def buildLncRNAGeneSetStats(infile, outfile):
'''
counts:
no. of transcripts
no. genes
average number of exons per transcript
average number of exons per gene
no. multi-exon transcripts
no. single exon transcripts
no. multi-exon genes
no. single exon genes
in the coding and lncRNA genesets
'''
outf = open(outfile, "w")
outf.write("\t".join([
"no_transcripts", "no_genes", "no_exons_per_transcript",
"no_exons_per_gene", "no_single_exon_transcripts",
"no_multi_exon_transcripts", "no_single_exon_genes",
"no_multi_exon_genes"
]) + "\n")
# For pep8 purposes
x = list(
map(str, [
PipelineLncRNA.CounterTranscripts(infile).count(),
PipelineLncRNA.CounterGenes(infile).count(),
PipelineLncRNA.CounterExonsPerTranscript(infile).count(),
PipelineLncRNA.CounterExonsPerGene(infile).count(),
PipelineLncRNA.CounterSingleExonTranscripts(infile).count(),
PipelineLncRNA.CounterMultiExonTranscripts(infile).count(),
PipelineLncRNA.CounterSingleExonGenes(infile).count(),
PipelineLncRNA.CounterMultiExonGenes(infile).count()
]))
outf.write("\t".join(x))
def __call__(self, track, slice=None):
return odict((("single_exon",
PipelineLncRNA.CounterSingleExonGenes(
os.path.join("gtfs", track) + ".gtf.gz").count()),
("multi_exon",
PipelineLncRNA.CounterMultiExonGenes(
os.path.join("gtfs", track) + ".gtf.gz").count())))
def buildRefcodingGeneSetStats(infile, outfile):
'''
counts:
no. of transcripts
no. genes
average number of exons per transcript
average number of exons per gene
no. multi-exon transcripts
no. single exon transcripts
no. multi-exon genes
no. single exon genes
in the coding and lncRNA genesets
'''
# calculate exon status for refcoding genes.
tmpf = P.getTempFilename(".") + ".gz"
PipelineLncRNA.flagExonStatus(infile, tmpf)
outf = IOTools.openFile(outfile, "w")
outf.write("\t".join([
"no_transcripts", "no_genes", "no_exons_per_transcript",
"no_exons_per_gene", "no_single_exon_transcripts",
"no_multi_exon_transcripts", "no_single_exon_genes",
"no_multi_exon_genes"
]) + "\n")
outf.write("\t".join(
map(str, [
PipelineLncRNA.CounterTranscripts(tmpf).count(),
PipelineLncRNA.CounterGenes(tmpf).count(),
PipelineLncRNA.CounterExonsPerTranscript(tmpf).count(),
PipelineLncRNA.CounterExonsPerGene(tmpf).count(),
PipelineLncRNA.CounterSingleExonTranscripts(tmpf).count(),
PipelineLncRNA.CounterMultiExonTranscripts(tmpf).count(),
PipelineLncRNA.CounterSingleExonGenes(tmpf).count(),
PipelineLncRNA.CounterMultiExonGenes(tmpf).count()
])))
os.unlink(tmpf)
os.unlink(tmpf + ".log")
os.unlink(P.snip(tmpf, ".gz"))