Mercurial > repos > iuc > virannot_blast2tsv

annotate otu.py @ 3:f8ebd1e802d7 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 16701bfbffd605805e847897799251ab748f559f
author iuc
date Sun, 08 Sep 2024 14:09:19 +0000
parents e889010415a1
children bb29ae8708b5
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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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e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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3
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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4 # Name: virAnnot_otu
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5 # Author: 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 # Reuirements: Ete3 toolkit and external apps
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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7 # Aims: Create viral OTUs based on RPS and Blast annotations
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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e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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10 import argparse
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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11 import csv
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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12 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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13 import os
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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14 import random
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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15 import re
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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17 import pandas as pd
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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18 import xlsxwriter
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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19 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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20 from Bio.Align.Applications import ClustalOmegaCommandline
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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21 from ete3 import NodeStyle, SeqGroup, SeqMotifFace, Tree, TreeStyle
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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24 def main():
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25 """
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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26 1 - retrieve info (sequence, query_id, taxo) from RPS file
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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27 2 - align protein sequences of the same domain, calculate
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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28 matrix of distances, generate trees
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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29 3 - get statistics (read number) per otu
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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30 4 - create HTML report
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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31 """
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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32 options = _set_options()
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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33 _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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34 hits_collection = _cut_sequence(options)
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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35 _align_sequences(options, hits_collection)
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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36 _get_stats(options, hits_collection)
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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37 _create_html(options, hits_collection)
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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38
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39
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40 def _cut_sequence(options):
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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41 """
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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42 Retrieve viral hits and sequences from RPS files
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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43 """
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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44 log.info("Cut sequences")
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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45 i = 0 # keep track of iterations over rps files to use the corresponding fasta file
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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46 collection = {}
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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47 options.rps.sort()
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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48 for rps_file in options.rps:
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49 log.debug("Reading rps file " + str(rps_file))
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50 with open(rps_file[0], 'r') as rps_current_file:
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51 rps_reader = csv.reader(rps_current_file, delimiter='\t')
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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52 headers = 0
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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53 for row in rps_reader:
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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54 if headers == 0:
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55 # headers
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56 headers += 1
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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57 else:
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58 if row[1] == "no_hit":
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59 pass
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60 else:
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61 query_id = row[0]
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62 cdd_id = row[2]
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63 startQ = int(row[5])
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64 endQ = int(row[6])
