Mercurial > repos > greg > cfsan_snp_pipeline_quast_select

comparison cfsan_snp_pipeline_quast_select.py @ 0:fedc60909fbe draft default tip

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author greg
date Tue, 17 Oct 2023 14:13:45 +0000
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-1:000000000000 0:fedc60909fbe
1 #!/usr/bin/env python
2
3 import csv
4 import sys
5
6
7 def pick(rows, key, reverse=False):
8 sorted_rows = sorted(rows, key=lambda r: r[key], reverse=reverse)
9 return sorted_rows[0]['Assembly']
10
11
12 def int_or_str(token):
13 try:
14 return int(token)
15 except ValueError:
16 return str(token)
17
18
19 if __name__ == '__main__':
20 path, criterion = sys.argv[1:]
21 # QUAST tables have sample info as columns, so we need to transpose the table.
22 rows = list(zip(*csv.reader(open(path, "r"), delimiter='\t', dialect='excel')))
23 hed = rows.pop(0)
24 dict_rows = [{h: int_or_str(r[i]) for i, h in enumerate(hed)} for r in rows]
25 if "fewest" in criterion:
26 # If it's a count, we want the fewest.
27 reverse = False
28 else:
29 # Otherwise it's a length and we want the longest.
30 reverse = True
31 print(pick(dict_rows, criterion, reverse))