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annotate unipept.py @ 7:75b3b3d0adbf draft

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"planemo upload for repository http://unipept.ugent.be/apidocs commit b6707ea113b2a89b0bb8072dfcc9ceeef4a1b708"
author galaxyp
date Tue, 06 Apr 2021 16:13:57 +0000
parents 9aaa46d45472
children 7863f1abcdda
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1 #!/usr/bin/env python
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2 """
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3 #
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4 # Author:
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5 #
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6 # James E Johnson
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7 #
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8 #------------------------------------------------------------------------------
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9 """
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10 import json
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11 import optparse
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12 import re
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13 import sys
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14 import urllib.error
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15 import urllib.parse
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16 import urllib.request
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18
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19 try:
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20 import xml.etree.cElementTree as ET
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21 except ImportError:
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22 import xml.etree.ElementTree as ET
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23
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25 def warn_err(msg, exit_code=1):
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26 sys.stderr.write(msg)
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27 if exit_code:
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28 sys.exit(exit_code)
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31 go_types = ['biological process', 'molecular function', 'cellular component']
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32 ipr_types = ['Domain', 'Family', 'Homologous_superfamily', 'Repeat', 'Conserved_site', 'Active_site', 'Binding_site', 'PTM']
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33 ec_name_dict = {
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34 '1': 'Oxidoreductase',
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35 '1.1': 'act on the CH-OH group of donors',
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36 '1.2': 'act on the aldehyde or oxo group of donors',
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37 '1.3': 'act on the CH-CH group of donors',
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38 '1.4': 'act on the CH-NH2 group of donors',
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39 '1.5': 'act on CH-NH group of donors',
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40 '1.6': 'act on NADH or NADPH',
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41 '1.7': 'act on other nitrogenous compounds as donors',
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42 '1.8': 'act on a sulfur group of donors',
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43 '1.9': 'act on a heme group of donors',
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44 '1.10': 'act on diphenols and related substances as donors',
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45 '1.11': 'act on peroxide as an acceptor -- peroxidases',
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46 '1.12': 'act on hydrogen as a donor',
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47 '1.13': 'act on single donors with incorporation of molecular oxygen',
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48 '1.14': 'act on paired donors with incorporation of molecular oxygen',
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49 '1.15': 'act on superoxide radicals as acceptors',
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50 '1.16': 'oxidize metal ions',
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51 '1.17': 'act on CH or CH2 groups',
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52 '1.18': 'act on iron-sulfur proteins as donors',
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53 '1.19': 'act on reduced flavodoxin as donor',
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54 '1.20': 'act on phosphorus or arsenic as donors',
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55 '1.21': 'act on X-H and Y-H to form an X-Y bond',
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56 '1.97': 'other oxidoreductases',
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57 '2': 'Transferase',
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58 '2.1': 'transfer one-carbon groups, Methylase',
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59 '2.2': 'transfer aldehyde or ketone groups',
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60 '2.3': 'acyltransferases',
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61 '2.4': 'glycosyltransferases',
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62 '2.5': 'transfer alkyl or aryl groups, other than methyl groups',
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63 '2.6': 'transfer nitrogenous groups',
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64 '2.7': 'transfer phosphorus-containing groups',
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65 '2.8': 'transfer sulfur-containing groups',
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66 '2.9': 'transfer selenium-containing groups',
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67 '3': 'Hydrolase',
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68 '3.1': 'act on ester bonds',
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69 '3.2': 'act on sugars - glycosylases',
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70 '3.3': 'act on ether bonds',
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71 '3.4': 'act on peptide bonds - Peptidase',
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72 '3.5': 'act on carbon-nitrogen bonds, other than peptide bonds',
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73 '3.6': 'act on acid anhydrides',
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74 '3.7': 'act on carbon-carbon bonds',
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75 '3.8': 'act on halide bonds',
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76 '3.9': 'act on phosphorus-nitrogen bonds',
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77 '3.10': 'act on sulfur-nitrogen bonds',
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78 '3.11': 'act on carbon-phosphorus bonds',
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79 '3.12': 'act on sulfur-sulfur bonds',
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80 '3.13': 'act on carbon-sulfur bonds',
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81 '4': 'Lyase',
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82 '4.1': 'carbon-carbon lyases',
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83 '4.2': 'carbon-oxygen lyases',
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84 '4.3': 'carbon-nitrogen lyases',
