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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,84 @@ | ||
| #!/usr/bin/python | ||
| # File created on 31 Jan 2014. | ||
|
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| __author__ = "Erick Cardenas Poire" | ||
| __copyright__ = "Copyright 2014" | ||
| __credits__ = [""] | ||
| __version__ = "1.0" | ||
| __maintainer__ = "Erick Cardenas Poire" | ||
| __status__ = "Release" | ||
|
|
||
| from Bio import SeqIO | ||
| import sys | ||
| from os import makedirs, sys, listdir, environ, path | ||
| import re | ||
| import inspect | ||
| from commands import getstatusoutput | ||
| from optparse import OptionParser | ||
| import shutil | ||
|
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| #config = load_config() | ||
| script_info = {} | ||
| script_info['brief_description'] = """Adds coverage information from one file and modifies fasta header""" | ||
| script_info['script_description'] = """Adds coverage information from one file and modifies fasta header | ||
| REQUIRED: You must have a fasta and coverage file with same base name""" | ||
| script_info['script_usage'] = [] | ||
|
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| usage= """ | ||
| Need to run it like this: | ||
| ./add.coverage.to.fasta.py -i input_file | ||
| For more options: ./add.coverage.to.fasta.py -h""" | ||
|
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| parser = OptionParser(usage) | ||
| parser.add_option("-i", "--input_file", dest = "input_fp", | ||
| help = 'the input fasta file/input dir [REQUIRED]') | ||
|
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|
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| #creates an input output pair if input is just an input file | ||
| def create_an_inputs_and_output(input_file): | ||
| input_output = [] | ||
| shortname = re.sub('[.](fasta$|fas$|fna$|faa$|fsa$|fa$)','',input_file, re.I) #finds file format removes extension, case insensitive search | ||
| coverage_input_file = shortname+".cov" | ||
| output_file = shortname + ".new.fasta" | ||
| input_output.append(input_file) | ||
| input_output.append(coverage_input_file) | ||
| input_output.append(output_file) | ||
| return input_output | ||
|
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||
| # checks if the supplied arguments are adequate | ||
| def valid_arguments(opts, args): | ||
| if opts.input_fp == None: | ||
| return True | ||
| else: | ||
| return False | ||
|
|
||
| def main(argv): | ||
| (opts, args) = parser.parse_args() | ||
| if valid_arguments(opts, args): | ||
| print usage | ||
| sys.exit(0) | ||
|
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| # initialize the input directory or file | ||
| input_fp = opts.input_fp | ||
| list_of_files = create_an_inputs_and_output(input_fp) | ||
|
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| # Creates coverage dictionary | ||
| coverage_dictionary = {} | ||
| coverage_file_in = open(list_of_files[1],'r') | ||
| for line in coverage_file_in: | ||
| line = line.split('\t') | ||
| seq_ID = line[0] | ||
| seq_coverage = line[1] | ||
| coverage_dictionary[seq_ID] = seq_coverage | ||
| coverage_file_in.close() | ||
|
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| fileout = open(list_of_files[2], 'w') | ||
| for seq_record in SeqIO.parse(list_of_files[0], format = "fasta"): | ||
| seq_name = seq_record.id | ||
| coverage = coverage_dictionary.get(seq_name,0) | ||
| description = "coverage=" + coverage | ||
| fileout.write('>%s %s\n%s\n' %(seq_record.id, description, seq_record.seq)) | ||
| fileout.close() | ||
|
|
||
| # the main function | ||
| main(sys.argv[1:]) |
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