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65 frame = float(row[7])
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66 description = row[8]
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67 superkingdom = row[9]
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68 match = re.search("Viruses", superkingdom)
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69 # if contig is viral then retrieve sequence
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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70 if match:
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71 options.fasta.sort()
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72 seq = _retrieve_fasta_seq(options.fasta[i][0], query_id)
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73 seq_length = len(seq)
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74 if endQ < seq_length:
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75 seq = seq[startQ - 1:endQ]
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76 else:
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77 seq = seq[startQ - 1:seq_length]
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78 if frame < 0:
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79 seq = seq.reverse_complement()
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80 prot = seq.translate()
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81 if len(prot) >= options.min_protein_length:
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82 log.debug("Add " + query_id + " to collection")
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83 if cdd_id not in collection:
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84 collection[cdd_id] = {}
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85 collection[cdd_id][query_id] = {}
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86 collection[cdd_id][query_id]["nuccleotide"] = seq
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87 collection[cdd_id][query_id]["protein"] = prot
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
88 collection[cdd_id][query_id]["full_description"] = description
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
89 if options.blast is not None:
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
90 options.blast.sort()
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
91 with open(options.blast[i][0], 'r') as blast_current_file:
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
92 blast_reader = csv.reader(blast_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
93 for b_query in blast_reader:
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
94 if b_query[1] == query_id:
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
95 collection[cdd_id][query_id]["nb"] = b_query[2]
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
96 if len(b_query) > 10:
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
97 collection[cdd_id][query_id]["taxonomy"] = b_query[14]
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
98 else:
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
99 collection[cdd_id][query_id]["taxonomy"] = "Unknown"
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
100 else:
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
101 if "nb" not in collection[cdd_id][query_id]:
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
102 collection[cdd_id][query_id]["nb"] = 0
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
103 if "taxonomy" not in collection[cdd_id][query_id]:
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
104 collection[cdd_id][query_id]["taxonomy"] = "Unknown"
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
105 else:
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
106 log.info("No blast file")
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
107 collection[cdd_id][query_id]["taxonomy"] = "Unknown"
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
108 collection[cdd_id][query_id]["nb"] = 0
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
109
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
110 collection[cdd_id]["short_description"] = description.split(",")[0] + description.split(",")[1] # keep pfamXXX and RdRp 1
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
111 collection[cdd_id]["full_description"] = description
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
112 i += 1
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
113 return collection
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
114
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
115
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
116 def _retrieve_fasta_seq(fasta_file, query_id):
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
117 """
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
118 From fasta file retrieve specific sequence with id
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
119 """
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
120 contigs_list = SeqIO.to_dict(SeqIO.parse(open(fasta_file), 'fasta'))
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
121 try:
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
122 seq = contigs_list[query_id].seq
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
123 except KeyError:
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
124 print("KeyError for " + query_id + " file " + fasta_file)
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
125 else:
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
126 return seq
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
127
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
128
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
129 def _create_tree(tree, fasta, out, color):
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
130 """
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
131 Create phylogenic tree from multiple alignments
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
132 """
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
133 try:
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
134 f = open(tree, 'r')
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
135 except IOError:
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
136 log.info("Unknown file: " + tree + ". You may have less than 2 sequences to align.")
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
137 return
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
138
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
139 line = ""
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
140 for word in f:
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
141 line += word.strip()
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
142
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
143 f.close()
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
144 seqs = SeqGroup(fasta, format="fasta")
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
145 t = Tree(tree)
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
146 ts = TreeStyle()
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
147 ts.show_branch_length = True
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
148 colors = _parse_color_file(color)