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85 '4.4': 'carbon-sulfur lyases',
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86 '4.5': 'carbon-halide lyases',
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87 '4.6': 'phosphorus-oxygen lyases',
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88 '5': 'Isomerase',
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89 '5.1': 'racemases and epimerases',
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90 '5.2': 'cis-trans-isomerases',
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91 '5.3': 'intramolecular oxidoreductases',
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92 '5.4': 'intramolecular transferases -- mutases',
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93 '5.5': 'intramolecular lyases',
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94 '5.99': 'other isomerases',
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95 '6': 'Ligase',
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96 '6.1': 'form carbon-oxygen bonds',
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97 '6.2': 'form carbon-sulfur bonds',
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98 '6.3': 'form carbon-nitrogen bonds',
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99 '6.4': 'form carbon-carbon bonds',
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100 '6.5': 'form phosphoric ester bonds',
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101 '6.6': 'form nitrogen-metal bonds',
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102 }
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103 pept2lca_column_order = ['peptide', 'taxon_rank', 'taxon_id', 'taxon_name']
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104 pept2lca_extra_column_order = ['peptide', 'superkingdom', 'kingdom', 'subkingdom', 'superphylum', 'phylum', 'subphylum', 'superclass', 'class', 'subclass', 'infraclass', 'superorder', 'order', 'suborder', 'infraorder', 'parvorder', 'superfamily', 'family', 'subfamily', 'tribe', 'subtribe', 'genus', 'subgenus', 'species_group', 'species_subgroup', 'species', 'subspecies', 'varietas', 'forma']
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105 pept2lca_all_column_order = pept2lca_column_order + pept2lca_extra_column_order[2:]
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106 pept2prot_column_order = ['peptide', 'uniprot_id', 'taxon_id']
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107 pept2prot_extra_column_order = pept2prot_column_order + ['taxon_name', 'ec_references', 'go_references', 'refseq_ids', 'refseq_protein_ids', 'insdc_ids', 'insdc_protein_ids']
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108 pept2ec_column_order = [['peptide', 'total_protein_count'], ['ec_number', 'protein_count']]
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109 pept2ec_extra_column_order = [['peptide', 'total_protein_count'], ['ec_number', 'protein_count', 'name']]
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110 pept2go_column_order = [['peptide', 'total_protein_count'], ['go_term', 'protein_count']]
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111 pept2go_extra_column_order = [['peptide', 'total_protein_count'], ['go_term', 'protein_count', 'name']]
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112 pept2interpro_column_order = [['peptide', 'total_protein_count'], ['code', 'protein_count']]
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113 pept2interpro_extra_column_order = [['peptide', 'total_protein_count'], ['code', 'protein_count', 'type', 'name']]
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114 pept2funct_column_order = ['peptide', 'total_protein_count', 'ec', 'go', 'ipr']
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115
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116
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117 def __main__():
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118 version = '4.3'
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119 pep_pat = '^([ABCDEFGHIKLMNPQRSTVWXYZ]+)$'
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120
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121 def read_tabular(filepath, col):
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122 peptides = []
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123 with open(filepath) as fp:
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124 for i, line in enumerate(fp):
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125 if line.strip() == '' or line.startswith('#'):
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126 continue
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127 fields = line.rstrip('\n').split('\t')
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128 peptide = fields[col]
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129 if not re.match(pep_pat, peptide):
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130 warn_err('"%s" is not a peptide (line %d column %d of tabular file: %s)\n' % (peptide, i, col, filepath), exit_code=invalid_ec)
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131 peptides.append(peptide)
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132 return peptides
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133
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134 def get_fasta_entries(fp):
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135 name, seq = None, []
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136 for line in fp:
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137 line = line.rstrip()
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138 if line.startswith(">"):
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139 if name:
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140 yield (name, ''.join(seq))
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141 name, seq = line, []
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142 else:
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143 seq.append(line)
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144 if name:
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145 yield (name, ''.join(seq))
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146
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147 def read_fasta(filepath):
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148 peptides = []
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149 with open(filepath) as fp:
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150 for id, peptide in get_fasta_entries(fp):
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151 if not re.match(pep_pat, peptide):
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152 warn_err('"%s" is not a peptide (id %s of fasta file: %s)\n' % (peptide, id, filepath), exit_code=invalid_ec)
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153 peptides.append(peptide)
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154 return peptides
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155
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156 def read_mzid(fp):
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157 peptides = []
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158 for event, elem in ET.iterparse(fp):
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159 if event == 'end':
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160 if re.search('PeptideSequence', elem.tag):
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161 peptides.append(elem.text)
