Mercurial > repos > sanbi-uwc > confil
changeset 3:53a61865e86e draft
planemo upload for repository https://github.com/COMBAT-TB/confil commit cb48efaef286f70c94607cb583a61bb9e3d71604
| author | sanbi-uwc |
|---|---|
| date | Wed, 27 Feb 2019 06:20:05 -0500 |
| parents | ca3c6f955c3e |
| children | eaf51f9aff10 |
| files | LICENSE README.md conda/conda_upload.sh conda/meta.yaml confil.xml confil/__init__.py confil/confil.py confil/kraken.py confil/report.py requirements.txt setup.cfg setup.py test/test_data/test_file.tab test/test_data/test_file_1.fastq test/test_data/test_file_2.fastq test/test_report.py test/test_runner.py |
| diffstat | 16 files changed, 1023 insertions(+), 2 deletions(-) [+] |
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If not, see <https://www.gnu.org/licenses/>. + +Also add information on how to contact you by electronic and paper mail. + + If the program does terminal interaction, make it output a short +notice like this when it starts in an interactive mode: + + <program> Copyright (C) <year> <name of author> + This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. + This is free software, and you are welcome to redistribute it + under certain conditions; type `show c' for details. + +The hypothetical commands `show w' and `show c' should show the appropriate +parts of the General Public License. Of course, your program's commands +might be different; for a GUI interface, you would use an "about box". + + You should also get your employer (if you work as a programmer) or school, +if any, to sign a "copyright disclaimer" for the program, if necessary. +For more information on this, and how to apply and follow the GNU GPL, see +<https://www.gnu.org/licenses/>. + + The GNU General Public License does not permit incorporating your program +into proprietary programs. If your program is a subroutine library, you +may consider it more useful to permit linking proprietary applications with +the library. If this is what you want to do, use the GNU Lesser General +Public License instead of this License. But first, please read +<https://www.gnu.org/licenses/why-not-lgpl.html>.
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.md Wed Feb 27 06:20:05 2019 -0500 @@ -0,0 +1,26 @@ +# confil + +[](https://travis-ci.org/COMBAT-TB/confil) +[](https://anaconda.org/thoba/confil) + +:no_entry_sign: :construction: **For in-house use** + +`confil` parses a [kraken2](https://ccb.jhu.edu/software/kraken2/) report and determines contamination based on a specified cutoff. + +## Requirements + +- kraken2 + +## Up and running + +```sh +$ git clone https://github.com/COMBAT-TB/confil.git +... +$ cd confil +$ virtualenv envname +$ source envname/bin/activate +$ pip install -r requirements.txt +$ python setup.py install +$ confil --help +$ confil --threads 1 --paired --cutoff 80 fastq_1.fastq fastq_2.fastq +```
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/conda/conda_upload.sh Wed Feb 27 06:20:05 2019 -0500 @@ -0,0 +1,14 @@ +set -e +# Only need to change these two variables +PKG_NAME=confil +USER=thoba + +OS=$TRAVIS_OS_NAME-64 + +conda config --set anaconda_upload no +DEV='dev' +DATE=`date +%Y%m%d` +export VERSION=$DEV$DATE +export CONDA_BLD_PATH=$HOME/miniconda/conda-bld +conda build . +anaconda -t $CONDA_UPLOAD_TOKEN upload -u $USER $CONDA_BLD_PATH/$OS/$PKG_NAME-*.tar.bz2 --force