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
149 node_names = t.get_leaf_names()
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
150 for name in node_names:
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
151 seq = seqs.get_seq(name)
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
152 seqFace = SeqMotifFace(seq, seq_format="()")
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
153 node = t.get_leaves_by_name(name)
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
154 for i in range(0, len(node)):
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
155 if name in colors:
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
156 ns = NodeStyle()
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
157 ns['bgcolor'] = colors[name]
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
158 node[i].set_style(ns)
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
159 node[i].add_face(seqFace, 0, 'aligned')
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
160
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
161 t.render(out, tree_style=ts)
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
162
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
163
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
164 def _parse_color_file(file):
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
165 fh = open(file)
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
166 reader = csv.reader(fh, delimiter="\t")
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
167 data = list(reader)
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
168 colors = {}
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
169 for i in range(0, len(data)):
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
170 colors[data[i][0]] = data[i][1]
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
171
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
172 return colors
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
173
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
174
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
175 def _align_sequences(options, hits_collection):
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176 """
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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177 Align hit sequences with pfam reference
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178 """
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parents:
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179 log.info("Align sequences")
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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180 if not os.path.exists(options.output):
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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181 os.mkdir(options.output)
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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182 color_by_sample = {}
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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183 for cdd_id in hits_collection:
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184 cdd_output = options.output + "/" + hits_collection[cdd_id]["short_description"].replace(" ", "_")
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185 if not os.path.exists(cdd_output):
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186 os.mkdir(cdd_output)
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187 if os.path.exists(cdd_output + "/seq_to_align.fasta"):
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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188 os.remove(cdd_output + "/seq_to_align.fasta")
3
f8ebd1e802d7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 16701bfbffd605805e847897799251ab748f559f
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parents: 0
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189 if os.path.exists(cdd_output + "/seq_nucc.fasta"):
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190 os.remove(cdd_output + "/seq_nucc.fasta")
0
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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191 file_seq_to_align = cdd_output + "/seq_to_align.fasta"
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192 file_color_config = cdd_output + "/color_config.txt"
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193 f = open(file_seq_to_align, "a")
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194 f_c = open(file_color_config, "w+")
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195 log.info("Writing to " + file_seq_to_align)
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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196 count = 0 # count number of contig per domain
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197 for query_id in hits_collection[cdd_id]:
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198 if query_id not in ["short_description", "full_description"]:
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199 sample = query_id.split("_")[0] # get sample from SAMPLE_IdCONTIG
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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parents:
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200 sample_color = "#" + ''.join([random.choice('ABCDEF0123456789') for i in range(6)])
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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201 # same color for each contig of the same sample
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202 if sample not in color_by_sample.keys():
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iuc
parents:
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203 color_by_sample[sample] = sample_color
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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parents:
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204 f.write(">" + query_id + "\n")
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
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205 f.write(str(hits_collection[cdd_id][query_id]["protein"]) + "\n")
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
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206 f_c.write(query_id + '\t' + color_by_sample[sample] + '\n')
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
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207 count += 1
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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208 f.close()
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iuc
parents:
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209 f_c.close()
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210 file_seq_aligned = cdd_output + '/seq_aligned.final_tree.fa'
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
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211 tree_file = cdd_output + '/tree.dnd'
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parents:
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212 file_cluster = cdd_output + '/otu_cluster.csv'