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162 return peptides
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163
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164 def read_pepxml(fp):
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165 peptides = []
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166 for event, elem in ET.iterparse(fp):
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167 if event == 'end':
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168 if re.search('search_hit', elem.tag):
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169 peptides.append(elem.get('peptide'))
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170 return peptides
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171
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172 def best_match(peptide, matches):
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173 if not matches:
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174 return None
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175 elif len(matches) == 1:
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176 return matches[0].copy()
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177 elif 'taxon_rank' in matches[0]:
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178 # find the most specific match (peptide is always the first column order field)
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179 for col in reversed(pept2lca_extra_column_order[1:]):
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180 col_id = col + "_id" if options.extra else col
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181 for match in matches:
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182 if 'taxon_rank' in match and match['taxon_rank'] == col:
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183 return match.copy()
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184 if col_id in match and match[col_id]:
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185 return match.copy()
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186 else:
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187 return sorted(matches, key=lambda x: len(x['peptide']))[-1].copy()
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188 return None
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189
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190 def get_taxon_json(resp):
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191 found_keys = set()
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192 for i, pdict in enumerate(resp):
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193 found_keys |= set(pdict.keys())
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194 taxa_cols = []
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195 for col in pept2lca_extra_column_order[-1:0:-1]:
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196 if col + '_id' in found_keys:
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197 taxa_cols.append(col)
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198 id_to_node = dict()
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199
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200 def get_node(id, name, rank, child, seq):
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201 if id not in id_to_node:
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202 data = {'count': 0, 'self_count': 0, 'valid_taxon': 1, 'rank': rank, 'sequences': []}
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203 node = {'id': id, 'name': name, 'children': [], 'kids': [], 'data': data}
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204 id_to_node[id] = node
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205 else:
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206 node = id_to_node[id]
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207 node['data']['count'] += 1
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208 if seq is not None and seq not in node['data']['sequences']:
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209 node['data']['sequences'].append(seq)
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210 if child is None:
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211 node['data']['self_count'] += 1
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212 elif child['id'] not in node['kids']:
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213 node['kids'].append(child['id'])
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214 node['children'].append(child)
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215 return node
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216 root = get_node(1, 'root', 'no rank', None, None)
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217 for i, pdict in enumerate(resp):
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218 sequence = pdict.get('peptide', pdict.get('tryptic_peptide', None))
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219 seq = sequence
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220 child = None
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221 for col in taxa_cols:
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222 col_id = col + '_id'
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223 if col_id in pdict and pdict.get(col_id):
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224 col_name = col if col in found_keys else col + '_name'
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225 child = get_node(pdict.get(col_id, None), pdict.get(col_name, ''), col, child, seq)
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226 seq = None
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227 if child is not None:
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228 get_node(1, 'root', 'no rank', child, None)
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229 return root
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230
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231 def get_ec_json(resp):
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232 ecMap = dict()
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233 for pdict in resp:
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234 if 'ec' in pdict:
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235 for ec in pdict['ec']:
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236 ec_number = ec['ec_number']
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237 if ec_number not in ecMap:
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238 ecMap[ec_number] = []
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239 ecMap[ec_number].append(pdict)
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240
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241 def get_ids(ec):
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242 ids = []
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243 i = len(ec)
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244 while i >= 0:
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245 ids.append(ec[:i])
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246 i = ec.rfind('.', 0, i - 1)
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247 return ids
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248 id_to_node = dict()
4
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249
5
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250 def get_node(id, name, child, seq):
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251 if id not in id_to_node:
