def buildCoverageStats(infile, outfile):
'''Generate coverage statistics for regions of interest from a
bed file using Picard'''
# TS check whether this is always required or specific to current baits file
# baits file requires modification to make picard accept it
# this is performed before CalculateHsMetrics
to_cluster = USECLUSTER
baits = PARAMS["roi_baits"]
modified_baits = infile + "_temp_baits_final.bed"
regions = PARAMS["roi_regions"]
statement = '''samtools view -H %(infile)s > %(infile)s_temp_header.txt;
awk 'NR>2' %(baits)s |
awk -F '\\t' 'BEGIN { OFS="\\t" } {print $1,$2,$3,"+",$4;}'
> %(infile)s_temp_baits.bed;
cat %(infile)s_temp_header.txt %(infile)s_temp_baits.bed
> %(modified_baits)s; checkpoint ;
rm -rf %(infile)s_temp_baits.bed %(infile)s_temp_header.txt
'''
P.run()
PipelineMappingQC.buildPicardCoverageStats(
infile, outfile, modified_baits, modified_baits)
IOTools.zapFile(modified_baits)
def buildCoverageStats(infile, outfile):
'''Generate coverage statistics for regions of interest from a
bed file using Picard'''
# TS check whether this is always required or specific to current baits
# file
# baits file requires modification to make picard accept it
# this is performed before CalculateHsMetrics
to_cluster = USECLUSTER
baits = PARAMS["roi_baits"]
modified_baits = infile + "_temp_baits_final.bed"
regions = PARAMS["roi_regions"]
statement = '''samtools view -H %(infile)s > %(infile)s_temp_header.txt;
awk 'NR>2' %(baits)s |
awk -F '\\t' 'BEGIN { OFS="\\t" } {print $1,$2,$3,"+",$4;}'
> %(infile)s_temp_baits.bed;
cat %(infile)s_temp_header.txt %(infile)s_temp_baits.bed
> %(modified_baits)s; checkpoint ;
rm -rf %(infile)s_temp_baits.bed %(infile)s_temp_header.txt
'''
P.run()
PipelineMappingQC.buildPicardCoverageStats(infile, outfile, modified_baits,
modified_baits)
IOTools.zapFile(modified_baits)
def buildPicardStats(infile, outfile):
'''build alignment stats using picard.
Note that picards counts reads but they are in fact alignments.
'''
if PARAMS["pool_reads"]:
reffile = os.path.join(
os.path.dirname(infile), "agg-agg-agg.filtered.contigs.fa")
else:
reffile = P.snip(infile, ".bam") + ".fa"
PipelineMappingQC.buildPicardAlignmentStats(infile,
outfile,
reffile)
def runPicardOnRealigned(infile, outfile):
to_cluster = USECLUSTER
job_options = getGATKOptions()
# TS no multithreading so why 6 threads?
# job_threads = 6
tmpdir_gatk = P.getTempDir('/ifs/scratch')
# threads = PARAMS["gatk_threads"]
outfile_tumor = outfile.replace("Control", PARAMS["mutect_tumour"])
infile_tumor = infile.replace("Control", PARAMS["mutect_tumour"])
track = P.snip(os.path.basename(infile), ".bam")
track_tumor = track.replace("Control", PARAMS["mutect_tumour"])
genome = "%s/%s.fa" % (PARAMS["bwa_index_dir"],
PARAMS["genome"])
PipelineMappingQC.buildPicardAlignmentStats(infile, outfile, genome)
PipelineMappingQC.buildPicardAlignmentStats(infile_tumor,
outfile_tumor, genome)
# check above functions then remove statement
statement = '''
cat %(infile)s
| python %%(scriptsdir)s/bam2bam.py -v 0 --method=set-sequence
| CollectMultipleMetrics
INPUT=/dev/stdin
REFERENCE_SEQUENCE=%%(bwa_index_dir)s/%%(genome)s.fa
ASSUME_SORTED=true
OUTPUT=%(outfile)s
VALIDATION_STRINGENCY=SILENT
>& %(outfile)s;
cat %(infile_tumor)s
| python %%(scriptsdir)s/bam2bam.py -v 0
--method=set-sequence --output-sam
| CollectMultipleMetrics
INPUT=/dev/stdin
REFERENCE_SEQUENCE=%%(bwa_index_dir)s/%%(genome)s.fa
ASSUME_SORTED=true
OUTPUT=%(outfile_tumor)s
VALIDATION_STRINGENCY=SILENT
>& %(outfile_tumor)s;''' % locals()
def runPicardOnRealigned(infile, outfile):
to_cluster = USECLUSTER
job_memory = PARAMS["gatk_memory"]
tmpdir_gatk = P.getTempDir()
outfile_tumor = outfile.replace(PARAMS["sample_control"],
PARAMS["sample_tumour"])