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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213 # create alignment for domain with more than 1 contigs
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214 if count > 1:
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iuc
parents:
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215 log.info("Run clustal omega...")
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parents:
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216 clustalo_cmd = ClustalOmegaCommandline("clustalo", infile=file_seq_to_align, outfile=file_seq_aligned,
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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217 guidetree_out=tree_file, seqtype="protein", force=True)
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218 log.debug(clustalo_cmd)
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219 stdout, stderr = clustalo_cmd()
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220 log.debug(stdout + stderr)
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221
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222 # create tree plot with colors
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223 file_matrix = cdd_output + "/identity_matrix.csv"
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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parents:
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224 log.info("Create tree...")
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
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225 _create_tree(tree_file, file_seq_aligned, tree_file + '.png', file_color_config)
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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parents:
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226 _compute_pairwise_distance(options, file_seq_aligned, file_matrix, cdd_id)
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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227 log.info("Retrieve OTUs...")
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228 # if os.path.exists(file_cluster):
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229 # os.remove(file_cluster)
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parents:
diff changeset
230 otu_cmd = os.path.join(options.tool_path, 'seek_otu.R') + ' ' + file_matrix + ' ' + file_cluster + ' ' + str(options.perc)
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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parents:
diff changeset
231 log.debug(otu_cmd)
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232 os.system(otu_cmd)
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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parents:
diff changeset
233 # only one contig
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parents:
diff changeset
234 else:
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
235 mv_cmd = 'cp ' + file_seq_to_align + ' ' + file_seq_aligned
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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parents:
diff changeset
236 log.debug(mv_cmd)
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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parents:
diff changeset
237 os.system(mv_cmd)
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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diff changeset
238
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parents:
diff changeset
239 f = open(file_cluster, "w+")
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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parents:
diff changeset
240 f.write('OTU_1,1,' + list(hits_collection[cdd_id].keys())[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
241 f.close()
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242
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243
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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parents:
diff changeset
244 def _compute_pairwise_distance(options, file_seq_aligned, file_matrix, cdd_id):
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
245 """
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
246 Calculate paiwise distance between aligned protein sequences
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
247 from a cdd_id
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
248 """
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
249 log.info("Compute pairwise distance of " + cdd_id)
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
250 matrix = {}
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
251 for k1 in SeqIO.parse(file_seq_aligned, "fasta"):
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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parents:
diff changeset
252 row = []
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
253 for k2 in SeqIO.parse(file_seq_aligned, "fasta"):
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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parents:
diff changeset
254 identic = 0
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
255 compared = 0
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
256 keep_pos = 0
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
257 for base in k1:
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iuc
parents:
diff changeset
258 base2 = k2[keep_pos]
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iuc
parents:
diff changeset
259 # mutation, next
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
260 if base == 'X' or base2 == 'X':
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
261 keep_pos += 1
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
262 continue
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
263 # gap in both sequences, next
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
264 if base == '-' and base2 == '-':
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
265 keep_pos += 1
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
266 continue
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
267 # gap in one of the sequence, next
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
268 if base == '-' or base2 == '-':
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
269 keep_pos += 1
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
270 continue
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
271 # identity
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
272 if base == base2:
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
273 identic += 1
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
274 compared += 1
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
275 keep_pos += 1
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
276 # set minimum overlap to 20
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
277 if compared == 0 or compared < 20:
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
278 percentIdentity = 0
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
279 else:
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
280 percentIdentity = (identic / compared) * 100
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
