Merge 9c5d75e into 028a72d

errors.py

@@ -0,0 +1,7 @@
+#!/usr/bin/env python
+
+class QCError(RuntimeError):
+    '''Indicates a failure at a QC step.'''
+
+    def __init__(self, reason):
+        super(QCError, self).__init__(reason)

pipes/WDL/workflows/tasks/tasks_taxon_filter.wdl

@@ -83,8 +83,11 @@ task deplete_taxa {
 #   level or greater for the virus of interest)
 # ======================================================================
 task filter_to_taxon {
-  File reads_unmapped_bam
-  File lastal_db_fasta
+  File     reads_unmapped_bam
+  File     lastal_db_fasta
+  Boolean? error_on_reads_in_neg_control = false
+  Int? negative_control_reads_threshold = 0
+  String? neg_control_prefixes_space_separated = "neg water NTC"
 
   # do this in two steps in case the input doesn't actually have "cleaned" in the name
   String bam_basename = basename(basename(reads_unmapped_bam, ".bam"), ".cleaned")
@@ -95,10 +98,21 @@ task filter_to_taxon {
     # find 90% memory
     mem_in_mb=`/opt/viral-ngs/source/docker/calc_mem.py mb 90`
 
+    if [[ "${error_on_reads_in_neg_control}" == "true" ]]; then
+      ERROR_ON_NEG_CONTROL_ARGS="--errorOnReadsInNegControl"
+      if [[ -n "${negative_control_reads_threshold}" ]]; then
+        ERROR_ON_NEG_CONTROL_ARGS="$ERROR_ON_NEG_CONTROL_ARGS ${'--negativeControlReadsThreshold=' + negative_control_reads_threshold}"
+      fi
+      if [[ -n "${neg_control_prefixes_space_separated}" ]]; then
+        ERROR_ON_NEG_CONTROL_ARGS="$ERROR_ON_NEG_CONTROL_ARGS ${'--negControlPrefixes=' + neg_control_prefixes_space_separated}"
+      fi      
+    fi
+
     taxon_filter.py filter_lastal_bam \
       ${reads_unmapped_bam} \
       ${lastal_db_fasta} \
       ${bam_basename}.taxfilt.bam \
+      $ERROR_ON_NEG_CONTROL_ARGS \
       --JVMmemory="$mem_in_mb"m \
       --loglevel=DEBUG
 

taxon_filter.py

@@ -34,14 +34,15 @@
 import tools.samtools
 from util.file import mkstempfname
 import read_utils
+from errors import QCError
 
 log = logging.getLogger(__name__)
 
+
 # =======================
 # ***  deplete_human  ***
 # =======================
 
-
 def parser_deplete(parser=argparse.ArgumentParser()):
     parser.add_argument('inBam', help='Input BAM file.')
     parser.add_argument('revertBam', nargs='?', help='Output BAM: read markup reverted with Picard.')
@@ -172,11 +173,15 @@ def filter_lastal_bam(
     min_length_for_initial_matches=5,
     max_length_for_initial_matches=50,
     max_initial_matches_per_position=100,
+    error_on_reads_in_neg_control=False,
+    neg_control_prefixes=None, #set below: "neg","water","NTC"
+    negative_control_reads_threshold=0,
     JVMmemory=None, threads=None
 ):
     ''' Restrict input reads to those that align to the given
         reference database using LASTAL.
     '''
+    neg_control_prefixes = neg_control_prefixes or ["neg","water","NTC"]
 
     with util.file.tmp_dir('-lastdb') as tmp_db_dir:
         # index db if necessary
@@ -185,6 +190,8 @@ def filter_lastal_bam(
             db = lastdb.build_database(db, os.path.join(tmp_db_dir, 'lastdb'))
 
         with util.file.tempfname('.read_ids.txt') as hitList:
+            number_of_hits=0
+
             # look for lastal hits in BAM and write to temp file
             with open(hitList, 'wt') as outf:
                 for read_id in tools.last.Lastal().get_hits(
@@ -195,8 +202,16 @@ def filter_lastal_bam(
                         max_initial_matches_per_position,
                         threads=threads
                     ):
+                    number_of_hits+=1
                     outf.write(read_id + '\n')
 
+            if error_on_reads_in_neg_control:
+                sample_name=os.path.basename(inBam)
+                if any(sample_name.lower().startswith(prefix.lower()) for prefix in neg_control_prefixes):
+                    if number_of_hits > max(0,negative_control_reads_threshold):
+                        log.warning("Error raised due to reads in negative control; re-run this without '--errorOnReadsInNegControl' if this execution should succeed.")
+                        raise QCError("The sample '{}' appears to be a negative control, but it contains {} reads after filtering to desired taxa.".format(sample_name,number_of_hits))
+
             # filter original BAM file against keep list
             tools.picard.FilterSamReadsTool().execute(inBam, False, hitList, outBam, JVMmemory=JVMmemory)
 
@@ -233,6 +248,26 @@ def parser_filter_lastal_bam(parser=argparse.ArgumentParser()):
         type=int,
         default=100
     )
+    parser.add_argument(
+        '--errorOnReadsInNegControl',
+        dest="error_on_reads_in_neg_control",
+        help='If specified, the function will return an error if there are reads after filtering for samples with names containing: (water,neg,ntc) (default: %(default)s)',
+        action="store_true",
+    )
+    parser.add_argument(
+        '--negativeControlReadsThreshold',
+        dest="negative_control_reads_threshold",
+        help='maximum number of reads (single-end) or read pairs (paired-end) to tolerate in samples identified as negative controls (default: %(default)s)',
+        type=int,
+        default=0
+    )
+    parser.add_argument(
+        '--negControlPrefixes',
+        dest="neg_control_prefixes",
+        default=["neg","water","NTC"],
+        nargs='*',
+        help='Bam file name prefixes to interpret as negative controls, space-separated (default: %(default)s)'
+    )
     parser.add_argument(
         '--JVMmemory',
         default=tools.picard.FilterSamReadsTool.jvmMemDefault,