Mercurial > repos > iuc > gff_to_prot
comparison gff_to_prot.py @ 0:99810cf51f2e draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
author | iuc |
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date | Mon, 22 Apr 2019 14:42:21 -0400 |
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-1:000000000000 | 0:99810cf51f2e |
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1 #!/usr/bin/env python | |
2 import csv | |
3 import os | |
4 import sys | |
5 | |
6 | |
7 def get_description(line, parent): | |
8 cols = line.split('\t') | |
9 labels = {} | |
10 for pair in cols[8].split(";"): | |
11 k, v = pair.split('=') | |
12 labels[k] = v | |
13 | |
14 if (cols[2]) == "CDS" and labels["Parent"] == parent: | |
15 return labels.get("Note", '-') | |
16 return '-' | |
17 | |
18 | |
19 def convert_to_prot_table(fname, output_name): | |
20 gff_file = open(fname) | |
21 output_file = open(output_name, 'w') | |
22 writer = csv.writer(output_file, delimiter='\t') | |
23 lines = gff_file.readlines() | |
24 gff_file.close() | |
25 for i, line in enumerate(lines): | |
26 line = line.strip() | |
27 if line.startswith('#'): | |
28 continue | |
29 cols = line.split('\t') | |
30 if (len(cols) < 9): | |
31 print("Ignoring invalid row with entries: {0}".format(cols)) | |
32 elif (cols[2]) == "region": | |
33 continue | |
34 elif (cols[2]) == "CDS": | |
35 continue | |
36 elif (cols[2]) == "gene": | |
37 start = int(cols[3]) | |
38 end = int(cols[4]) | |
39 strand = cols[6].strip() | |
40 labels = {} | |
41 diff = int(abs(end - start) / 3) # What is this called? | |
42 for pair in cols[8].split(";"): | |
43 k, v = pair.split('=') | |
44 labels[k.strip()] = v.strip() | |
45 | |
46 Rv = labels["locus_tag"].strip() # error out if not found | |
47 gene = labels.get('Name', '') | |
48 desc = get_description(lines[i + 1], labels.get("ID", "")) if (i + 1) < len(lines) else '-' | |
49 vals = [desc, start, end, strand, diff, '-', '-', gene, Rv, '-'] | |
50 writer.writerow(vals) | |
51 output_file.close() | |
52 | |
53 | |
54 if __name__ == "__main__": | |
55 usage_string = "Usage: python gff-prot-converter.py <gff filename> <output filename>" | |
56 | |
57 if len(sys.argv) < 3: | |
58 print(usage_string) | |
59 sys.exit(0) | |
60 file_name = sys.argv[1] | |
61 if not os.path.exists(file_name): | |
62 print("File not found. Exiting...") | |
63 print(usage_string) | |
64 sys.exit(0) | |
65 convert_to_prot_table(file_name, sys.argv[2]) |