Mercurial > repos > iuc > virannot_otu

annotate rps2tsv.py @ 4:adcf06db3030 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 7036ce0e06b6dc64332b1a5642fc58928523c5c6
author iuc
date Tue, 13 May 2025 11:52:27 +0000
parents 40fb54cc6628
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
1 #!/usr/bin/env python3
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
2
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
3
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
4 # Name: rps2ecsv
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
5 # Author: Marie Lefebvre - INRAE
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
6 # Aims: Convert rpsblast xml output to csv and add taxonomy
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
7
4
adcf06db3030 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 7036ce0e06b6dc64332b1a5642fc58928523c5c6
iuc
parents: 3
diff changeset
8 """Module which converts rpsblast xml output to tsv and add taxonomy"""
0
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
9
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
10 import argparse
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
11 import json
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
12 import logging as log
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
13 from urllib import request
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
14 from urllib.error import HTTPError, URLError
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
15
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
16 from Bio.Blast import NCBIXML
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
17 from ete3 import NCBITaxa
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
18
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
19 ncbi = NCBITaxa()
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
20
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
21
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
22 def main():
4
adcf06db3030 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 7036ce0e06b6dc64332b1a5642fc58928523c5c6
iuc
parents: 3
diff changeset
23 """
adcf06db3030 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 7036ce0e06b6dc64332b1a5642fc58928523c5c6
iuc
parents: 3
diff changeset
24 Main function
adcf06db3030 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 7036ce0e06b6dc64332b1a5642fc58928523c5c6
iuc
parents: 3
diff changeset
25 """
0
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
26 options = _set_options()
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
27 _set_log_level(options.verbosity)
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
28 hits = _read_xml(options)
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
29 _write_tsv(options, hits)
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
30
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
31
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
32 def _read_xml(options):
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
33 """
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
34 Parse XML RPSblast results file
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
35 """
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
36 log.info("Read XML file " + options.xml_file)
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
37 xml = open(options.xml_file, 'r')
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
38 records = NCBIXML.parse(xml)
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
39 xml_results = {}
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
40 for blast_record in records:
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
41 for aln in blast_record.alignments:
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
42 for hit in aln.hsps:
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
43 hsp = {}
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
44 hit_evalue = hit.expect
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
45 if hit_evalue > options.max_evalue:
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
46 continue
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
47 hit_frame = hit.frame[0] # frame
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
48 hit_evalue = hit.expect # evalue
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
49 hit_startQ = hit.query_start
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
50 hit_endQ = hit.query_end
4
adcf06db3030 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 7036ce0e06b6dc64332b1a5642fc58928523c5c6
iuc
parents: 3
diff changeset
51 hit_identity = hit.identities
adcf06db3030 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 7036ce0e06b6dc64332b1a5642fc58928523c5c6
iuc
parents: 3
diff changeset
52 hit_aln_length = hit.align_length
adcf06db3030 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 7036ce0e06b6dc64332b1a5642fc58928523c5c6
iuc
parents: 3
diff changeset
53 pident = "%0.3f" % (100 * float(hit_identity) / float(hit_aln_length))
adcf06db3030 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 7036ce0e06b6dc64332b1a5642fc58928523c5c6
iuc
parents: 3
diff changeset
54 if float(pident) < 0.1:
adcf06db3030 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 7036ce0e06b6dc64332b1a5642fc58928523c5c6
iuc
parents: 3
diff changeset
55 continue
adcf06db3030 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 7036ce0e06b6dc64332b1a5642fc58928523c5c6
iuc
parents: 3
diff changeset
56 hsp["pident"] = pident
0
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
57 hsp["frame"] = hit_frame
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
58 hsp["evalue"] = hit_evalue
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
59 hsp["startQ"] = hit_startQ
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
60 hsp["endQ"] = hit_endQ
3
