import os
def get_data(filename):
"""Returns a filehandler from ../data/filename if it exists"""
pass
if __name__ == '__main__':
import argparse
import fasta_reader
from common import is_valid_file
parser = argparse.ArgumentParser(
description='Compute GC content of a DNA sequence')
parser.add_argument('files',
nargs='+',
help='File or list of files to be processed',
type=lambda f: is_valid_file(f, parser))
args = parser.parse_args()
readers = []
for file in args.files:
reader = fasta_reader.FastaReader()
reader.read_file(file)
readers.append(reader)
for reader in readers:
for name, sequence in reader.sequences.items():
print(sequence.gc_content)
print(sequence.c_count + sequence.t_count + sequence.a_count +
sequence.g_count)
if hit_def not in data:
data[hit_def] = {'bits': bits, 'expect': expect, 'query': query}
elif data[hit_def]['expect'] > expect:
data[hit_def] = {'bits': bits, 'expect': expect, 'query': query}
return data
if __name__ == '__main__':
from common import is_valid_file
import argparse
from Bio.Blast import NCBIXML
import re
parser = argparse.ArgumentParser(description='Parse Blast Query Result XML file')
parser.add_argument('field', help='Field to search in the blast hit list')
parser.add_argument('file', type=lambda f: is_valid_file(f, parser), help='XML file to parse')
args = parser.parse_args()
E_THRESH = 1e-20
fd = open(args.file)
data = {}
output_string = "{:<10}{:<15}{:<10}{}"
result = NCBIXML.parse(fd)
for record in result:
for alignment in record.alignments:
if is_match(args.field, alignment):
for hsp in alignment.hsps:
if hsp.expect < E_THRESH:
update_min(data, record.query, re.search('(?<=\|)\w+', alignment.hit_def).group(0), hsp.bits, hsp.expect)
for k, v in data.items():
print(