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comparison fasta2database.py @ 10:d0431a839606 draft

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author petr-novak
date Wed, 14 Aug 2019 11:24:15 -0400
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9:ed4d9ede9cb4 10:d0431a839606
1 #!/usr/bin/env python3
2 '''
3 Helper script to create DANTE databese which can be used in second iteration
4 '''
5 import sys
6
7 fasta_input = sys.argv[1]
8 db_fasta_output_file = sys.argv[2]
9 db_classification_file = sys.argv[3]
10 classification_table = set()
11 # fasta header will be reformatted to correct REXdb classification
12 with open(fasta_input, 'r') as f, open(db_fasta_output_file, 'w') as out:
13 for line in f:
14 if line[0] == ">":
15 ## modify header
16 name, domain, classification = line.split(" ")
17 name_clean=name[1:].replace("-","_")
18 new_header = ">NA-{}__{}\n".format(domain, name_clean)
19 classification_string = "\t".join(classification.split("|"))
20 classification_table.add("{}\t{}".format(name_clean, classification_string))
21 out.write(new_header)
22 else:
23 out.write(line)
24 with open(db_classification_file, 'w') as f:
25 f.writelines(classification_table)