40fb54cc6628 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 16701bfbffd605805e847897799251ab748f559f
iuc
parents: 2
diff changeset
61 hsp["query_id"] = blast_record.query
0
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
62 hsp["cdd_id"] = aln.hit_def.split(",")[0]
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
63 hsp["hit_id"] = aln.hit_id
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
64 hsp["query_length"] = blast_record.query_length # length of the query
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
65 hsp["description"] = aln.hit_def
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
66 hsp["accession"] = aln.accession
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
67 hsp["pfam_id"] = hsp["description"].split(",")[0].replace("pfam", "PF")
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
68 log.info("Requeting Interpro for " + hsp["pfam_id"])
2
735a21808348 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit ab5e1189217b6ed5f1c5d7c5ff6b79b6a4c18cff
iuc
parents: 0
diff changeset
69 url = "https://www.ebi.ac.uk/interpro/api/taxonomy/uniprot/entry/pfam/" + hsp["pfam_id"]
0
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
70 req = request.Request(url)
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
71 try:
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
72 response = request.urlopen(req)
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
73 except HTTPError as e:
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
74 log.debug('Http error for interpro: ', e.code)
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
75 except URLError as e:
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
76 log.debug('Url error for interpro: ', e.reason)
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
77 else:
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
78 encoded_response = response.read()
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
79 decoded_response = encoded_response.decode()
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
80 payload = json.loads(decoded_response)
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
81 kingdoms = []
2
735a21808348 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit ab5e1189217b6ed5f1c5d7c5ff6b79b6a4c18cff
iuc
parents: 0
diff changeset
82 for item in payload["results"][:6]:
735a21808348 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit ab5e1189217b6ed5f1c5d7c5ff6b79b6a4c18cff
iuc
parents: 0
diff changeset
83 if item["metadata"]["parent"] is not None:
735a21808348 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit ab5e1189217b6ed5f1c5d7c5ff6b79b6a4c18cff
iuc
parents: 0
diff changeset
84 lineage_parent = item["metadata"]["parent"]
735a21808348 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit ab5e1189217b6ed5f1c5d7c5ff6b79b6a4c18cff
iuc
parents: 0
diff changeset
85 translation = ncbi.get_taxid_translator([int(lineage_parent)])
735a21808348 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit ab5e1189217b6ed5f1c5d7c5ff6b79b6a4c18cff
iuc
parents: 0
diff changeset
86 names = list(translation.values())
735a21808348 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit ab5e1189217b6ed5f1c5d7c5ff6b79b6a4c18cff
iuc
parents: 0
diff changeset
87 if len(names) > 0:
735a21808348 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit ab5e1189217b6ed5f1c5d7c5ff6b79b6a4c18cff
iuc
parents: 0
diff changeset
88 if names[0] == "root":
735a21808348 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit ab5e1189217b6ed5f1c5d7c5ff6b79b6a4c18cff
iuc
parents: 0
diff changeset
89 taxonomy = names[1:] # remove 'root' at the begining
735a21808348 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit ab5e1189217b6ed5f1c5d7c5ff6b79b6a4c18cff
iuc
parents: 0
diff changeset
90 else:
735a21808348 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit ab5e1189217b6ed5f1c5d7c5ff6b79b6a4c18cff
iuc
parents: 0
diff changeset
91 taxonomy = names
735a21808348 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit ab5e1189217b6ed5f1c5d7c5ff6b79b6a4c18cff
iuc
parents: 0
diff changeset
92 else:
735a21808348 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit ab5e1189217b6ed5f1c5d7c5ff6b79b6a4c18cff
iuc
parents: 0
diff changeset
93 taxonomy = names
735a21808348 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit ab5e1189217b6ed5f1c5d7c5ff6b79b6a4c18cff
iuc
parents: 0
diff changeset
94 if len(taxonomy) != 0:
735a21808348 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit ab5e1189217b6ed5f1c5d7c5ff6b79b6a4c18cff
iuc
parents: 0
diff changeset
95 kingdoms.append(taxonomy[0])
4
adcf06db3030 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 7036ce0e06b6dc64332b1a5642fc58928523c5c6
iuc
parents: 3
diff changeset
96 # {'Pseudomonadota': 9, 'cellular organisms': 4}
adcf06db3030 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 7036ce0e06b6dc64332b1a5642fc58928523c5c6
iuc
parents: 3
diff changeset
97 frequency = {kingdom: kingdoms.count(kingdom) for kingdom in kingdoms}
0
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
98 sorted_freq = dict(sorted(frequency.items(), key=lambda x: x[1], reverse=True))
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
99 concat_freq = ";".join("{}({})".format(k, v) for k, v in sorted_freq.items())
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
100 hsp["taxonomy"] = concat_freq
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
101 xml_results[hsp["query_id"]] = hsp
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
102 return xml_results
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
103
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
104
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
105 def _write_tsv(options, hits):
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
106 """
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
