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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)
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__()