Mercurial > repos > iuc > virannot_blast2tsv

annotate blast2tsv.py @ 0:e889010415a1 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
author iuc
date Mon, 04 Mar 2024 19:55:52 +0000
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children 77c3ef9b0ed7
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e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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1 #!/usr/bin/env python3
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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2
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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4 # Name: blast2tsv
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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5 # Author(s): Sebastien Theil, Marie Lefebvre - INRAE
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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6 # Aims: Convert blast xml output to tsv and add taxonomy
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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7
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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8
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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9 import argparse
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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10 import csv
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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11 import logging as log
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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12 import os
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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14 from Bio import Entrez
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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15 from Bio import SeqIO
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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16 from Bio.Blast import NCBIXML
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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17 from ete3 import NCBITaxa
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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18
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19 ncbi = NCBITaxa()
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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21
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22 def main():
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23 options = _set_options()
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24 _set_log_level(options.verbosity)
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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25 hits = _read_xml(options)
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26 _write_tsv(options, hits)
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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28
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29 def _guess_database(accession):
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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30 """Guess the correct database for querying based off the format of the accession"""
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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31 database_mappings_refseq = {'AC_': 'nuccore', 'NC_': 'nuccore', 'NG_': 'nuccore',
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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32 'NT_': 'nuccore', 'NW_': 'nuccore', 'NZ_': 'nuccore',
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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33 'AP_': 'protein', 'NP_': 'protein', 'YP_': 'protein',
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34 'XP_': 'protein', 'WP_': 'protein'}
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35 return database_mappings_refseq[accession[0:3]]
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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36
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37
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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38 def _read_xml(options):
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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39 """
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40 Parse XML blast results file
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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41 Keep only the first hit
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42 """
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43 log.info("Read XML file.")
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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44 results = open(options.xml_file, 'r')
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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45 records = NCBIXML.parse(results)
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46 xml_results = {}
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47 for blast_record in records:
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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48 for aln in blast_record.alignments:
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49 hit_count = 1
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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50 for hit in aln.hsps:
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51 hsp = {}
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52 if hit_count == 1:
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53 first_hit_frame = hit.frame[1] if len(hit.frame) > 0 else 0 # strand
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54 cumul_hit_identity = hit.identities if hit.identities else 0
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55 cumul_hit_score = hit.bits # hit score
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56 cumul_hit_evalue = hit.expect # evalue
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57 cumul_hit_length = hit.align_length if hit.align_length is not None else 0
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58 hit_count = hit_count + 1
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59 else:
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60 # all HSPs in different strand than 1st HSPs will be discarded.
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61 if (first_hit_frame > 0 and hit.frame[1] > 0) or (first_hit_frame < 0 and hit.frame[1] < 0):
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62 cumul_hit_identity = cumul_hit_identity + hit.identities
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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63 cumul_hit_length = cumul_hit_length + hit.align_length
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64 cumul_hit_evalue = cumul_hit_evalue + hit.expect
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65 cumul_hit_score = cumul_hit_score + hit.bits
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66 hit_count = hit_count + 1
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67 if hit_count == 1:
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68 final_hit_count = hit_count
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69 elif hit_count > 1:
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70 final_hit_count = hit_count - 1
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71 hsp["evalue"] = cumul_hit_evalue / final_hit_count # The smaller the E-value, the better the match
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72 hsp["query_id"] = blast_record.query_id
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73 hsp["query_length"] = blast_record.query_length # length of the query
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74 hsp["accession"] = aln.accession.replace("ref|", "")
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75 hsp["description"] = aln.hit_def
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76 hsp["hit_length"] = aln.length # length of the hit
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77 hsp["hsp_length"] = hit.align_length # length of the hsp alignment
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78 hsp["queryOverlap"] = _get_overlap_value(options.algo, hsp, 'hsp', hsp["query_length"])[0]
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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79 if cumul_hit_length == 0:
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80 hsp["percentIdentity"] = round(cumul_hit_identity, 1) # identity percentage
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81 else:
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82 hsp["percentIdentity"] = round(cumul_hit_identity / cumul_hit_length * 100, 1) # identity percentage
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83 hsp["score"] = cumul_hit_score # The higher the bit-score, the better the sequence similarity
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84 hsp["num_hsps"] = final_hit_count
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
85 hsp["hit_cumul_length"] = cumul_hit_length
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
86 hsp["hitOverlap"] = _get_overlap_value(options.algo, hsp, 'hit', hsp["query_length"])[1]
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
87 db = _guess_database(hsp["accession"])
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
88 try:
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
89 handle = Entrez.esummary(db=db, id=hsp["accession"])
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
90 taxid = str(int(Entrez.read(handle)[0]['TaxId']))
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
91 handle.close()
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
92 log.info("Taxid found for " + hsp["accession"])
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
93 lineage = ncbi.get_lineage(taxid)
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
94 names = ncbi.get_taxid_translator(lineage)
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
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95 ordered = [names[tid] for tid in lineage]
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
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96 taxonomy = ordered[1:]
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
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97 hsp["tax_id"] = taxid
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