107 Write output
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
108 """
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
109 log.info("Write output file " + options.output)
4
adcf06db3030 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 7036ce0e06b6dc64332b1a5642fc58928523c5c6
iuc
parents: 3
diff changeset
110 headers = "#query_id\tquery_length\tcdd_id\thit_id\tevalue\tstartQ\tendQ\tframe\tdescription\tsuperkingdom\tpident\n"
0
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
111 f = open(options.output, "w+")
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
112 f.write(headers)
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
113 for h in hits:
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
114 f.write(h + "\t" + str(hits[h]["query_length"]) + "\t")
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
115 f.write(hits[h]["cdd_id"] + "\t" + hits[h]["hit_id"] + "\t" + str(hits[h]["evalue"]) + "\t")
4
adcf06db3030 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 7036ce0e06b6dc64332b1a5642fc58928523c5c6
iuc
parents: 3
diff changeset
116 f.write(str(hits[h]["startQ"]) + "\t" + str(hits[h]["endQ"]) + "\t"
adcf06db3030 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 7036ce0e06b6dc64332b1a5642fc58928523c5c6
iuc
parents: 3
diff changeset
117 + str(hits[h]["frame"]) + "\t")
adcf06db3030 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 7036ce0e06b6dc64332b1a5642fc58928523c5c6
iuc
parents: 3
diff changeset
118 f.write(hits[h]["description"] + "\t" + hits[h]["taxonomy"] + "\t" + hits[h]["pident"])
0
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
119 f.write("\n")
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
120 f.close()
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
121
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
122
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
123 def _set_options():
4
adcf06db3030 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 7036ce0e06b6dc64332b1a5642fc58928523c5c6
iuc
parents: 3
diff changeset
124 """
adcf06db3030 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 7036ce0e06b6dc64332b1a5642fc58928523c5c6
iuc
parents: 3
diff changeset
125 Script parameters
adcf06db3030 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 7036ce0e06b6dc64332b1a5642fc58928523c5c6
iuc
parents: 3
diff changeset
126 """
0
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
127 parser = argparse.ArgumentParser()
4
adcf06db3030 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 7036ce0e06b6dc64332b1a5642fc58928523c5c6
iuc
parents: 3
diff changeset
128 parser.add_argument('-x', '--xml', help='XML files with results of blast', action='store',
adcf06db3030 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 7036ce0e06b6dc64332b1a5642fc58928523c5c6
iuc
parents: 3
diff changeset
129 required=True, dest='xml_file')
adcf06db3030 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 7036ce0e06b6dc64332b1a5642fc58928523c5c6
iuc
parents: 3
diff changeset
130 parser.add_argument('-e', '--max_evalue', help='Max evalue', action='store',
adcf06db3030 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 7036ce0e06b6dc64332b1a5642fc58928523c5c6
iuc
parents: 3
diff changeset
131 type=float, default=0.0001, dest='max_evalue')
adcf06db3030 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 7036ce0e06b6dc64332b1a5642fc58928523c5c6
iuc
parents: 3
diff changeset
132 parser.add_argument('-o', '--out', help='The output file (.tab).', action='store',
adcf06db3030 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 7036ce0e06b6dc64332b1a5642fc58928523c5c6
iuc
parents: 3
diff changeset
133 type=str, default='./rps2tsv_output.tab', dest='output')
adcf06db3030 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 7036ce0e06b6dc64332b1a5642fc58928523c5c6
iuc
parents: 3
diff changeset
134 parser.add_argument('-v', '--verbosity', help='Verbose level', action='store',
adcf06db3030 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 7036ce0e06b6dc64332b1a5642fc58928523c5c6
iuc
parents: 3
diff changeset
135 type=int, choices=[1, 2, 3, 4], default=1)
0
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
136 args = parser.parse_args()
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
137 return args
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
138
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
139
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
140 def _set_log_level(verbosity):
4
adcf06db3030 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 7036ce0e06b6dc64332b1a5642fc58928523c5c6
iuc
parents: 3
diff changeset
141 """
adcf06db3030 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 7036ce0e06b6dc64332b1a5642fc58928523c5c6
iuc
parents: 3
diff changeset
142 Debbug
adcf06db3030 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 7036ce0e06b6dc64332b1a5642fc58928523c5c6
iuc
parents: 3
diff changeset
143 """
0
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
144 if verbosity == 1:
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
145 log_format = '%(asctime)s %(levelname)-8s %(message)s'
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
146 log.basicConfig(level=log.INFO, format=log_format)
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
147 elif verbosity == 3:
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
148 log_format = '%(filename)s:%(lineno)s - %(asctime)s %(levelname)-8s %(message)s'
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
149 log.basicConfig(level=log.DEBUG, format=log_format)
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
150
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
151
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
152 if __name__ == "__main__":
c9dac9b2e01c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
153 main()