Newer
Older
#
# * --------------------------------------------------------------------------
# * Licensed under MIT (https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/LICENSE.md)
# * --------------------------------------------------------------------------
#
from __future__ import print_function
from collections import OrderedDict
import re
EPILOG = '''
For more details:
%(prog)s --help
'''
# SETTINGS
logger = logging.getLogger(__name__)
logger.addHandler(logging.NullHandler())
logger.propagate = False
logger.setLevel(logging.INFO)
SOFTWARE_REGEX = {
'Nextflow': ['version_nextflow.txt', r"(\S+)"],
'Trim Galore!': ['trimReads_vf/version_trimgalore.txt', r"version (\S+)"],
'Cutadapt': ['trimReads_vf/version_cutadapt.txt', r"Version (\S+)"],
'BWA': ['alignReads_vf/version_bwa.txt', r"Version: (\S+)"],
'Samtools': ['alignReads_vf/version_samtools.txt', r"samtools (\S+)"],
'Sambamba': ['filterReads_vf/version_sambamba.txt', r"sambamba (\S+)"],
'BEDTools': ['convertReads_vf/version_bedtools.txt', r"bedtools v(\S+)"],
'R': ['crossReads_vf/version_r.txt', r"R version (\S+)"],
'SPP': ['crossReads_vf/version_spp.txt', r"\[1\] ‘(1.14)’"],
'MACS2': ['callPeaksMACS_vf/version_macs.txt', r"macs2 (\S+)"],
'bedGraphToBigWig': ['callPeaksMACS_vf/version_bedGraphToBigWig.txt', r"bedGraphToBigWig v (\S+)"],
'ChIPseeker': ['peakAnnotation_vf/version_ChIPseeker.txt', r"Version (\S+)\""],
'MEME-ChIP': ['motifSearch_vf/version_memechip.txt', r"Version (\S+)"],
'DiffBind': ['diffPeaks_vf/version_DiffBind.txt', r"Version (\S+)\""],
'deepTools': ['experimentQC_vf/version_deeptools.txt', r"deeptools (\S+)"],
'Python': ['version_python.txt', r"Python (\S+)"],
'MultiQC': ['version_multiqc.txt', r"multiqc, version (\S+)"],
def get_args():
'''Define arguments.'''
parser = argparse.ArgumentParser(
description=__doc__, epilog=EPILOG,
formatter_class=argparse.RawDescriptionHelpFormatter)
parser.add_argument('-o', '--output',
help="The out file name.",
required=True)
parser.add_argument('-t', '--test',
help='Used for testing purposes',
default=False,
action='store_true')
args = parser.parse_args()
return args
'''Check if version files are found.'''
logger.info("Running file check.")
software_files = np.array(list(SOFTWARE_REGEX.values()))[:,0]
extra_files = set(files) - set(software_files)
logger.error('Missing regex: %s', list(extra_files))
raise Exception("Missing regex: %s" % list(extra_files))
def main():
args = get_args()
output = args.output
out_filename = output + '_mqc.yaml'
results = OrderedDict()
results['Nextflow'] = '<span style="color:#999999;\">Not Run</span>'
results['Trim Galore!'] = '<span style="color:#999999;\">Not Run</span>'
results['Cutadapt'] = '<span style="color:#999999;\">Not Run</span>'
results['BWA'] = '<span style="color:#999999;\">Not Run</span>'
results['Samtools'] = '<span style="color:#999999;\">Not Run</span>'
results['Sambamba'] = '<span style="color:#999999;\">Not Run</span>'
results['BEDTools'] = '<span style="color:#999999;\">Not Run</span>'
results['R'] = '<span style="color:#999999;\">Not Run</span>'
results['SPP'] = '<span style="color:#999999;\">Not Run</span>'
results['MACS2'] = '<span style="color:#999999;\">Not Run</span>'
results['bedGraphToBigWig'] = '<span style="color:#999999;\">Not Run</span>'
results['ChIPseeker'] = '<span style="color:#999999;\">Not Run</span>'
results['MEME-ChIP'] = '<span style="color:#999999;\">Not Run</span>'
results['DiffBind'] = '<span style="color:#999999;\">Not Run</span>'
results['deepTools'] = '<span style="color:#999999;\">Not Run</span>'
results['MultiQC'] = '<span style="color:#999999;\">Not Run</span>'
results['Python'] = '<span style="color:#999999;\">Not Run</span>'
# list all files
files = glob.glob('**/*.txt', recursive=True)
# Search each file using its regex
for k, v in SOFTWARE_REGEX.items():
if os.path.isfile(v[0]):
with open(v[0]) as x:
versions = x.read()
match = re.search(v[1], versions)
if match:
results[k] = "v{}".format(match.group(1))
# Dump to YAML
print(
'''
id: 'Software Versions'
section_name: 'Software Versions'
section_href: 'https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/'
plot_type: 'html'
description: 'are collected at run time from the software output.'
data: |
<dl class="dl-horizontal">
'''
, file = open(out_filename, "w"))
for k, v in results.items():
print(" <dt>{}</dt><dd>{}</dd>".format(k, v), file = open(out_filename, "a"))
print(" </dl>", file = open(out_filename, "a"))
if __name__ == '__main__':
main()