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#!/usr/bin/env python
from __future__ import division
__author__ = "Greg Caporaso"
__copyright__ = "Copyright 2011, The PyCogent project"
__credits__ = ["Greg Caporaso"]
__license__ = "GPL"
__version__ = "1.6.0dev"
__maintainer__ = "Greg Caporaso"
__email__ = "gregcaporaso@gmail.com"
__status__ = "Development"
from glob import glob
from cogent.util.option_parsing import (
parse_command_line_parameters,
make_option)
from cogent.parse.fasta import MinimalFastaParser
script_info = {}
script_info['brief_description'] = "Count sequences in one or more fasta files."
script_info['script_description'] = "This script counts the number of sequences in one or more fasta files and prints the results to stdout."
script_info['script_usage'] = [\
("Count sequences in one file",
"Count the sequences in a fasta file and write results to stdout.",
"%prog -i in.fasta"),
("Count sequences in two file",
"Count the sequences in two fasta files and write results to stdout.",
"%prog -i in1.fasta,in2.fasta"),
("Count the sequences in many fasta files",
"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']= "Tabular data is written to stdout."
script_info['required_options'] = [
make_option('-i','--input_fps',
help='the input filepaths (comma-separated)'),
]
script_info['optional_options'] = [
make_option('--suppress_errors',action='store_true',\
help='Suppress warnings about missing files [default: %default]',
default=False)
]
script_info['version'] = __version__
def main():
option_parser, opts, args =\
parse_command_line_parameters(**script_info)
suppress_errors = opts.suppress_errors
input_fps = []
for input_fp in opts.input_fps.split(','):
input_fps.extend(glob(input_fp))
for input_fp in input_fps:
i = 0
try:
input_f = open(input_fp,'U')
except IOError,e:
if suppress_errors:
continue
else:
print input_fp, e
for s in MinimalFastaParser(input_f):
i += 1
print input_fp, i
if __name__ == "__main__":
main()
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