14 +247,12 @@ def _copy_to_casava( """ fwd_path_in = os.path.join(tmp_dir, filenames[0]) fwd_path_out = os.path.join(casava_result_path, f'{filenames[0]}.gz') - rewrite_fastq(fwd_path_in, fwd_path_out) - os.remove(fwd_path_in) + _rewrite_fastq(fwd_path_in, fwd_path_out) if len(filenames) > 1: rev_path_in = os.path.join(tmp_dir, filenames[1]) rev_path_out = os.path.join(casava_result_path, f'{filenames[1]}.gz') - rewrite_fastq(rev_path_in, rev_path_out) - os.remove(rev_path_in) + _rewrite_fastq(rev_path_in, rev_path_out) def _write2casava_dir( diff --git a/q2_fondue/tests/data/SRR123456.fastq b/q2_fondue/tests/data/SRR123456.fastq index a67e0bb..da697ce 100644 --- a/q2_fondue/tests/data/SRR123456.fastq +++ b/q2_fondue/tests/data/SRR123456.fastq @@ -9,4 +9,4 @@ A='=4<;<<<;3==B:<5<<9@9A988497;867=<;<-EA/:9A<&C=1A)9EA3#EA2GC7*65:08?7C<==@;$5<<9?7<=<;A=(A91<=<=FB/=@;$=8-C==B;<===B;=8@<&:GC6)<3:B;<@;$=<5:D=;D=7:==D=;8<<<<+;:A<<9A65:08?7C<==@;$5<<9?7<=<;A=(A91<=<=FB/=@;$=8-C==B;<===B;=8@<&:GC6)<3:B;<@;$=<5:D=;D=7:==D=;8<<<<+;:A<<9A65:08?7C<==@;$5<<9?7<=<;A=(A91<=<=FB/=@;$=8-C==B;<===B;=8@<&:GC6)<3:B;<@;$=<5:D=;D=7:==D=;8<<<<+;:A<<9A65:08?7C<==@;$5<<9?7<=<;A=(A91<=<=FB/=@;$=8-C==B;<===B;=8@<&:GC6)<3:B;<@;$=<5:D=;D=7:==D=;8<<<<+;:A<<9A65:08?7C<==@;$5<<9?7<=<;A=(A91<=<=FB/=@;$=8-C==B;<===B;=8@<&:GC6)<3:B;<@;$=<5:D=;D=7:==D=;8<<<<+;:A<<9A65:08?7C<==@;$5<<9?7<=<;A=(A91<=<=FB/=@;$=8-C==B;<===B;=8@<&:GC6)<3:B;<@;$=<5:D=;D=7:==D=;8<<<<+;:A<<9A65:08?7C<==@;$5<<9?7<=<;A=(A91<=<=FB/=@;$=8-C==B;<===B;=8@<&:GC6)<3:B;<@;$=<5:D=;D=7:==D=;8<<<<+;:A<<9A65:08?7C<==@;$5<<9?7<=<;A=(A91<=<=FB/=@;$=8-C==B;<===B;=8@<&:GC6)<3:B;<@;$=<5:D=;D=7:==D=;8<<<<+;:A<<9A>EA/GFGGHG///E@EEE>/?1BGB1B>F2B1G1212FGFFHH @ERR3018303.94 Bgsng7131.m10_1839802 length=250 TACGTAGGTGGCAAGCGTTGTCCGGATTTACTGGGCGTAAAGGGAGCGTAGGCGGACTTTTAAGTGAGATGTGAAATACCCGGGCTCAACTTGGGTGCTGCATTTCAAACTGGAAGTCTAGAGTGCAGGAGAGGAGAATGGAATTCCTAGTGTAGCGGTGAAATGCGTAGAGATTAGGAAGAACACCAGTGGCGAAGGCGATTCTCTGGACTGTAACTGACGCTGAGGCTCGAAAGCGTGGGGAGCAAAC +ERR3018303.94 Bgsng7131.m10_1839802 length=250 -CBBCCFFCFFCFGGGGGGGGGGHGGGGGHHHHHHHHGGFGHHGGGGGGGGGGHGGGGGHHHFGHHGHHGHHHHHHEGHHHHGGGFGHGHGGHGHHGEFFHGHHHHHGHGGHGHHHHHHHGHFHHHHHGGFFHGDFGHFHGHHGHHGHHHHHHHFHHGDGGGFGHGHFGD?EFCHGHHFCGHFHHGGGGGGGFFGFADAED?CFFFFFFFB;BEBFFFFFF/ADFAAFEFEFF@BADFFFFFFFAABEFF: \ No newline at end of file +CBBCCFFCFFCFGGGGGGGGGGHGGGGGHHHHHHHHGGFGHHGGGGGGGGGGHGGGGGHHHFGHHGHHGHHHHHHEGHHHHGGGFGHGHGGHGHHGEFFHGHHHHHGHGGHGHHHHHHHGHFHHHHHGGFFHGDFGHFHGHHGHHGHHHHHHHFHHGDGGGFGHGHFGD?EFCHGHHFCGHFHHGGGGGGGFFGFADAED?CFFFFFFFB;BEBFFFFFF/ADFAAFEFEFF@BADFFFFFFFAABEFF: diff --git a/q2_fondue/tests/data/testaccHYB_1.fastq b/q2_fondue/tests/data/testaccHYB_1.fastq index aa42ad1..299e688 100644 --- a/q2_fondue/tests/data/testaccHYB_1.fastq +++ b/q2_fondue/tests/data/testaccHYB_1.fastq @@ -13,4 +13,4 @@ AAAAAFF@@F1C1EEGGGG?AAFEGGCGHG2GGHHHEGGGHHHG//EGGGGGGGGGGGF1BFDGHF21E2FHBGGG11BB @ERR3018303.91 Bgsng7131.m10_3716454 length=250 TACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGAAGGCGAAGGCAGCCCCTTGGGAATGTACTGACGCTCATGTGCGAAAGCGTGGGGGGCAAAC +ERR3018303.91 Bgsng7131.m10_3716454 length=250 -BBBBBBBBBBBBGGGGEGGFFGHGGGGGHHDHGHHGGGGGHHHGGCEGGGGGGGGGGGGHHHBFHH4GGHGHHHHHHHHGG??EEEGHHHHG0GGGFFHFHDGHHHHGFGHDGEHFFEHHGGHHHFHHGGG.FFGGGFCF.FFFFFFBF/BFFFBFF;AFEFFFFEDADFEFFFFFBB9FDBFBBFF?.BDDEAFBC9.AD.EDFFFBBE?BFFF/BBFFF9?.DD/BFFFFF@@DB.9;BAF---@EFF \ No newline at end of file +BBBBBBBBBBBBGGGGEGGFFGHGGGGGHHDHGHHGGGGGHHHGGCEGGGGGGGGGGGGHHHBFHH4GGHGHHHHHHHHGG??EEEGHHHHG0GGGFFHFHDGHHHHGFGHDGEHFFEHHGGHHHFHHGGG.FFGGGFCF.FFFFFFBF/BFFFBFF;AFEFFFFEDADFEFFFFFBB9FDBFBBFF?.BDDEAFBC9.AD.EDFFFBBE?BFFF/BBFFF9?.DD/BFFFFF@@DB.9;BAF---@EFF diff --git a/q2_fondue/tests/data/testaccHYB_2.fastq b/q2_fondue/tests/data/testaccHYB_2.fastq index 1c2ce98..9c2c051 100644 --- a/q2_fondue/tests/data/testaccHYB_2.fastq +++ b/q2_fondue/tests/data/testaccHYB_2.fastq @@ -13,4 +13,4 @@ GGGHHHHGHHHHGGGGGGGGGHHGGGGGHHHHHHHHGGGGHHHGGGGGGGGGGGGGGGGFFHHHDGHHHHHHGGHHHHHH @ERR3018303.91 Bgsng7131.m10_3716454 length=231 TACGTAGGTGGCAAGCGTTATCCGGATTTATTGGGCGTAAAGAGAGTGCAGGCGGTTTTCTAAGTCTGATGTGAAAGCCTTCGGCTTAACCGGAGAAGTGCATCGGAAACTGGATAACTTGAGTGCAGAAGAGGGTAGTGGAACTCCATGTGTAGCGGTGGAATGCGTAGATATATGGAAGAACACCAGTGGCGAAGGCGGCTACCTGGTCTGCAACTGACGCTGAGACTC +ERR3018303.91 Bgsng7131.m10_3716454 length=231 -GGGHHHHGHGGHHHGHGGGGHHHGGGGGGHEGHHHHGFGGHHHHHGHHHHHHGGGEFGGGHGHGGFHGEDG4GEGH3BECGEHG@CCBHBGFG/BF1=FDGF1=FDG65:08?7C<==@;$5<<9?7<=<;A=(A91<=<=FB/=@;$=8-C==B;<===B;=8@<&:GC6)<3:B;<@;$=<5:D=;D=7:==D=;8<<<<+;:A<<9A65:08?7C<==@;$5<<9?7<=<;A=(A91<=<=FB/=@;$=8-C==B;<===B;=8@<&:GC6)<3:B;<@;$=<5:D=;D=7:==D=;8<<<<+;:A<<9A65:08?7C<==@;$5<<9?7<=<;A=(A91<=<=FB/=@;$=8-C==B;<===B;=8@<&:GC6)<3:B;<@;$=<5:D=;D=7:==D=;8<<<<+;:A<<9A65:08?7C<==@;$5<<9?7<=<;A=(A91<=<=FB/=@;$=8-C==B;<===B;=8@<&:GC6)<3:B;<@;$=<5:D=;D=7:==D=;8<<<<+;:A<<9A