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252 data = {'count': 0, 'self_count': 0, 'sequences': []}
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253 node = {'id': id, 'name': name, 'children': [], 'kids': [], 'data': data}
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254 id_to_node[id] = node
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255 else:
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256 node = id_to_node[id]
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257 node['data']['count'] += 1
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258 if seq is not None and seq not in node['data']['sequences']:
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259 node['data']['sequences'].append(seq)
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260 if child is None:
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261 node['data']['self_count'] += 1
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262 elif child['id'] not in node['kids']:
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263 node['kids'].append(child['id'])
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264 node['children'].append(child)
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265 return node
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266 root = get_node(0, '-.-.-.-', None, None)
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267 for i in range(1, 7):
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268 child = get_node(str(i), '%s\n%s' % (str(i), ec_name_dict[str(i)]), None, None)
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269 get_node(0, '-.-.-.-', child, None)
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270 for i, pdict in enumerate(resp):
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271 sequence = pdict.get('peptide', pdict.get('tryptic_peptide', None))
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272 seq = sequence
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273 if 'ec' in pdict:
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274 for ec in pdict['ec']:
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275 child = None
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276 ec_number = ec['ec_number']
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277 for ec_id in get_ids(ec_number):
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278 ec_name = str(ec_id)
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279 child = get_node(ec_id, ec_name, child, seq)
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280 seq = None
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281 if child:
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282 get_node(0, '-.-.-.-', child, None)
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283 return root
4
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284
5
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285 def get_taxon_dict(resp, column_order, extra=False, names=False):
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286 found_keys = set()
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287 results = []
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288 for i, pdict in enumerate(resp):
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289 results.append(pdict)
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290 found_keys |= set(pdict.keys())
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291 # print >> sys.stderr, "%s\n%s" % (pdict.keys(), found_keys)
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292 column_names = []
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293 column_keys = []
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294 for col in column_order:
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295 if col in found_keys:
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296 column_names.append(col)
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297 column_keys.append(col)
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298 elif names:
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299 col_id = col + '_id'
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300 col_name = col + '_name'
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301 if extra:
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302 if col_id in found_keys:
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303 column_names.append(col_id)
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304 column_keys.append(col_id)
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305 if names:
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306 if col_name in found_keys:
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307 column_names.append(col)
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308 column_keys.append(col_name)
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309 else:
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310 if col + '_name' in found_keys:
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311 column_names.append(col)
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312 column_keys.append(col + '_name')
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313 elif col + '_id' in found_keys:
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314 column_names.append(col)
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315 column_keys.append(col + '_id')
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316 # print >> sys.stderr, "%s\n%s" % (column_names, column_keys)
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317 taxa = dict() # peptide: [taxonomy]
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318 for i, pdict in enumerate(results):
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319 peptide = pdict['peptide'] if 'peptide' in pdict else None
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320 if peptide and peptide not in taxa:
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321 vals = [str(pdict[x]) if x in pdict and pdict[x] else '' for x in column_keys]
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322 taxa[peptide] = vals
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323 return (taxa, column_names)
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324
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325 def get_ec_dict(resp, extra=False):
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326 ec_cols = ['ec_numbers', 'ec_protein_counts']
4
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327 if extra:
5
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328 ec_cols.append('ec_names')
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329 ec_dict = dict()
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330 for i, pdict in enumerate(resp):
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331 peptide = pdict['peptide']
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332 ec_numbers = []
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333 protein_counts = []
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334 ec_names = []
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335 if 'ec' in pdict:
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336 for ec in pdict['ec']:
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337 ec_numbers.append(ec['ec_number'])
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338 protein_counts.append(str(ec['protein_count']))
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339 if extra:
6
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340 ec_names.append(ec['name'] if 'name' in ec and ec['name'] else '')