281 row.append(percentIdentity)
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
282 matrix[k1.id] = row
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
283 log.debug("Write " + file_matrix)
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
284 f = open(file_matrix, "w+")
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
285 for row in matrix:
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
286 f.write(row + ',' + ', '.join(map(str, matrix[row])) + "\n")
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
287 f.close()
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
288
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
289
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
290 def _get_stats(options, hits_collection):
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
291 """
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
292 Retrieve annotation and number of read
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
293 for each OTUs
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
294 """
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
295 file_xlsx = options.output + '/otu_stats.xlsx' # Create a workbook
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
296 workbook = xlsxwriter.Workbook(file_xlsx)
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
297 log.info("Writing stats to " + file_xlsx)
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
298 for cdd_id in hits_collection:
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
299 otu_collection = {}
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
300 cdd_output = options.output + "/" + hits_collection[cdd_id]["short_description"].replace(" ", "_")
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
301 worksheet = workbook.add_worksheet(hits_collection[cdd_id]["short_description"]) # add a worksheet
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
302 file_cluster = cdd_output + '/otu_cluster.csv'
3
f8ebd1e802d7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 16701bfbffd605805e847897799251ab748f559f
iuc
parents: 0
diff changeset
303 file_fasta_nucc = cdd_output + '/representative_nucc.fasta'
0
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
304 with open(file_cluster, 'r') as clust:
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
305 otu_reader = csv.reader(clust, delimiter=',')
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
306 samples_list = []
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
307 for row in otu_reader:
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
308 contigs_list = row[2:len(row) - 1] # remove last empty column
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
309 otu_collection[row[0]] = {} # key -> otu number
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
310 otu_collection[row[0]]['contigs_list'] = contigs_list
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
311 for contig in contigs_list:
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
312 sample = contig.split('_')[0]
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
313 samples_list.append(sample) if sample not in samples_list else samples_list
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
314 if sample not in otu_collection[row[0]]:
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
315 otu_collection[row[0]][sample] = {}
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
316 otu_collection[row[0]][sample][contig] = {}
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
317 # add read number of the contig and annotation
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
318 if 'nb' in hits_collection[cdd_id][contig]:
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
319 otu_collection[row[0]][sample][contig]['nb'] = hits_collection[cdd_id][contig]["nb"]
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
320 else:
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
321 otu_collection[row[0]][sample][contig]['nb'] = 0
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
322 if 'taxonomy' in hits_collection[cdd_id][contig]:
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
323 otu_collection[row[0]][sample][contig]['taxonomy'] = hits_collection[cdd_id][contig]["taxonomy"]
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
324 else:
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
325 otu_collection[row[0]][sample][contig]['taxonomy'] = 'unknown'
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
326 else:
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
327 otu_collection[row[0]][sample][contig] = {}
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
328 # add read number of the contig and annotation
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
329 if 'nb' in hits_collection[cdd_id][contig]:
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
330 otu_collection[row[0]][sample][contig]['nb'] = hits_collection[cdd_id][contig]["nb"]
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
331 else:
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
332 otu_collection[row[0]][sample][contig]['nb'] = 0
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
333 if 'taxonomy' in hits_collection[cdd_id][contig]:
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
334 otu_collection[row[0]][sample][contig]['taxonomy'] = hits_collection[cdd_id][contig]["taxonomy"]
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
335 else:
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
336 otu_collection[row[0]][sample][contig]['taxonomy'] = 'unknown'
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
337 if 'taxonomy' in hits_collection[cdd_id][contig]:
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
338 otu_collection[row[0]]['global_taxonomy'] = hits_collection[cdd_id][contig]["taxonomy"]
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
339 else:
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
340 otu_collection[row[0]]['global_taxonomy'] = 'unknown'
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
341
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
342 # calculate total number of reads for each sample of each OTU
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
343 for otu in otu_collection:
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
344 for sample in otu_collection[otu]:
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
345 if sample not in ['contigs_list', 'global_taxonomy']:
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
346 total_nb_read = 0
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
347 for contig in otu_collection[otu][sample]:
3
f8ebd1e802d7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 16701bfbffd605805e847897799251ab748f559f
iuc
parents: 0
diff changeset
348 if otu_collection[otu][sample][contig]['nb'] == '':
f8ebd1e802d7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 16701bfbffd605805e847897799251ab748f559f
iuc
parents: 0
diff changeset
349 otu_collection[otu][sample][contig]['nb'] = 0
0
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
350 total_nb_read += int(otu_collection[otu][sample][contig]['nb'])
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
