Mercurial > repos > cpt > cpt_blast_to_xmfa

annotate blast2pxmfa.py @ 1:c66d6978a5f8 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
author cpt
date Mon, 05 Jun 2023 02:14:17 +0000
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
1
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
1 #!/usr/bin/env python
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
2 import os
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
3 import argparse
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
4 from CPT_GFFParser import gffParse, gffWrite
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
5 from Bio import SeqIO
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
6 from Bio.SeqRecord import SeqRecord
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
7 from gff3 import feature_lambda, feature_test_true
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
8 from Bio.Align.Applications import ClustalwCommandline
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
9 from Bio import AlignIO
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
10 import tempfile
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
11 import logging
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
12
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
13 log = logging.getLogger()
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
14 log.setLevel(logging.DEBUG)
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
15
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
16
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
17 def parse_gff3(annotations, genome):
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
18 annotations.seek(0)
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
19 genome.seek(0)
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
20
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
21 data = {}
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
22 seq_dict = SeqIO.to_dict(SeqIO.parse(genome, "fasta"))
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
23 for record in gffParse(annotations, base_dict=seq_dict):
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
24 for feature in feature_lambda(
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
25 record.features, feature_test_true, {}, subfeatures=False
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
26 ):
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
27 data[feature.id] = {
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
28 "rec": record.id,
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
29 "loc": feature.location,
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
30 "seq": feature.extract(record).seq.translate(table=11, cds=False)[0:-1],
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
31 }
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
32 return data
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
33
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
34
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
35 def get_seqids(genome):
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
36 genome.seek(0)
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
37 recids = []
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
38 for record in SeqIO.parse(genome, "fasta"):
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
39 recids.append(record.id)
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
40 return recids
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
41
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
42
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
43 def gen_relationships(blast):
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
44 for row in blast:
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
45 line = row.split("\t")
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
46 yield {"from": line[0], "to": line[1], "pident": line[2], "evalue": line[10]}
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
47
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
48
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
49 def cluster_relationships(data):
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
50 generated_clusters_ids = []
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
51
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
52 for relationship in data:
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
53 hit = False
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
54 relationship_set = set((relationship["from"], relationship["to"]))
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
55 for idx, cluster in enumerate(generated_clusters_ids):
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
56 if relationship["from"] in cluster or relationship["to"] in cluster:
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
57 generated_clusters_ids[idx] = cluster.__or__(relationship_set)
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
58 hit = True
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
59 break
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
60
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
61 if not hit:
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
62 generated_clusters_ids.append(relationship_set)
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
63 return generated_clusters_ids
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
64
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
65
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
66 def align_sequences(SequenceList):
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
67 # No sense in aligning one sequence.
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
68 if len(SequenceList) < 2:
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
69 return None
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
70
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
71 # Clustal mangles IDs. Fricking Clustal. Specifically it truncates them
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
72 # meaning we have to RE-ID every single sequence that goes into it. Lovely.
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
73 id_map = {}
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
74 for idx, seq in enumerate(SequenceList):
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
75 id_map[str(idx)] = seq.id
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
76 seq.id = str(idx)
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
77
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
78 t_fa = tempfile.NamedTemporaryFile(prefix="blastxmfa.", delete=False)
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
79 t_aln = tempfile.NamedTemporaryFile(prefix="blastxmfa.", delete=False)
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
80 # Write fasta to file
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
81 SeqIO.write(SequenceList, str.encode(t_fa.name), "fasta")
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
82 # Flush & close
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
83 t_fa.flush()
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
84 t_fa.close()
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
85 t_aln.close()
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
86
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
87 # Build clustal CLI
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
88 d = ClustalwCommandline(infile=t_fa.name, outfile=t_aln.name)
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
89 logging.debug(d)
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
90 # Call clustal
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
91 d()
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
92 # Get our alignment back
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
93 try:
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
94 aln = AlignIO.read(t_aln.name, "clustal")
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
95 # Now we replace the IDs with the correct, full length ones
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
96 for a in aln:
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
97 a.id = id_map[a.id]
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
98 # Cleanup
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
99 os.unlink(t_fa.name)
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
100 os.unlink(t_aln.name)
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
101 return aln
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
102 except Exception as e:
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
103 logging.error("%s, %s", e, t_fa.name)
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
104 os.unlink(t_aln.name)
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
105 return None
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
106
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
107
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
108 def split_by_n(seq, n):
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
109 """A generator to divide a sequence into chunks of n units."""
