Merge branch '12-tagAlign' into 'master'

Resolve "Make tagAlign files"

Closes #12

See merge request !10

workflow/conf/biohpc.config

@@ -21,7 +21,11 @@ process {
   }
   $experimentQC {
     module = ['python/3.6.1-2-anaconda', 'deeptools/2.5.0.1']
-    executor = 'local'
+    cpus = 32
+  }
+  $convertReads {
+    module = ['python/3.6.1-2-anaconda',  'samtools/1.4.1', 'bedtools/2.26.0']
+    cpus = 32
   }
 }
 

workflow/main.nf

@@ -144,6 +144,7 @@ process filterReads {
   output:
 
   set sampleId, file('*.bam'), file('*.bai'), biosample, factor, treatment, replicate, controlId into dedupReads
+  set sampleId, file('*.bam'), biosample, factor, treatment, replicate, controlId into convertReads
   file '*flagstat.qc' into dedupReadsStats
   file '*pbc.qc' into dedupReadsComplexity
   file '*dup.qc' into dupReads
@@ -189,3 +190,32 @@ process experimentQC {
   """
 
 }
+
+// Convert reads to bam
+process convertReads {
+
+  tag "$sampleId-$replicate"
+  publishDir "$baseDir/output/${task.process}", mode: 'copy'
+
+  input:
+
+  set sampleId, deduped, biosample, factor, treatment, replicate, controlId from convertReads
+
+  output:
+
+  set sampleId, file('*.tagAlign.gz'), file('*.bed{pe,se}.gz'), biosample, factor, treatment, replicate, controlId into tagReads
+
+  script:
+
+  if (pairedEnd) {
+    """
+    python3 $baseDir/scripts/convert_reads.py -b $deduped -p
+    """
+  }
+  else {
+    """
+    python3 $baseDir/scripts/convert_reads.py -b $deduped
+    """
+  }
+
+}

workflow/scripts/convert_reads.py

+#!/usr/bin/env python3
+
+'''Convert tagAlign files for further processing.'''
+
+import os
+import argparse
+import shutil
+import shlex
+import logging
+from multiprocessing import cpu_count
+import utils
+
+EPILOG = '''
+For more details:
+        %(prog)s --help
+'''
+
+# SETTINGS
+
+logger = logging.getLogger(__name__)
+logger.addHandler(logging.NullHandler())
+logger.propagate = False
+logger.setLevel(logging.INFO)
+
+
+def get_args():
+    '''Define arguments.'''
+    parser = argparse.ArgumentParser(
+        description=__doc__, epilog=EPILOG,
+        formatter_class=argparse.RawDescriptionHelpFormatter)
+
+    parser.add_argument('-b', '--bam',
+                        help="The bam file to run filtering and qc on.",
+                        required=True)
+
+    parser.add_argument('-p', '--paired',
+                        help="True/False if paired-end or single end.",
+                        default=False,
+                        action='store_true')
+
+    args = parser.parse_args()
+    return args
+
+# Functions
+
+
+def check_tools():
+    '''Checks for required componenets on user system'''
+
+    logger.info('Checking for required libraries and components on this system')
+
+    bedtools_path = shutil.which("bedtools")
+    if bedtools_path:
+        logger.info('Found bedtools: %s', bedtools_path)
+    else:
+        logger.error('Missing bedtools')
+        raise Exception('Missing bedtools')
+
+    samtools_path = shutil.which("samtools")
+    if samtools_path:
+        logger.info('Found samtools: %s', samtools_path)
+    else:
+        logger.error('Missing samtools')
+        raise Exception('Missing samtools')
+
+
+def convert_mapped(bam, tag_filename):
+    '''Use bedtools to convert to tagAlign.'''
+
+    out, err = utils.run_pipe([
+        "bamToBed -i %s" % (bam),
+        r"""awk 'BEGIN{OFS="\t"}{$4="N";$5="1000";print $0}'""",
+        "gzip -nc"], outfile=tag_filename)
+
+
+def convert_mapped_pe(bam, bam_basename):
+    '''Use bedtools to convert to tagAlign PE data.'''
+
+    bedpe_filename = bam_basename + ".bedpe.gz"
+
+    # Name sort bam to make BEDPE
+    nmsrt_bam_filename = bam_basename + ".nmsrt.bam"
+    samtools_sort_command = \
+        "samtools sort -n -@%d -o %s %s" \
+        % (cpu_count(), nmsrt_bam_filename, bam)
+
+    logger.info(samtools_sort_command)
+    utils.check_output(shlex.split(samtools_sort_command))
+
+    out, err = utils.run_pipe([
+        "bamToBed -bedpe -mate1 -i %s" % (nmsrt_bam_filename),
+        "gzip -nc"],
+        outfile=bedpe_filename)
+
+
+def main():
+    args = get_args()
+    paired = args.paired
+    bam = args.bam
+
+    # Create a file handler
+    handler = logging.FileHandler('convert_reads.log')
+    logger.addHandler(handler)
+
+    # Check if tools are present
+    check_tools()
+
+    # Convert PE or SE to tagAlign
+    bam_basename = os.path.basename(
+        utils.strip_extensions(bam, ['.bam']))
+
+    tag_filename = bam_basename + 'tagAlign.gz'
+    convert_mapped(bam, tag_filename)
+
+    if paired:  # paired-end data
+        convert_mapped_pe(bam, bam_basename)
+    else:
+        bedse_filename =  bam_basename + ".bedse.gz"
+        shutil(tag_filename, bedse_filename)
+
+
+if __name__ == '__main__':
+    main()

workflow/tests/test_convert_reads.py

+#!/usr/bin/env python3
+
+import pytest
+import os
+
+test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
+                '/../output/convertReads/'
+
+
+def test_convert_reads_singleend():
+    assert os.path.exists(os.path.join(test_output_path, 'ENCFF646LXU.tagAlign.gz'))
+    assert os.path.exists(os.path.join(test_output_path, 'ENCFF646LXU.bedse.gz'))
+
+
+def test_map_qc_pairedend():
+    # Do the same thing for paired end data
+    # Also check that bedpe exists
+    pass