351 otu_collection[otu][sample]['total_nb_read'] = total_nb_read
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
352 row = 0
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
353 column = 0
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
354 item = '#OTU_name'
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
355 worksheet.write(row, column, item)
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
356 for samp in samples_list:
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
357 column += 1
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
358 worksheet.write(row, column, samp)
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
359 worksheet.write(row, column + 1, 'taxonomy')
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
360 worksheet.write(row, column + 2, 'contigs_list')
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
361 row = 1
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
362 # column = 0
3
f8ebd1e802d7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 16701bfbffd605805e847897799251ab748f559f
iuc
parents: 0
diff changeset
363 with open(file_fasta_nucc, "w+") as f_nucc:
f8ebd1e802d7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 16701bfbffd605805e847897799251ab748f559f
iuc
parents: 0
diff changeset
364 for otu in otu_collection:
f8ebd1e802d7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 16701bfbffd605805e847897799251ab748f559f
iuc
parents: 0
diff changeset
365 log.info(otu)
f8ebd1e802d7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 16701bfbffd605805e847897799251ab748f559f
iuc
parents: 0
diff changeset
366 if isinstance(otu_collection[otu], dict):
f8ebd1e802d7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 16701bfbffd605805e847897799251ab748f559f
iuc
parents: 0
diff changeset
367 column = 0
f8ebd1e802d7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 16701bfbffd605805e847897799251ab748f559f
iuc
parents: 0
diff changeset
368 worksheet.write(row, column, otu)
f8ebd1e802d7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 16701bfbffd605805e847897799251ab748f559f
iuc
parents: 0
diff changeset
369 # prepare table with 0 in each cells
f8ebd1e802d7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 16701bfbffd605805e847897799251ab748f559f
iuc
parents: 0
diff changeset
370 for sample in otu_collection[otu]:
f8ebd1e802d7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 16701bfbffd605805e847897799251ab748f559f
iuc
parents: 0
diff changeset
371 column = 1
f8ebd1e802d7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 16701bfbffd605805e847897799251ab748f559f
iuc
parents: 0
diff changeset
372 for samp in samples_list:
f8ebd1e802d7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 16701bfbffd605805e847897799251ab748f559f
iuc
parents: 0
diff changeset
373 worksheet.write(row, column, 0)
f8ebd1e802d7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 16701bfbffd605805e847897799251ab748f559f
iuc
parents: 0
diff changeset
374 column += 1
f8ebd1e802d7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 16701bfbffd605805e847897799251ab748f559f
iuc
parents: 0
diff changeset
375 # fill in table with nb of read for each sample and each OTU
f8ebd1e802d7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 16701bfbffd605805e847897799251ab748f559f
iuc
parents: 0
diff changeset
376 for sample in otu_collection[otu]:
f8ebd1e802d7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 16701bfbffd605805e847897799251ab748f559f
iuc
parents: 0
diff changeset
377 column = 1
f8ebd1e802d7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 16701bfbffd605805e847897799251ab748f559f
iuc
parents: 0
diff changeset
378 for samp in samples_list:
f8ebd1e802d7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 16701bfbffd605805e847897799251ab748f559f
iuc
parents: 0
diff changeset
379 if samp == sample:
f8ebd1e802d7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 16701bfbffd605805e847897799251ab748f559f
iuc
parents: 0
diff changeset
380 worksheet.write(row, column, otu_collection[otu][sample]['total_nb_read'])
f8ebd1e802d7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 16701bfbffd605805e847897799251ab748f559f
iuc
parents: 0
diff changeset
381 column += 1
f8ebd1e802d7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 16701bfbffd605805e847897799251ab748f559f
iuc
parents: 0
diff changeset
382 worksheet.write(row, len(samples_list) + 1, otu_collection[otu]['global_taxonomy'].replace(';', ' '))
f8ebd1e802d7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 16701bfbffd605805e847897799251ab748f559f
iuc
parents: 0
diff changeset
383 worksheet.write(row, len(samples_list) + 2, ",".join(otu_collection[otu]['contigs_list']))
f8ebd1e802d7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 16701bfbffd605805e847897799251ab748f559f
iuc
parents: 0
diff changeset
384 row += 1
f8ebd1e802d7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 16701bfbffd605805e847897799251ab748f559f
iuc
parents: 0
diff changeset
385 f_nucc.write(">" + cdd_id + "_" + otu + "_" + otu_collection[otu]['contigs_list'][0] + "\n")
f8ebd1e802d7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 16701bfbffd605805e847897799251ab748f559f
iuc
parents: 0
diff changeset
386 f_nucc.write(str(hits_collection[cdd_id][otu_collection[otu]['contigs_list'][0]]['nuccleotide']) + "\n")
0
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
387 workbook.close()
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
388 read_file = pd.ExcelFile(file_xlsx)
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
389 for sheet in read_file.sheet_names:
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
390 cluster_nb_reads_file = options.output + "/" + sheet.replace(" ", "_") + "/cluster_nb_reads_files.tab"
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
391 data_xls = pd.read_excel(file_xlsx, sheet, dtype=str, index_col=None)
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
392 data_xls.to_csv(cluster_nb_reads_file, encoding='utf-8', index=False, sep='\t')
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
393
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
394
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
395 def _create_html(options, hits_collection):
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
396 """
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
397 Create HTML file with all results
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
398 """
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
399 # create mapping file with all informations to use to create HTML report
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
400 map_file_path = options.output + "/map.txt"
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
401 if os.path.exists(map_file_path):
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
402 os.remove(map_file_path)
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
403
3
f8ebd1e802d7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 16701bfbffd605805e847897799251ab748f559f
iuc
parents: 0
diff changeset
404 with open(map_file_path, "w+") as map_file:
f8ebd1e802d7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 16701bfbffd605805e847897799251ab748f559f
iuc
parents: 0
diff changeset