5
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341 vals = [','.join(ec_numbers), ','.join(protein_counts)]
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342 if extra:
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343 vals.append(','.join(ec_names))
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344 ec_dict[peptide] = vals
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345 return (ec_dict, ec_cols)
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346
5
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347 def get_go_dict(resp, extra=False):
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348 go_cols = ['go_terms', 'go_protein_counts']
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349 if extra:
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350 go_cols.append('go_names')
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351 go_dict = dict()
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352 for i, pdict in enumerate(resp):
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353 peptide = pdict['peptide']
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354 go_terms = []
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355 protein_counts = []
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356 go_names = []
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357 if 'go' in pdict:
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358 for go in pdict['go']:
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359 if 'go_term' in go:
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360 go_terms.append(go['go_term'])
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361 protein_counts.append(str(go['protein_count']))
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362 if extra:
6
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363 go_names.append(go['name'] if 'name' in go and go['name'] else '')
5
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364 else:
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365 for go_type in go_types:
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366 if go_type in go:
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367 for _go in go[go_type]:
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368 go_terms.append(_go['go_term'])
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369 protein_counts.append(str(_go['protein_count']))
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diff changeset
370 if extra:
6
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371 go_names.append(_go['name'] if 'name' in _go and _go['name'] else '')
5
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372 vals = [','.join(go_terms), ','.join(protein_counts)]
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diff changeset
373 if extra:
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374 vals.append(','.join(go_names))
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375 go_dict[peptide] = vals
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376 return (go_dict, go_cols)
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377
5
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378 def get_ipr_dict(resp, extra=False):
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379 ipr_cols = ['ipr_codes', 'ipr_protein_counts']
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380 if extra:
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381 ipr_cols.append('ipr_types')
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382 ipr_cols.append('ipr_names')
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383 ipr_dict = dict()
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384 for i, pdict in enumerate(resp):
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385 peptide = pdict['peptide']
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386 ipr_codes = []
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387 protein_counts = []
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388 ipr_names = []
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389 ipr_types = []
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390 if 'ipr' in pdict:
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391 for ipr in pdict['ipr']:
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392 if 'code' in ipr:
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393 ipr_codes.append(ipr['code'])
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394 protein_counts.append(str(ipr['protein_count']))
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diff changeset
395 if extra:
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396 ipr_types.append(ipr['type'] if 'type' in ipr else '')
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397 ipr_names.append(ipr['name'] if 'name' in ipr else '')
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398 else:
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diff changeset
399 for ipr_type in ipr_types:
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400 if ipr_type in ipr:
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diff changeset
401 for _ipr in ipr[ipr_type]:
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402 ipr_codes.append(_ipr['code'])
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403 protein_counts.append(str(_ipr['protein_count']))
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404 if extra:
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405 ipr_types.append(ipr_type)
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406 ipr_names.append(_ipr['name'] if 'name' in _ipr else '')
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diff changeset
407 vals = [','.join(ipr_codes), ','.join(protein_counts)]
4
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408 if extra:
5
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diff changeset
409 vals.append(','.join(ipr_types))
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410 vals.append(','.join(ipr_names))
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411 ipr_dict[peptide] = vals
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412 return (ipr_dict, ipr_cols)
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413
5
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414 def write_ec_table(outfile, resp, column_order):
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415 with open(outfile, 'w') as fh:
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416 for i, pdict in enumerate(resp):
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417 if 'ec' in pdict:
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418 tvals = [str(pdict[x]) if x in pdict and pdict[x] else '' for x in column_order[0]]
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419 for ec in pdict['ec']:
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420 vals = [str(ec[x]) if x in ec and ec[x] else '' for x in column_order[-1]]
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421 fh.write('%s\n' % '\t'.join(tvals + vals))
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422
5
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423 def write_go_table(outfile, resp, column_order):
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424 with open(outfile, 'w') as fh:
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425 for i, pdict in enumerate(resp):
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426 if 'go' in pdict:
