def counts2bedgraph(infile, outfile, track, probe):
'''Generate windowed bedgraph around each probe for each track'''
track = P.snip(track, ".tsv")
PipelineCaptureC.interactions2BedGraph(track, probe,
PARAMS["database_name"],
outfile)
def getProbeFragments(infiles, outfile):
'''Fetch the fragments that contain the probes. Entries will be named for
the probe'''
probes, digest = infiles
lookup = P.snip(outfile, "bed.gz") + "lookup.tsv"
PipelineCaptureC.fetchProbeFragments(probes, digest, outfile, lookup)
def countInteractions(infiles, outfile):
'''Count the number of interactions. Read pairs must map to only
two fragments, one each for each primary alignment in the pair'''
reads, digest, probes = infiles
metrics = P.snip(outfile, ".tsv.gz") + ".metrics.tsv"
PipelineCaptureC.countInteractions(reads, digest, probes,
outfile, metrics,
submit=True,
job_memory="4G")
def digest2fragments(infile, outfile):
genome = PARAMS["annotations_interface_contigs_tsv"]
outfile = P.snip(outfile, ".gz")
PipelineCaptureC.sites2fragments(infile, genome, outfile)
statement = '''uniq %(outfile)s > bgzip %(outfile)s.gz;
def qunatifyAnomileies(infiles, outfile):
''' Quantify level of undigested and self ligated fragments'''
bam, probes = infiles
PipelineCaptureC.quantifyAnomolies(bam, probes, outfile)
def digest2fragments(infile, outfile):
genome = PARAMS["annotations_interface_contigs_tsv"]
outfile = P.snip(outfile, ".gz")
PipelineCaptureC.sites2fragments(infile, genome, outfile)
statement = '''uniq %(outfile)s > bgzip %(outfile)s.gz;