def rename_sequences( sequence_file ):
records = read_sequences( sequence_file )
if any([r.name.strip().endswith('|quiver') for r in records]):
records = [rename_record(r) for r in records]
output_file = get_output_file( sequence_file )
write_sequences( records, output_file )
return output_file
else:
return sequence_file
def exons_to_cDNA( exon_file ):
"""
Combine a multi-Fasta of Exon sequences into a mock cDNA
"""
output_type = get_file_type( exon_file )
output_file = _get_output_file( exon_file, output_type )
records = _parse_exon_records( exon_file, output_type )
log.info("Combinging %s exons sequences to cDNA" % len(records))
if len( records ):
sorted_records = _sort_records( records )
cDNA_record = _combine_records( sorted_records )
log.info("Writing cDNA sequence out to %s" % output_file)
write_sequences( cDNA_record, output_file )
def exons_to_cDNA(exon_file):
"""
Combine a multi-Fasta of Exon sequences into a mock cDNA
"""
output_type = get_file_type(exon_file)
output_file = _get_output_file(exon_file, output_type)
records = _parse_exon_records(exon_file, output_type)
log.info("Combinging %s exons sequences to cDNA" % len(records))
if len(records):
sorted_records = _sort_records(records)
cDNA_record = _combine_records(sorted_records)
log.info("Writing cDNA sequence out to %s" % output_file)
write_sequences(cDNA_record, output_file)