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
110 # http://stackoverflow.com/questions/9475241/split-python-string-every-nth-character
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
111 while seq:
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
112 yield seq[:n]
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
113 seq = seq[n:]
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
114
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
115
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
116 def larger_than_one(it):
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
117 for item in it:
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
118 if len(item) > 1:
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
119 yield item
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
120
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
121
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
122 def smaller_than_3n(x, it):
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
123 THRESH = 3 * x
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
124 for item in it:
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
125 if len(item) <= THRESH:
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
126 yield item
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
127 else:
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
128 log.warn(
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
129 "Cluster with %s (>%s) members, seems excessive", len(item), THRESH
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
130 )
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
131
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
132
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
133 class XmfaWriter(object):
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
134 HEADER_TPL = "> {seqnum}:{start}-{end} {strand} {file} # {realname}\n"
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
135
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
136 def __init__(self, handle):
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
137 self.output = handle
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
138 self.output.write("#FormatVersion Mauve1\n")
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
139
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
140 def write(self, seqnum, start, end, strand, file, realname, sequence):
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
141 self.output.write(
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
142 self.HEADER_TPL.format(
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
143 seqnum=seqnum,
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
144 start=start,
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
145 end=end,
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
146 strand=strand,
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
147 file=file,
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
148 realname=realname,
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
149 )
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
150 )
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
151
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
152 for line in split_by_n(sequence, 80):
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
153 self.output.write(line + "\n")
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
154
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
155 def end(self):
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
156 self.output.write("=\n")
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
157
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
158
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
159 def blast2pxmfa(blast, fasta, gff3, output, genomic=False):
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
160 logging.info("Parsing sequence")
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
161 locations = parse_gff3(gff3, fasta)
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
162 logging.info("Parsed locations, clustering")
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
163 recids = get_seqids(fasta)
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
164 logging.info("Found %s records in fasta", len(recids))
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
165
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
166 xmw = XmfaWriter(output)
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
167
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
168 # First let's generate some blastclust style clusters.
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
169 clusters = list(
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
170 smaller_than_3n(
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
171 len(recids),
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
172 larger_than_one(cluster_relationships(gen_relationships(blast))),
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
173 )
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
174 )
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
175 logging.debug("%s clusters generated", len(clusters))
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
176
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
177 def sortIndexForFeatId(element):
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
178 # Will not work correctly if genome length is >1mb
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
179 general = recids.index(locations[element]["rec"]) * 1000000
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
180 specific = locations[element]["loc"].start
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
181 return general + specific
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
182
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
183 for idx, cluster in enumerate(clusters):
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
184 logging.debug("Cluster %s/%s, size=%s", idx + 1, len(clusters), len(cluster))
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
185 # We're considering 1 LCB :: 1 cluster
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
186 seqs = []
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
187 for element in cluster:
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
188 if element not in locations:
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
189 logging.warning("Could not find this feature %s", element)
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
190 continue
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
191
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
192 sr = SeqRecord(
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
193 locations[element]["seq"],
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
194 id=element,
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
195 description="[{0.start}:{0.end}:{0.strand}]".format(
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
196 locations[element]["loc"]
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
197 ),
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
198 )
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
199 seqs.append(sr)
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
200
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
201 aligned_seqs = align_sequences(seqs)
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
202 if aligned_seqs is None:
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
203 logging.error("Error aligning cluster [%s]", "".join(cluster))
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
204 continue
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
205
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
206 sortedCluster = sorted(cluster, key=lambda x: sortIndexForFeatId(x))
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
207 sortedAligned = sorted(aligned_seqs, key=lambda x: sortIndexForFeatId(x.id))
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
208 # print(sortedCluster, [x.id for x in sortedAligned])
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
209
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
210 # Pre-check the asserts.
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
211 goodToGo = all(
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
212 [
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
213 element == aligned_seq.id
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
214 for (element, aligned_seq) in zip(sortedCluster, sortedAligned)
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
215 ]
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
216 )
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
217 if not goodToGo:
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
218 logging.info(
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
219 "Skipping one grouping: %s != %s",
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
220 ",".join(sortedCluster),
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
221 ",".join([x.id for x in sortedAligned]),
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
222 )
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
223 # Skip this look
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
224 continue
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
225 # print(aligned_seqs)
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
226 for element, aligned_seq in zip(sortedCluster, sortedAligned):
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
227 if element not in locations:
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
228 logging.warning("Could not find this feature %s", element)
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
229 continue
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
230
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
231 eloc = locations[element]
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
232 xmw.write(
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
233 seqnum=recids.index(eloc["rec"]) + 1,
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
234 start=eloc["loc"].start,
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
235 end=eloc["loc"].end,
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
236 strand="+" if eloc["loc"].strand == 1 else "-",
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
237 file=eloc["rec"] + ".fa",
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
238 realname=element,
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
239 sequence=str(aligned_seq.seq),
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
240 )
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
241 xmw.end()
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
242
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
243
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
244 if __name__ == "__main__":
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
245 parser = argparse.ArgumentParser(
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
246 description="Convert Blast TSV to protein XMFA", epilog=""
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
247 )
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
248 parser.add_argument("blast", type=argparse.FileType("r"), help="Blast TSV Output")
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
249 parser.add_argument("fasta", type=argparse.FileType("r"), help="Blast Input Fasta")
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
250 parser.add_argument("gff3", type=argparse.FileType("r"), help="GFF3 Gene Calls")
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
251 parser.add_argument(
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
252 "--genomic",
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
253 action="store_true",
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
254 help="Further reduce protein results into genomic-level results.",
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
255 )
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
256 parser.add_argument(
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
257 "output", type=argparse.FileType("w"), help="Output file or - for stdout"
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
258 )
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
259 args = parser.parse_args()
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
260
c66d6978a5f8 planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
cpt
parents:
diff changeset
261 blast2pxmfa(**vars(args))