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/conda/meta.yaml Wed Feb 27 06:20:05 2019 -0500 @@ -0,0 +1,27 @@ +package: + name: confil + version: {{ environ['VERSION'] }} + +source: + fn: confil-0.0.1.tar.gz + url: https://github.com/COMBAT-TB/confil/archive/0.0.1.tar.gz + +build: + script_env: + - VERSION + - CONDA_BLD_PATH + number: 0 + +requirements: + build: + - python + - click + run: + - python + - click + +about: + home: https://github.com/COMBAT-TB/confil + license_file: LICENSE + summary: "confil parses a kraken2 report and determines contamination based on a specified cutoff." + dev_url: https://github.com/COMBAT-TB/confil
--- a/confil.xml Thu Feb 14 04:36:14 2019 -0500 +++ b/confil.xml Wed Feb 27 06:20:05 2019 -0500 @@ -12,7 +12,7 @@ #set report_name = os.path.splitext(os.path.basename($input_type_conditional.single_input.element_identifier))[0] #set report_name = re.sub('_[0-9]+$', '', str(report_name)) + '.tab' - confil --threads $threads --cutoff $cutoff + python $__tool_directory__/confil/confil.py --threads $threads --cutoff $cutoff $input_type_conditional.single_input.element_identifier && mv $report_name '$output' @@ -23,7 +23,7 @@ #set report_name = os.path.splitext(os.path.basename($input_type_conditional.collection_input.forward.element_identifier))[0] #set report_name = re.sub('_[0-9]+$', '', str(report_name)) + '.tab' - confil --threads $threads --cutoff $cutoff --paired + python $__tool_directory__/confil/confil.py --threads $threads --cutoff $cutoff --paired $input_type_conditional.collection_input.forward.element_identifier $input_type_conditional.collection_input.reverse.element_identifier && mv $report_name '$output' #end if
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/confil/confil.py Wed Feb 27 06:20:05 2019 -0500 @@ -0,0 +1,46 @@ +import os + +import click + +from kraken import kraken_installed, run_kraken + +# TODO: Remove +KRAKEN2_DEFAULT_DB = "/tools/databases/kraken2/04092018/standard/" +OUT_DIR = os.path.abspath(os.curdir) +fastq_file_extensions = ['.fq', '.fastq'] + + +@click.command() +@click.option('--db', default=OUT_DIR, required=True, + help='Name for Kraken 2 DB', type=click.Path(exists=True), + show_default=True) +@click.option('--threads', default=1, help='Number of threads', + show_default=True) +@click.option('--cutoff', default=50, show_default=True, + help='Percentage of fragments covered') +@click.option('--paired', is_flag=True, + help='The filenames provided have paired-end reads') +@click.argument('seqfiles', nargs=-1, required=True) +def confil(db, threads, cutoff, paired, seqfiles): + """ + Checks sequence for contamination using specified cutoff. + """ + if kraken_installed(): + seqfiles = [os.path.abspath(seqfile) for seqfile in seqfiles] + if len(seqfiles) > 2 and not paired: + raise ValueError( + "Expecting no more than 2 FASTQ files. We got {}.\n{}".format( + len(seqfiles), seqfiles)) + if paired and len(seqfiles) < 2: + raise ValueError( + "Expecting 2 paired FASTQ files. We got {}.\n{}".format( + len(seqfiles), seqfiles)) + click.secho('Using a cutoff of {}% for contamination!\n'.format( + cutoff), fg='green') + # run kraken and read/parse report + run_kraken(db=db, threads=threads, cutoff=cutoff, + paired=paired, seqfiles=seqfiles) + + +if __name__ == '__main__': + confil()
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/confil/kraken.py Wed Feb 27 06:20:05 2019 -0500 @@ -0,0 +1,59 @@ +import distutils.spawn +import os +import re +from shlex import split +from subprocess import PIPE, Popen + +import click + +from report import parse_report + +OUT_DIR = os.path.abspath(os.curdir) + + +def kraken_installed(): + # check if `kraken2` is in path + # TODO remove python + installed = distutils.spawn.find_executable("python") + if not installed: + raise OSError("kraken2 is not installed.") + return installed + + +def run_kraken(db, threads, cutoff, paired, seqfiles): + # Using the sample name to track report + seq_name = [os.path.splitext(os.path.basename(seq))[0] + for seq in seqfiles][0] + # remove _ and numbers + seq_name = re.sub('_[0-9]+$', '', seq_name) + # building cmd + cmd = "kraken2 --threads {threads} --db {db} --output {seq_name}.out --report {seq_name}.tab ".format( + threads=threads, db=db, seq_name=seq_name) + if paired: + cmd += "--paired --classified-out {}_cseqs#.fq ".format(seq_name) + cmd += "{seqfiles}".format(seqfiles=' '.join(seqfiles)) + click.secho("Executing kraken2: \n{}\n".format( + split(cmd)), fg='bright_yellow') + + # TODO: remove + test_file = "https://raw.githubusercontent.com/COMBAT-TB/confil/master/test/test_data/test_file.tab" + out_file = os.path.join(OUT_DIR, "{}.tab".format(seq_name)) + mock_cmd = 'wget {} -O {}'.format(test_file, out_file) + cmd = mock_cmd + click.secho("Executing mock_cmd: \n{}\n".format(split(cmd)), fg='red') + + p = Popen(split(cmd), stdout=PIPE, stderr=PIPE, close_fds=True) + while True: + output = p.stdout.readline() + if output == '' and p.poll() is not None: + break + if output: + click.echo(output) + returncode = p.poll() + if returncode != 0: + error = p.stderr.readline() + raise OSError("Kraken2 launch error:\n{}\n".format(error)) + # parse kraken report + report_file = os.path.join(OUT_DIR, "{}.tab".format(seq_name)) + parse_report(report_file=report_file, cutoff=cutoff) + return returncode
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/confil/report.py Wed Feb 27 06:20:05 2019 -0500 @@ -0,0 +1,38 @@ +import os + +import click + + +def parse_report(report_file, cutoff): + file_name = os.path.splitext(os.path.basename(report_file))[0] + hit = None + if os.stat(report_file).st_size > 0 and report_file.endswith(".tab"): + click.secho("Processing {} with cutoff of {}...\n".format( + report_file, cutoff), fg='green') + with open(report_file, 'r') as report: + for line in report: + line = [str(e).strip() for e in line.split('\t')] + if len(line) > 1: + click.secho('{}'.format(line), fg='green') + # Percentage of fragments covered by the clade rooted at this taxon + percentage = int(float(line[0])) + # Number of fragments covered by the clade rooted at this taxon + # num_covered = int(float(line[1])) + # Number of fragments assigned directly to this taxon + # num_assigned = int(float(line[2])) + # NCBI taxonomic ID number + # ncbi_tax = int(float(line[3])) + # Indented scientific name (Mycobacterium\n) + name = str(line[5]).strip() + if percentage < cutoff and 'Mycobacterium' in name: + click.secho('\n{}%: {} is contaminated!\n'.format( + percentage, file_name), fg='red') + raise SystemExit('{}%: {} is contaminated!\n'.format( + percentage, file_name)) + if percentage >= cutoff and 'Mycobacterium' in name: + click.secho('\n{}%: {} is not contaminated!\n'.format( + percentage, file_name), fg='green') + hit = line + break + click.secho('Hit: {}'.format(hit), fg='green') + return hit
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/requirements.txt Wed Feb 27 06:20:05 2019 -0500 @@ -0,0 +1,2 @@ +Click==7.0 +pytest==4.2.0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/setup.cfg Wed Feb 27 06:20:05 2019 -0500 @@ -0,0 +1,9 @@ +[metadata] +description-file = README.md + +[egg_info] +tag_build = .dev +tag_date = 1 + +[aliases] +release = egg_info -Db ''
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/setup.py Wed Feb 27 06:20:05 2019 -0500 @@ -0,0 +1,23 @@ +from setuptools import find_packages, setup + +with open("README.md", "r") as fh: + long_description = fh.read() + +setup( + name='confil', + version='0.0.1', + url='https://github.com/COMBAT-TB/confil', + description='Contamination filter', + long_description=long_description, + long_description_content_type="text/markdown", + keywords='contamination, filter', + py_modules=['confil'], + packages=find_packages(), + include_package_data=True, + install_requires=[ + 'click' + ], + entry_points={ + 'console_scripts': ['confil=confil.confil:confil'] + }, +)
