def _create_gtf_from_transcripts(self,
gtf_path,
exons_by_transcript,
genes=None,
strands=None):
gtf = tests.gtf.GTF()
gtf.path = gtf_path
transcripts = list()
for i, exons_for_transcript in enumerate(exons_by_transcript):
transcript = tests.gtf.Transcript()
transcript.chromosome = '1'
strand_i = '+'
if strands is not None:
strand_i = strands[i]
transcript.strand = strand_i
gene_i = 1
if genes is not None:
gene_i = genes[i]
transcript.gene_id = tests.util.gene_id_str(gene_i)
transcript.gene_name = tests.util.gene_name_str(gene_i)
transcript.transcript_id = tests.util.transcript_id_str(i)
transcript.exons = exons_for_transcript
transcripts.append(transcript)
gtf.transcripts = transcripts
error = gtf.write()
self.assertFalse(error)
return gtf
def _create_gtf(self, gtf_path):
gtf = tests.gtf.GTF()
gtf.path = gtf_path
transcript_1 = tests.gtf.Transcript()
transcript_1.chromosome = '1'
transcript_1.strand = '+'
transcript_1.gene_id = tests.util.gene_id_str(1)
transcript_1.gene_name = tests.util.gene_name_str(1)
transcript_1.transcript_id = tests.util.transcript_id_str(1)
transcript_1.exons = [(1, 100), (201, 300), (401, 500)]
gtf.transcripts = [transcript_1]
error = gtf.write()
self.assertFalse(error)
return gtf
def _create_gtf_from_transcripts(self, gtf_path, exons_by_transcript):
gtf = tests.gtf.GTF()
gtf.path = gtf_path
transcripts = list()
for i, exons_for_transcript in enumerate(exons_by_transcript):
transcript = tests.gtf.Transcript()
transcript.chromosome = '1'
transcript.strand = '+'
transcript.gene_id = tests.util.gene_id_str(1)
transcript.gene_name = tests.util.gene_name_str(1)
transcript.transcript_id = tests.util.transcript_id_str(i)
transcript.exons = exons_for_transcript
transcripts.append(transcript)
gtf.transcripts = transcripts
error = gtf.write()
self.assertFalse(error)
return gtf