98 hsp["taxonomy"] = ';'.join(taxonomy)
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
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99 hsp["organism"] = taxonomy[-1]
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
100 except RuntimeError:
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
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101 hsp["tax_id"] = ""
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
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102 hsp["taxonomy"] = ""
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
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103 hsp["organism"] = ""
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
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104 log.warning("RuntimeError - Taxid not found for " + hsp["accession"])
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
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105 if hsp["evalue"] <= options.max_evalue and hsp["queryOverlap"] >= options.min_qov and \
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
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106 hsp["hitOverlap"] >= options.min_hov and hsp["score"] >= options.min_score:
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
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107 xml_results[hsp["query_id"]] = hsp
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
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108 else:
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iuc
parents:
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109 xml_results[hsp["query_id"]] = [hsp["query_length"]]
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
110
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
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111 return xml_results
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
112
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
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113
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
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114 def _get_overlap_value(algo, hsp, type, qlength):
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
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115 """
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
116 Set hsp or hit overlap values for hit and query
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
117 Return array [query_overlap, hit_overlap]
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
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118 """
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
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119 if type == 'hsp':
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
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120 q_align_len = qlength
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
121 h_align_len = hsp["hsp_length"]
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
122 else:
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
123 q_align_len = qlength
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
124 h_align_len = hsp["hit_cumul_length"]
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
125
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
126 if algo == 'BLASTX':
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
127 if q_align_len:
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
128 query_overlap = (q_align_len * 3 / q_align_len) * 100
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
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129 if hsp["hit_length"]:
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
130 hit_overlap = (h_align_len / hsp["hit_length"]) * 100
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
131 elif algo == 'TBLASTN':
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
132 if q_align_len:
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
133 query_overlap = (q_align_len / q_align_len) * 100
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
134 if hsp["hit_length"]:
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
135 hit_overlap = (h_align_len * 3 / hsp["hit_length"]) * 100
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
136 elif algo == 'TBLASTX':
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
137 if q_align_len:
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
138 query_overlap = (q_align_len * 3 / hsp["hsp_length"]) * 100
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
139 if hsp["hit_length"]:
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
140 hit_overlap = (h_align_len * 3 / hsp["hit_length"]) * 100
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
141 else:
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
142 if q_align_len:
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
143 query_overlap = (q_align_len / q_align_len) * 100
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
144 if hsp["hit_length"]:
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
145 hit_overlap = (h_align_len / hsp["hit_length"]) * 100
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
146 if query_overlap is None:
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
147 query_overlap = 0
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
148 if query_overlap > 100:
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
149 query_overlap = 100
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
150 if 'hit_overlap' not in locals():
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
151 hit_overlap = 0
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
152 if hit_overlap > 100:
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
153 hit_overlap = 100
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parents:
diff changeset
154
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
155 return [round(query_overlap, 0), round(hit_overlap, 0)]
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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parents:
diff changeset
156
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parents:
diff changeset
157
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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parents:
diff changeset
158 def _write_tsv(options, hits):
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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parents:
diff changeset
159 """
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
160 Write output
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
161 """
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
162 # get a list of contig without corresponding number of mapped reads
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
163 if options.rn_file is not None:
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
164 with open(options.rn_file) as rn:
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
165 rows = (line.split('\t') for line in rn)
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
166 rn_list = {row[0]: row[1:] for row in rows}
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
167 fasta = SeqIO.to_dict(SeqIO.parse(open(options.fasta_file), 'fasta'))
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
168 headers = "#algo\tquery_id\tnb_reads\tquery_length\taccession\tdescription\torganism\tpercentIdentity\tnb_hsps\tqueryOverlap\thitOverlap\tevalue\tscore\ttax_id\ttaxonomy\tsequence\n"
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
169 if not os.path.exists(options.output):
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
170 os.mkdir(options.output)
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
171 tsv_file = options.output + "/blast2tsv_output.tab"
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
172 log.info("Write output file: " + tsv_file)
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
173 f = open(tsv_file, "w+")
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
174 f.write(headers)
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
175 for h in hits:
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
176 if options.rn_file is not None:
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
177 read_nb = ''.join(rn_list[h]).replace("\n", "")
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
178 else:
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
179 read_nb = ''
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
180 if len(hits[h]) > 1:
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
181 f.write(options.algo + "\t" + h + "\t" + read_nb + "\t" + str(hits[h]["query_length"]) + "\t")
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
182 f.write(hits[h]["accession"] + "\t" + hits[h]["description"] + "\t")
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
183 f.write(hits[h]["organism"] + "\t" + str(hits[h]["percentIdentity"]) + "\t")
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
184 f.write(str(hits[h]["num_hsps"]) + "\t" + str(hits[h]["queryOverlap"]) + "\t")
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
185 f.write(str(hits[h]["hitOverlap"]) + "\t" + str(hits[h]["evalue"]) + "\t")
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
186 f.write(str(hits[h]["score"]) + "\t" + str(hits[h]["tax_id"]) + "\t")
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
187 if h in fasta:
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
188 f.write(hits[h]["taxonomy"] + "\t" + str(fasta[h].seq))
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
189 else:
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
190 f.write(hits[h]["taxonomy"] + "\t\"\"")
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
191 f.write("\n")
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
192 else:
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
193 f.write(options.algo + "\t" + h + "\t" + read_nb + "\t" + str(hits[h])[1:-1] + "\t")
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
194 f.write("\n")
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
195 f.close()
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
196 _create_abundance(options, tsv_file)
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
197
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
198
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
199 def _create_abundance(options, tsv_file):
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
200 """
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
201 extract values from tsv files
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
202 and create abundance files
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
203 """
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
204 log.info("Calculating abundance.")
