Mercurial > repos > george-weingart > lefse

comparison home/ubuntu/lefse_to_export/qiime2lefse.py @ 1:db64b6287cd6 draft

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Modified datatypes
author george-weingart
date Wed, 20 Aug 2014 16:56:51 -0400
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0:e7cd19afda2e 1:db64b6287cd6
1 #!/usr/bin/env python
2
3 import sys
4
5 def read_params(args):
6 import argparse as ap
7 import textwrap
8
9 p = ap.ArgumentParser( description= "TBA" )
10
11 p.add_argument( '--in', metavar='INPUT_FILE', type=str,
12 nargs='?', default=sys.stdin,
13 help= "the Qiime OTU table file "
14 "[ stdin if not present ]" )
15 p.add_argument( '--md', metavar='METADATA_FILE', type=str,
16 nargs='?', default=None,
17 help= "the Qiime OTU table file "
18 "[ only OTU table without metadata if not present ]" )
19 p.add_argument( '--out', metavar='OUTPUT_FILE', type=str,
20 nargs = '?', default=sys.stdout,
21 help= "the output file "
22 "[stdout if not present]")
23
24 p.add_argument( '-c', metavar="class attribute",
25 type=str,
26 help = "the attribute to use as class" )
27 p.add_argument( '-s', metavar="subclass attribute",
28 type=str,
29 help = "the attribute to use as subclass" )
30 p.add_argument( '-u', metavar="subject attribute",
31 type=str,
32 help = "the attribute to use as subject" )
33
34
35
36 return vars(p.parse_args())
37
38
39
40 def qiime2lefse( fin, fmd, fout, all_md, sel_md ):
41 with (fin if fin==sys.stdin else open(fin)) as inpf :
42 lines = [list(ll) for ll in
43 (zip(*[l.strip().split('\t')
44 for l in inpf.readlines()[1:]]) ) ]
45 for i,(l1,l2) in enumerate(zip( lines[0], lines[-1] )):
46 if not l2 == 'Consensus Lineage':
47 lines[-1][i] = l2+"|"+l1
48
49 data = dict([(l[0],l[1:]) for l in lines[1:]])
50
51 md = {}
52 if fmd:
53 with open(fmd) as inpf:
54 mdlines = [l.strip().split('\t') for l in inpf.readlines()]
55
56 mdf = mdlines[0][1:]
57
58 for l in mdlines:
59 mdd = dict(zip(mdf,l[1:]))
60 md[l[0]] = mdd
61
62 selected_md = md.values()[0].keys() if md else []
63
64 if not all_md:
65 selected_md = [s for s in sel_md if s]
66
67 out_m = [ selected_md +
68 list([d.replace(";","|").replace("\"","") for d in data[ 'Consensus Lineage' ]]) ]
69 for k,v in data.items():
70 if k == 'Consensus Lineage':
71 continue
72 out_m.append( [md[k][kmd] for kmd in selected_md] + list(v) )
73
74 with (fout if fout == sys.stdout else open( fout, "w" )) as outf:
75 for l in zip(*out_m):
76 outf.write( "\t".join(l) + "\n" )
77
78 if __name__ == '__main__':
79 pars = read_params( sys.argv )
80
81 qiime2lefse( fin = pars['in'],
82 fmd = pars['md'],
83 fout = pars['out'],
84 all_md = not pars['c'] and not pars['s'] and not pars['u'],
85 sel_md = [pars['c'],pars['s'],pars['u']])