Source code for galaxy.datatypes.converters.fastqsolexa_to_fasta_converter

#!/usr/bin/env python
"""
convert fastqsolexa file to separated sequence and quality files.

assume each sequence and quality score are contained in one line
the order should be:
1st line: @title_of_seq
2nd line: nucleotides
3rd line: +title_of_qualityscore (might be skipped)
4th line: quality scores
(in three forms: a. digits, b. ASCII codes, the first char as the coding base, c. ASCII codes without the first char.)

Usage:
%python fastqsolexa_to_fasta_converter.py <your_fastqsolexa_filename> <output_seq_filename> <output_score_filename>
"""
import sys

assert sys.version_info[:2] >= (2, 4)


[docs]def stop_err(msg): sys.exit("%s" % msg)
def __main__(): infile_name = sys.argv[1] fastq_block_lines = 0 seq_title_startswith = '' with open(infile_name) as fh, open(sys.argv[2], 'w') as outfile: for i, line in enumerate(fh): line = line.rstrip() # eliminate trailing space and new line characters if not line or line.startswith('#'): continue fastq_block_lines = (fastq_block_lines + 1) % 4 line_startswith = line[0:1] if fastq_block_lines == 1: # line 1 is sequence title if not seq_title_startswith: seq_title_startswith = line_startswith if seq_title_startswith != line_startswith: stop_err('Invalid fastqsolexa format at line %d: %s.' % (i + 1, line)) outfile.write('>%s\n' % line[1:]) elif fastq_block_lines == 2: # line 2 is nucleotides outfile.write('%s\n' % line) else: pass if __name__ == "__main__": __main__()