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427 tvals = [str(pdict[x]) if x in pdict and pdict[x] else '' for x in column_order[0]]
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428 for go in pdict['go']:
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429 if 'go_term' in go:
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430 vals = [str(go[x]) if x in go and go[x] else '' for x in column_order[-1]]
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431 fh.write('%s\n' % '\t'.join(tvals + vals))
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432 else:
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433 for go_type in go_types:
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434 if go_type in go:
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435 for _go in go[go_type]:
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436 vals = [str(_go[x]) if x in _go and _go[x] else '' for x in column_order[-1]]
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437 vals.append(go_type)
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438 fh.write('%s\n' % '\t'.join(tvals + vals))
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439
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440 def write_ipr_table(outfile, resp, column_order):
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441 with open(outfile, 'w') as fh:
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442 for i, pdict in enumerate(resp):
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443 if 'ipr' in pdict:
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444 tvals = [str(pdict[x]) if x in pdict and pdict[x] else '' for x in column_order[0]]
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445 for ipr in pdict['ipr']:
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446 if 'code' in ipr:
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447 vals = [str(ipr[x]) if x in ipr and ipr[x] else '' for x in column_order[-1]]
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448 fh.write('%s\n' % '\t'.join(tvals + vals))
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449 else:
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450 for ipr_type in ipr_types:
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451 if ipr_type in ipr:
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452 for _ipr in ipr[ipr_type]:
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453 vals = [str(_ipr[x]) if x in _ipr and _ipr[x] else '' for x in column_order[-1]]
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454 vals.append(ipr_type)
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455 fh.write('%s\n' % '\t'.join(tvals + vals))
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456
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457 # Parse Command Line
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458 parser = optparse.OptionParser()
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459 # unipept API choice
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460 parser.add_option('-a', '--api', dest='unipept', default='pept2lca', choices=['pept2lca', 'pept2taxa', 'pept2prot', 'pept2ec', 'pept2go', 'pept2interpro', 'pept2funct', 'peptinfo'],
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461 help='The unipept application: pept2lca, pept2taxa, pept2prot, pept2ec, pept2go, pept2funct, or peptinfo')
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462 # input files
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463 parser.add_option('-t', '--tabular', dest='tabular', default=None, help='A tabular file that contains a peptide column')
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464 parser.add_option('-c', '--column', dest='column', type='int', default=0, help='The column (zero-based) in the tabular file that contains peptide sequences')
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465 parser.add_option('-f', '--fasta', dest='fasta', default=None, help='A fasta file containing peptide sequences')
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466 parser.add_option('-m', '--mzid', dest='mzid', default=None, help='A mxIdentML file containing peptide sequences')
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467 parser.add_option('-p', '--pepxml', dest='pepxml', default=None, help='A pepxml file containing peptide sequences')
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468 # Unipept Flags
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469 parser.add_option('-e', '--equate_il', dest='equate_il', action='store_true', default=False, help='isoleucine (I) and leucine (L) are equated when matching tryptic peptides to UniProt records')
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470 parser.add_option('-x', '--extra', dest='extra', action='store_true', default=False, help='return the complete lineage of the taxonomic lowest common ancestor')
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471 parser.add_option('-n', '--names', dest='names', action='store_true', default=False, help='return the names of all ranks in the lineage of the taxonomic lowest common ancestor')
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472 parser.add_option('-D', '--domains', dest='domains', action='store_true', default=False, help='group response by GO namaspace: biological process, molecular function, cellular component')
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473 parser.add_option('-M', '--max_request', dest='max_request', type='int', default=200, help='The maximum number of entries per unipept request')
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474
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475 # output fields
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476 parser.add_option('-A', '--allfields', dest='allfields', action='store_true', default=False, help='inlcude fields: taxon_rank,taxon_id,taxon_name csv and tsv outputs')
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477 # Warn vs Error Flag
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478 parser.add_option('-S', '--strict', dest='strict', action='store_true', default=False, help='Print exit on invalid peptide')
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479 # output files
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480 parser.add_option('-J', '--json', dest='json', default=None, help='Output file path for json formatted results')
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481 parser.add_option('-j', '--ec_json', dest='ec_json', default=None, help='Output file path for json formatted results')
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482 parser.add_option('-E', '--ec_tsv', dest='ec_tsv', default=None, help='Output file path for EC TAB-separated-values (.tsv) formatted results')
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483 parser.add_option('-G', '--go_tsv', dest='go_tsv', default=None, help='Output file path for GO TAB-separated-values (.tsv) formatted results')
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484 parser.add_option('-I', '--ipr_tsv', dest='ipr_tsv', default=None, help='Output file path for InterPro TAB-separated-values (.tsv) formatted results')
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485 parser.add_option('-L', '--lineage_tsv', dest='lineage_tsv', default=None, help='Output file path for Lineage TAB-separated-values (.tsv) formatted results')
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486 parser.add_option('-T', '--tsv', dest='tsv', default=None, help='Output file path for TAB-separated-values (.tsv) formatted results')
