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#!/usr/bin/env python
# File created on 29 May 2011
from __future__ import division
__author__ = "Greg Caporaso"
__copyright__ = "Copyright 2011, The QIIME project"
__credits__ = ["Greg Caporaso"]
__license__ = "GPL"
__version__ = "1.4.0"
__maintainer__ = "Greg Caporaso"
__email__ = "gregcaporaso@gmail.com"
__status__ = "Release"
from glob import glob
from qiime.util import (parse_command_line_parameters,
make_option,
count_seqs_in_filepaths)
script_info = {}
script_info['brief_description'] = ""
script_info['script_description'] = ""
script_info['script_usage'] = [\
("",
"Count the sequences in a fasta file and write results to stdout.",
"%prog -i in.fasta"),
("",
"Count the sequences in a fasta file and a fastq file and write results to file. Note that fastq files can only be processed if they end with .fastq -- all other files are assumed to be fasta.",
"%prog -i in1.fasta,in2.fastq -o seq_counts.txt"),
("",
"Count the sequences all .fasta files in current directory and write results to stdout. Note that -i option must be quoted.",
"%prog -i \"*.fasta\"")]
script_info['output_description']= ""
script_info['required_options'] = [\
# Example required option
make_option('-i','--input_fps',
help='the input filepaths (comma-separated)'),
]
script_info['optional_options'] = [
# Example optional option
make_option('-o','--output_fp',type="new_filepath",
help='the output filepath [default: write to stdout]'),\
make_option('--suppress_errors',action='store_true',\
help='Suppress warnings about missing files [default: %default]',
default=False)
]
script_info['version'] = __version__
def format_output(count_data, total, inaccessible_filepaths, suppress_errors=False):
""" Output formatter """
lines = ['']
for c in count_data:
lines.append('%d : %s (Sequence lengths (mean +/- std): %1.4f +/- %1.4f)' %
(c[0][0],c[1],c[0][1],c[0][2]))
lines.append('%d : Total' % total)
if inaccessible_filepaths and not suppress_errors:
lines.append('')
lines.append(\
'Some files were not accessible. Do they exist? Do you have read permission?')
for inaccessible_filepath in inaccessible_filepaths:
lines.append(' %s' % inaccessible_filepath)
lines.append('')
return '\n'.join(lines)
def main():
option_parser, opts, args =\
parse_command_line_parameters(**script_info)
suppress_errors = opts.suppress_errors
input_fps = []
for e in opts.input_fps.split(','):
input_fps.extend(glob(e))
input_fps = set(input_fps)
if len(input_fps) == 0:
option_parser.error(\
"No filepaths match pattern(s) passed via -i: %s" % opts.input_fps)
output_fp = opts.output_fp
count_data, total, inaccessible_filepaths = count_seqs_in_filepaths(input_fps)
r = format_output(count_data, total, inaccessible_filepaths, suppress_errors)
if opts.output_fp:
f = open(output_fp,'w')
f.write(r)
f.close()
else:
print r
if __name__ == "__main__":
main()
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