infile_tumor = infile.replace(PARAMS["sample_control"],
PARAMS["sample_tumour"])
track = P.snip(os.path.basename(infile), ".bam")
track_tumor = track.replace(PARAMS["sample_control"],
PARAMS["sample_tumour"])
genome = "%s/%s.fa" % (PARAMS["bwa_index_dir"], PARAMS["genome"])
PipelineMappingQC.buildPicardAlignmentStats(infile, outfile, genome)
PipelineMappingQC.buildPicardAlignmentStats(infile_tumor, outfile_tumor,
genome)
def runPicardOnRealigned(infile, outfile):
to_cluster = USECLUSTER
job_memory = PARAMS["gatk_memory"]
tmpdir_gatk = P.getTempDir()
outfile_tumor = outfile.replace(
PARAMS["sample_control"], PARAMS["sample_tumour"])
infile_tumor = infile.replace(
PARAMS["sample_control"], PARAMS["sample_tumour"])
track = P.snip(os.path.basename(infile), ".bam")
track_tumor = track.replace(
PARAMS["sample_control"], PARAMS["sample_tumour"])
genome = "%s/%s.fa" % (PARAMS["bwa_index_dir"],
PARAMS["genome"])
PipelineMappingQC.buildPicardAlignmentStats(infile, outfile, genome)
PipelineMappingQC.buildPicardAlignmentStats(infile_tumor,
outfile_tumor, genome)
def buildBAMStats(infile, outfile):
'''Count number of reads mapped, duplicates, etc. '''
PipelineMappingQC.buildBAMStats(infile, outfile)
def buildPicardGCStats(infile, outfile):
'''Gather BAM file GC bias stats using Picard '''
PipelineMappingQC.buildPicardGCStats(
infile, outfile,
os.path.join(PARAMS["bwa_index_dir"], PARAMS["genome"] + ".fa"))
def loadPicardAlignmentStats(infiles, outfile):
'''Merge Picard alignment stats into single table and load into SQLite.'''
PipelineMappingQC.loadPicardAlignmentStats(infiles, outfile)
def buildPicardAlignmentStats(infile, outfile):
'''Gather BAM file alignment statistics using Picard '''
PipelineMappingQC.buildPicardAlignmentStats(
infile, outfile,
os.path.join(PARAMS["bwa_index_dir"], PARAMS["genome"] + ".fa"))
def loadPicardDuplicateStats(infiles, outfile):
'''Merge Picard duplicate stats into single table and load into SQLite.
'''
PipelineMappingQC.loadPicardDuplicateStats(infiles, outfile)
def loadCoverageStats(infiles, outfile):
PipelineMappingQC.loadPicardCoverageStats(infiles, outfile)
def buildPicardAlignmentStats(infile, outfile):
'''Gather BAM file alignment statistics using Picard '''
PipelineMappingQC.buildPicardAlignmentStats(infile, outfile,
os.path.join(PARAMS["bwa_index_dir"],
PARAMS["genome"] + ".fa"))
def loadBAMStats(infiles, outfile):
''' load bam statistics into bam_stats table '''
PipelineMappingQC.loadBAMStats(infiles, outfile)
def loadBAMStats(infiles, outfile):
'''Import bam statistics into SQLite'''
PipelineMappingQC.loadBAMStats(infiles, outfile)
def loadPicardAlignStats(infiles, outfile):
'''Merge Picard alignment stats into single table and load into SQLite.'''
PipelineMappingQC.loadPicardAlignmentStats(infiles, outfile)
def loadCoverageStats(infiles, outfile):
PipelineMappingQC.loadPicardCoverageStats(infiles, outfile)
def buildPicardGCStats(infile, outfile):
'''Gather BAM file GC bias stats using Picard '''
PipelineMappingQC.buildPicardGCStats(infile, outfile,
os.path.join(PARAMS["bwa_index_dir"],
PARAMS["genome"] + ".fa"))
def loadBAMStats(infiles, outfile):
'''Import bam statistics into SQLite'''
PipelineMappingQC.loadBAMStats(infiles, outfile)
def buildBAMStats(infile, outfile):
'''Count number of reads mapped, duplicates, etc. '''
PipelineMappingQC.buildBAMStats(infile, outfile)
def loadPicardDuplicateStats( infiles, outfile ):
'''Merge Picard duplicate stats into single table and load into SQLite.
'''
PipelineMappingQC.loadPicardDuplicateStats( infiles, outfile, pipeline_suffix = ".bed.gz" )
def loadPicardStats(infiles, outfile):
'''merge alignment stats into single tables.'''
PipelineMappingQC.loadPicardAlignmentStats(infiles, outfile)