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487 parser.add_option('-C', '--csv', dest='csv', default=None, help='Output file path for Comma-separated-values (.csv) formatted results')
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488 parser.add_option('-U', '--unmatched', dest='unmatched', default=None, help='Output file path for peptide with no matches')
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489 parser.add_option('-u', '--url', dest='url', default='http://api.unipept.ugent.be/api/v1/', help='unipept url http://api.unipept.ugent.be/api/v1/')
7
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490 parser.add_option('-P', '--peptide_match', dest='peptide_match', choices=['best', 'full', 'report'], default='best', help='Match whole peptide')
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491 parser.add_option('--unmatched_aa', dest='unmatched_aa', default=None, help='Show unmatched AA in peptide as')
5
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492 # debug
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493 parser.add_option('-g', '--get', dest='get', action='store_true', default=False, help='Use GET instead of POST')
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494 parser.add_option('-d', '--debug', dest='debug', action='store_true', default=False, help='Turning on debugging')
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495 parser.add_option('-v', '--version', dest='version', action='store_true', default=False, help='print version and exit')
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496 (options, args) = parser.parse_args()
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galaxyp
parents: 4
diff changeset
497 if options.version:
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
498 print('%s' % version)
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
499 sys.exit(0)
7
75b3b3d0adbf "planemo upload for repository http://unipept.ugent.be/apidocs commit b6707ea113b2a89b0bb8072dfcc9ceeef4a1b708"
galaxyp
parents: 6
diff changeset
500
75b3b3d0adbf "planemo upload for repository http://unipept.ugent.be/apidocs commit b6707ea113b2a89b0bb8072dfcc9ceeef4a1b708"
galaxyp
parents: 6
diff changeset
501 def tryptic_match_string(peptide, tryptic_matches):
75b3b3d0adbf "planemo upload for repository http://unipept.ugent.be/apidocs commit b6707ea113b2a89b0bb8072dfcc9ceeef4a1b708"
galaxyp
parents: 6
diff changeset
502 if options.unmatched_aa:
75b3b3d0adbf "planemo upload for repository http://unipept.ugent.be/apidocs commit b6707ea113b2a89b0bb8072dfcc9ceeef4a1b708"
galaxyp
parents: 6
diff changeset
503 p = peptide.lower()
75b3b3d0adbf "planemo upload for repository http://unipept.ugent.be/apidocs commit b6707ea113b2a89b0bb8072dfcc9ceeef4a1b708"
galaxyp
parents: 6
diff changeset
504 for m in tryptic_matches:
75b3b3d0adbf "planemo upload for repository http://unipept.ugent.be/apidocs commit b6707ea113b2a89b0bb8072dfcc9ceeef4a1b708"
galaxyp
parents: 6
diff changeset
505 p = p.replace(m.lower(), m)
75b3b3d0adbf "planemo upload for repository http://unipept.ugent.be/apidocs commit b6707ea113b2a89b0bb8072dfcc9ceeef4a1b708"
galaxyp
parents: 6
diff changeset
506 return re.sub('[a-z]', options.unmatched_aa, p)
75b3b3d0adbf "planemo upload for repository http://unipept.ugent.be/apidocs commit b6707ea113b2a89b0bb8072dfcc9ceeef4a1b708"
galaxyp
parents: 6
diff changeset
507 else:
75b3b3d0adbf "planemo upload for repository http://unipept.ugent.be/apidocs commit b6707ea113b2a89b0bb8072dfcc9ceeef4a1b708"
galaxyp
parents: 6
diff changeset
508 return ','.join(tryptic_matches)
75b3b3d0adbf "planemo upload for repository http://unipept.ugent.be/apidocs commit b6707ea113b2a89b0bb8072dfcc9ceeef4a1b708"
galaxyp
parents: 6
diff changeset
509
5
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
510 invalid_ec = 2 if options.strict else None
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
511 peptides = []
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
512 # Get peptide sequences
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
513 if options.mzid:
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
514 peptides += read_mzid(options.mzid)
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
515 if options.pepxml:
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
516 peptides += read_pepxml(options.pepxml)
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
517 if options.tabular:
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
518 peptides += read_tabular(options.tabular, options.column)
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
519 if options.fasta:
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
520 peptides += read_fasta(options.fasta)
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
521 if args and len(args) > 0:
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
522 for i, peptide in enumerate(args):
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
523 if not re.match(pep_pat, peptide):
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
524 warn_err('"%s" is not a peptide (arg %d)\n' % (peptide, i), exit_code=invalid_ec)
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
525 peptides.append(peptide)
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
526 if len(peptides) < 1:
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
527 warn_err("No peptides input!", exit_code=1)
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
528 column_order = pept2lca_column_order
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
529 if options.unipept == 'pept2prot':
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
530 column_order = pept2prot_extra_column_order if options.extra else pept2prot_column_order
4
4953dcd7dd39 planemo upload for repository http://unipept.ugent.be/apidocs commit e91b0fe16bf468b34884508652359b91847d1f95-dirty
galaxyp
parents: 3
diff changeset
531 else:
5
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
532 if options.extra or options.names:
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
533 column_order = pept2lca_all_column_order if options.allfields else pept2lca_extra_column_order
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
534 else:
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
535 column_order = pept2lca_column_order
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
536 # map to tryptic peptides
7
75b3b3d0adbf "planemo upload for repository http://unipept.ugent.be/apidocs commit b6707ea113b2a89b0bb8072dfcc9ceeef4a1b708"
galaxyp
parents: 6
diff changeset
537 if options.peptide_match == 'full':
75b3b3d0adbf "planemo upload for repository http://unipept.ugent.be/apidocs commit b6707ea113b2a89b0bb8072dfcc9ceeef4a1b708"
galaxyp
parents: 6
diff changeset
538 pepToParts = {p: [p] for p in peptides}
75b3b3d0adbf "planemo upload for repository http://unipept.ugent.be/apidocs commit b6707ea113b2a89b0bb8072dfcc9ceeef4a1b708"
galaxyp
parents: 6
diff changeset
539 else:
75b3b3d0adbf "planemo upload for repository http://unipept.ugent.be/apidocs commit b6707ea113b2a89b0bb8072dfcc9ceeef4a1b708"
galaxyp
parents: 6
diff changeset
540 pepToParts = {p: re.split('\n', re.sub(r'(?<=[RK])(?=[^P])', '\n', p)) for p in peptides}
75b3b3d0adbf "planemo upload for repository http://unipept.ugent.be/apidocs commit b6707ea113b2a89b0bb8072dfcc9ceeef4a1b708"
galaxyp
parents: 6
diff changeset
541 if options.debug:
75b3b3d0adbf "planemo upload for repository http://unipept.ugent.be/apidocs commit b6707ea113b2a89b0bb8072dfcc9ceeef4a1b708"
galaxyp
parents: 6
diff changeset