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
205 file_path = tsv_file
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
206 abundance = dict()
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
207 with open(tsv_file, 'r') as current_file:
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
208 log.debug("Reading " + file_path)
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
209 csv_reader = csv.reader(current_file, delimiter='\t')
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
210 line_count = 0
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
211 for row in csv_reader:
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
212 if line_count == 0:
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
213 # headers
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
214 line_count += 1
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
215 else:
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
216 # no annotation
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
217 if len(row) == 16:
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
218 if row[14] != "":
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
219 nb_reads = row[2]
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
220 if nb_reads == "":
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
221 current_reads_nb = 0
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
222 log.debug("No reads number for " + row[1])
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
223 else:
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
224 current_reads_nb = int(nb_reads)
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
225 contig_id = row[14]
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
226 if contig_id in abundance:
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
227 # add reads
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
228 abundance[contig_id]["reads_nb"] = abundance[row[14]]["reads_nb"] + current_reads_nb
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
229 abundance[contig_id]["contigs_nb"] = abundance[row[14]]["contigs_nb"] + 1
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
230 else:
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
231 # init reads for this taxo
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
232 abundance[contig_id] = {}
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
233 abundance[contig_id]["reads_nb"] = current_reads_nb
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
234 abundance[contig_id]["contigs_nb"] = 1
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
235 else:
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
236 log.debug("No annotations for contig " + row[1])
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
237 else:
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
238 log.debug("No annotations for contig " + row[1])
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
239 log.debug(abundance)
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
240 reads_file = open(options.output + "/blast2tsv_reads.txt", "w+")
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
241 for taxo in abundance:
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
242 reads_file.write(str(abundance[taxo]["reads_nb"]))
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
243 reads_file.write("\t")
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
244 reads_file.write("\t".join(taxo.split(";")))
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
245 reads_file.write("\n")
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
246 reads_file.close()
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
247 log.info("Abundance file created " + options.output + "/blast2tsv_reads.txt")
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
248 contigs_file = open(options.output + "/blast2tsv_contigs.txt", "w+")
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
249 for taxo in abundance:
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
250 contigs_file.write(str(abundance[taxo]["contigs_nb"]))
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
251 contigs_file.write("\t")
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
252 contigs_file.write("\t".join(taxo.split(";")))
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
253 contigs_file.write("\n")
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
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254 contigs_file.close()
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255 log.info("Abundance file created " + options.output + "/blast2tsv_contigs.txt")
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256
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257
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258 def _set_options():
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259 parser = argparse.ArgumentParser()
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260 parser.add_argument('-x', '--xml', help='XML files with results of blast', action='store', required=True, dest='xml_file')
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261 parser.add_argument('-rn', '--read-count', help='Tab-delimited file associating seqID with read number.', action='store', dest='rn_file')
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262 parser.add_argument('-c', '--contigs', help='FASTA file with contigs sequence.', action='store', required=True, dest='fasta_file')
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263 parser.add_argument('-me', '--max_evalue', help='Max evalue', action='store', type=float, default=0.0001, dest='max_evalue')
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264 parser.add_argument('-qov', '--min_query_overlap', help='Minimum query overlap', action='store', type=int, default=5, dest='min_qov')
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265 parser.add_argument('-mhov', '--min_hit_overlap', help='Minimum hit overlap', action='store', type=int, default=5, dest='min_hov')
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266 parser.add_argument('-s', '--min_score', help='Minimum score', action='store', type=int, default=30, dest='min_score')
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267 parser.add_argument('-a', '--algo', help='Blast type detection (BLASTN|BLASTP|BLASTX|TBLASTX|TBLASTN|DIAMONDX).', action='store', type=str, default='BLASTX', dest='algo')
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268 parser.add_argument('-o', '--out', help='The output file (.csv).', action='store', type=str, default='./blast2tsv', dest='output')
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269 parser.add_argument('-v', '--verbosity', help='Verbose level', action='store', type=int, choices=[1, 2, 3, 4], default=1)
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270 args = parser.parse_args()
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271 return args
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272
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273
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274 def _set_log_level(verbosity):
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275 if verbosity == 1:
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276 log_format = '%(asctime)s %(levelname)-8s %(message)s'
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277 log.basicConfig(level=log.INFO, format=log_format)
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278 elif verbosity == 3:
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279 log_format = '%(filename)s:%(lineno)s - %(asctime)s %(levelname)-8s %(message)s'
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280 log.basicConfig(level=log.DEBUG, format=log_format)
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281
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282
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283 if __name__ == "__main__":
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284 main()