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test/test_data/test_file.tab Wed Feb 27 06:20:05 2019 -0500 @@ -0,0 +1,16 @@ + 28.34 1198200 1198200 U 0 unclassified + 71.66 3030398 1705 R 1 root + 71.59 3027326 90 R1 131567 cellular organisms + 71.33 3016097 5832 D 2 Bacteria + 56.09 2371684 139 D1 1783272 Terrabacteria group + 55.96 2366280 32 P 201174 Actinobacteria + 55.96 2366229 970 C 1760 Actinobacteria + 55.90 2363912 491 O 85007 Corynebacteriales + 55.88 2363031 1244 F 1762 Mycobacteriaceae + 55.84 2361413 2074448 G 1763 Mycobacterium + 6.64 280596 161419 G1 77643 Mycobacterium tuberculosis complex + 2.50 105696 74351 S 1773 Mycobacterium tuberculosis + 0.16 6824 6824 S1 747369 Mycobacterium tuberculosis R1207 + 0.03 1383 827 S1 83332 Mycobacterium tuberculosis H37Rv + 0.01 266 266 S2 757419 Mycobacterium tuberculosis H37RvCO + \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test/test_data/test_file_1.fastq Wed Feb 27 06:20:05 2019 -0500 @@ -0,0 +1,16 @@ +@seq1 +AGTCGTGGTCATCGTGACTAGTCGATCTAGCTAGCTCTCTAGAGTGT ++ +;>@BCEFGHJKLMNOPQRSTUVWXYZ[\]^_?abcdefghijklmno +@seq2 +AGTCGTTGTCATCGTGACTAGTCGATCTAGCTAGCTCTCTAGAGTGT ++ +;>@BCElcH@KLMNOPQ>STZVWbYu[\]^_?a=;d?fghijklmno +@seq3 +AGTCGTCGTCATCGTGACTAGTCGATCTAGCTAGCTCTCTAGAGTGT ++ +7>@BCEFGHJKLMNOPQRSTUVWXYZ[\]^_?abcdefghijklmno +@seq4 +AGTCGTAGTCATCGTGACTAGTCGATCTAGCTAGCTCTCTAGAGTGT ++ +;>@BCEFGHJKLMNOPQRSTUVWXYZ[\]^_?abcdefghijklmno
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test/test_data/test_file_2.fastq Wed Feb 27 06:20:05 2019 -0500 @@ -0,0 +1,24 @@ +@seq1 +AAAGGTTTCTCTTTTGGAAATATCTAAATCCC ++ +!"#$%&\'()*+,-./0123456789:;<=>. +@seq2 +GGGTCTCCCAGAATGATTAGAGCCGTATAGGA ++ +?@ABCDEFGHIJK MNOPQRSTUVWXYZ[\\] +@seq3 +GCGGTTCAATACGATTACCACCATGATAAATA ++ +?Aa.1ghB2K!#lk(02GY[[II])Kwl+,5M +@seq4 +AGTCTTTTCCTCTAAAATAACATAGGATACTA ++ +ghY)N375Nh.,Ol>==/<:2#i&d%#KdNII +@seq5 +GAGGACTCATGGTAGGTATTTTACATGACATT ++ +IIgy%hf6#394bd&hNMWL$OPB63II*,+- +@seq6 +GGCCTACATTCATTTACGAGACTAATTAGGGA ++ +IIIIIgd6#5%jKO&.,D+s3aW=cdGB#a1$ \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test/test_report.py Wed Feb 27 06:20:05 2019 -0500 @@ -0,0 +1,24 @@ +import os + +import pytest + +from confil.report import parse_report +from test_runner import TEST_DATA_DIR + +TEST_REPORT = os.path.join(TEST_DATA_DIR, "test_file.tab") + +# test using a cutoff of 50% + + +@pytest.mark.parametrize("test_input, expected", [ + (type(parse_report(TEST_REPORT, 50)), list), + (parse_report(TEST_REPORT, 50)[5], 'Mycobacterium'), + (parse_report(TEST_REPORT, 50)[0], '55.84') +]) +def test_parse_report(test_input, expected): + assert test_input == expected + + +def test_parse_report_exception(): + with pytest.raises(SystemExit): + parse_report(TEST_REPORT, 90)
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test/test_runner.py Wed Feb 27 06:20:05 2019 -0500 @@ -0,0 +1,23 @@ +import os + +import pytest +from click.testing import CliRunner + +from confil.confil import confil + +CURR_DIR = os.path.dirname(os.path.abspath(__file__)) +TEST_DATA_DIR = os.path.join(CURR_DIR, "test_data/") + +FILE_1 = os.path.join(TEST_DATA_DIR, "test_file_1.fastq") +FILE_2 = os.path.join(TEST_DATA_DIR, "test_file_2.fastq") + + +@pytest.fixture(scope="module") +def cli_runner(): + runner = CliRunner() + return runner + + +def test_runner(cli_runner): + result = cli_runner.invoke(confil, ["--paired", FILE_1, FILE_2]) + assert result.exit_code == 0