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#!/usr/bin/env python3
# Sort the sequences by quality (percentage of number of N bases not called, descending) and by length (descending).
# The best sequence is the longest one, with no uncalled bases.
import os
import sys
import gzip
# import xxhash # Faster library
import hashlib
def open_gzipsafe(path_file):
if path_file.endswith('.gz'):
return gzip.open(path_file, 'rt')
else:
return open(path_file)
path_fasta = sys.argv[1]
hash_to_count_and_headers_dict = {}
header_to_seq_dict = {}
header_percCalledBases_seqLength_list = []
with open_gzipsafe(path_fasta) as f:
for fasta in f.read().strip('\n>').split('>'):
header = fasta.strip('\n').split('\n')[0]
sequence = ''.join(fasta.strip('\n').split('\n')[1:])
# hash = xxhash.xxh64(sequence).hexdigest() # Faster library
hash = hashlib.md5(sequence.encode('utf-8')).hexdigest()
if hash not in hash_to_count_and_headers_dict:
# New sequence
hash_to_count_and_headers_dict[hash] = [0, []]
header_to_seq_dict[header] = sequence
seq_len = len(sequence)
header_percCalledBases_seqLength_list.append([header, (seq_len - sequence.count('N')) / seq_len, seq_len])
hash_to_count_and_headers_dict[hash][0] += 1
hash_to_count_and_headers_dict[hash][1].append(header)
with open('dups.txt', 'w') as fw:
for count, header_list in hash_to_count_and_headers_dict.values():
fw.write('\t'.join([str(count), ', '.join(header_list)]) + '\n')
reversed_sorting = True if len(sys.argv) > 2 and sys.argv[2].lower() == 'true' else False
for header, percCalledBases, seqLength_list in sorted(
header_percCalledBases_seqLength_list, key=lambda x: (x[-2], x[-1]), reverse=reversed_sorting
):
sys.stdout.write('>{}\n{}\n'.format(header, header_to_seq_dict[header]))
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