405 headers = ['#cdd_id', 'align_files', 'tree_files', 'cluster_files', 'cluster_nb_reads_files', 'pairwise_files', 'description', 'full_description\n']
f8ebd1e802d7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 16701bfbffd605805e847897799251ab748f559f
iuc
parents: 0
diff changeset
406 map_file.write("\t".join(headers))
f8ebd1e802d7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 16701bfbffd605805e847897799251ab748f559f
iuc
parents: 0
diff changeset
407 for cdd_id in hits_collection:
f8ebd1e802d7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 16701bfbffd605805e847897799251ab748f559f
iuc
parents: 0
diff changeset
408 cdd_output = hits_collection[cdd_id]["short_description"].replace(" ", "_")
f8ebd1e802d7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 16701bfbffd605805e847897799251ab748f559f
iuc
parents: 0
diff changeset
409 short_description = cdd_output
f8ebd1e802d7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 16701bfbffd605805e847897799251ab748f559f
iuc
parents: 0
diff changeset
410 file_seq_aligned = cdd_output + '/seq_aligned.final_tree.fa'
f8ebd1e802d7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 16701bfbffd605805e847897799251ab748f559f
iuc
parents: 0
diff changeset
411 tree_file = cdd_output + '/tree.dnd.png'
f8ebd1e802d7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 16701bfbffd605805e847897799251ab748f559f
iuc
parents: 0
diff changeset
412 file_cluster = cdd_output + '/otu_cluster.csv'
f8ebd1e802d7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 16701bfbffd605805e847897799251ab748f559f
iuc
parents: 0
diff changeset
413 file_matrix = cdd_output + "/identity_matrix.csv"
f8ebd1e802d7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 16701bfbffd605805e847897799251ab748f559f
iuc
parents: 0
diff changeset
414 cluster_nb_reads_files = cdd_output + "/cluster_nb_reads_files.tab"
f8ebd1e802d7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 16701bfbffd605805e847897799251ab748f559f
iuc
parents: 0
diff changeset
415 map_file.write(cdd_id + "\t" + file_seq_aligned + "\t" + tree_file + "\t")
f8ebd1e802d7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 16701bfbffd605805e847897799251ab748f559f
iuc
parents: 0
diff changeset
416 map_file.write(file_cluster + "\t" + cluster_nb_reads_files + "\t" + file_matrix + "\t")
f8ebd1e802d7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 16701bfbffd605805e847897799251ab748f559f
iuc
parents: 0
diff changeset
417 map_file.write(short_description + "\t" + hits_collection[cdd_id]["full_description"] + "\n")
0
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
418 log.info("Writing HTML report")
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
419 html_cmd = os.path.join(options.tool_path, 'rps2tree_html.py') + ' -m ' + map_file_path + ' -o ' + options.output
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
420 log.debug(html_cmd)
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
421 os.system(html_cmd)
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
422
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
423
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
424 def _set_options():
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
425 parser = argparse.ArgumentParser()
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
426 parser.add_argument('-b', '--blast', help='TAB blast file from blast2ecsv module.', action='append', required=False, dest='blast', nargs='+')
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
diff changeset
427 parser.add_argument('-r', '--rps', help='TAB rpsblast file from rps2ecsv module.', action='append', required=True, dest='rps', nargs='+')
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
iuc
parents:
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428 parser.add_argument('-f', '--fasta', help='FASTA file with contigs', action='append', required=True, dest='fasta', nargs='+')
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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429 parser.add_argument('-p', '--percentage', help='Percentage similarity threshold for OTUs cutoff.', action='store', type=int, default=90, dest='perc')
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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430 parser.add_argument('-vp', '--viral_portion', help='Minimun portion of viral sequences in RPS domain to be included.', action='store', type=float, default=0.3, dest='viral_portion')
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431 parser.add_argument('-mpl', '--min_protein_length', help='Minimum query protein length.', action='store', type=int, default=100, dest='min_protein_length')
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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432 parser.add_argument('-tp', '--tool_path', help='Path to otu_seek.R', action='store', type=str, default='./', dest='tool_path')
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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433 parser.add_argument('-o', '--out', help='The output directory', action='store', type=str, default='./Rps2tree_OTU', dest='output')
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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434 parser.add_argument('-rgb', '--rgb-conf', help='Color palette for contigs coloration', action='store', type=str, default='rgb.txt', dest='file_rgb')
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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435 parser.add_argument('-v', '--verbosity', help='Verbose level', action='store', type=int, choices=[1, 2, 3, 4], default=1)
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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436 args = parser.parse_args()
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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437 return args
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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438
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439
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440 def _set_log_level(verbosity):
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441 if verbosity == 1:
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442 log_format = '%(asctime)s %(levelname)-8s %(message)s'
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443 log.basicConfig(level=log.INFO, format=log_format)
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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444 elif verbosity == 3:
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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445 log_format = '%(filename)s:%(lineno)s - %(asctime)s %(levelname)-8s %(message)s'
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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446 log.basicConfig(level=log.DEBUG, format=log_format)
e889010415a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd
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447
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448
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449 if __name__ == "__main__":
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450 main()