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)