542 print("column_order: %s\n" % (column_order), file=sys.stderr)
5
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
543 partToPeps = {}
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
544 for peptide, parts in pepToParts.items():
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
545 if options.debug:
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
546 print("peptide: %s\ttryptic: %s\n" % (peptide, parts), file=sys.stderr)
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
547 for part in parts:
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
548 if len(part) > 50:
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
549 warn_err("peptide: %s tryptic fragment len %d > 50 for %s\n" % (peptide, len(part), part), exit_code=None)
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
550 if 5 <= len(part) <= 50:
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
551 partToPeps.setdefault(part, []).append(peptide)
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
552 trypticPeptides = list(partToPeps.keys())
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
553 # unipept
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
554 unipept_resp = []
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
555 idx = list(range(0, len(trypticPeptides), options.max_request))
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
556 idx.append(len(trypticPeptides))
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
557 for i in range(len(idx) - 1):
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
558 post_data = []
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
559 if options.equate_il:
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
560 post_data.append(('equate_il', 'true'))
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
561 if options.names or options.json:
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
562 post_data.append(('extra', 'true'))
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
563 post_data.append(('names', 'true'))
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
564 elif options.extra or options.json:
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
565 post_data.append(('extra', 'true'))
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
566 if options.domains:
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
567 post_data.append(('domains', 'true'))
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
568 post_data += [('input[]', x) for x in trypticPeptides[idx[i]:idx[i + 1]]]
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
569 if options.debug:
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
570 print('post_data: %s\n' % (str(post_data)), file=sys.stderr)
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
571 headers = {'Content-Type': 'application/x-www-form-urlencoded', 'Accept': 'application/json'}
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
572 url = '%s/%s' % (options.url.rstrip('/'), options.unipept)
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
573 if options.get:
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
574 params = '&'.join(["%s=%s" % (i[0], i[1]) for i in post_data])
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
575 url = '%s.json?%s' % (url, params)
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
576 req = urllib.request.Request(url)
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
577 else:
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
578 url = '%s.json' % (url)
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
579 data = urllib.parse.urlencode(post_data).encode()
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
580 params = '&'.join(["%s=%s" % (i[0], i[1]) for i in post_data])
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
581 if options.debug:
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
582 print('data:\n%s\n' % (data), file=sys.stderr)
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
583 req = urllib.request.Request(url, headers=headers, data=urllib.parse.urlencode(post_data).encode(), method='POST')
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
584 if options.debug:
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
585 print("url: %s\n" % (str(url)), file=sys.stderr)
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
586 try:
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
587 resp = urllib.request.urlopen(req)
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
588 rdata = resp.read()
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
589 if options.debug:
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
590 print("%s %s\n" % (url, str(resp.getcode())), file=sys.stderr)
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
591 if resp.getcode() == 200:
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
592 if options.debug:
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
593 print("rdata: \n%s\n\n" % (rdata), file=sys.stderr)
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diff changeset
594 unipept_resp += json.loads(rdata)
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galaxyp
parents: 4
diff changeset
595 # unipept_resp += json.loads(urllib.request.urlopen(req).read())
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galaxyp
parents: 4
diff changeset
596 except Exception as e:
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galaxyp
parents: 4
diff changeset
597 warn_err('HTTP Error %s\n' % (str(e)), exit_code=None)
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galaxyp
parents: 4
diff changeset
598 unmatched_peptides = []
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galaxyp
parents: 4
diff changeset
599 peptideMatches = []
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galaxyp
parents: 4
diff changeset
600 if options.debug:
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galaxyp
parents: 4
diff changeset
601 print("unipept response: %s\n" % str(unipept_resp), file=sys.stderr)
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galaxyp
parents: 4
diff changeset
602 if options.unipept in ['pept2prot', 'pept2taxa']:
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galaxyp
parents: 4
diff changeset
603 dupkey = 'uniprot_id' if options.unipept == 'pept2prot' else 'taxon_id' # should only keep one of these per input peptide
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galaxyp
parents: 4
diff changeset
604 # multiple entries per trypticPeptide for pep2prot or pep2taxa
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galaxyp
parents: 4
diff changeset
605 mapping = {}
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galaxyp
parents: 4
diff changeset
606 for match in unipept_resp:
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galaxyp
parents: 4
diff changeset
607 mapping.setdefault(match['peptide'], []).append(match)
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galaxyp
parents: 4
diff changeset
608 for peptide in peptides:
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galaxyp
parents: 4
diff changeset
609 # Get the intersection of matches to the tryptic parts
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diff changeset
610 keyToMatch = None
7
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diff changeset
611 tryptic_match = []
5
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galaxyp
parents: 4
diff changeset
612 for part in pepToParts[peptide]:
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galaxyp
parents: 4
diff changeset
613 if part in mapping:
7
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diff changeset
614 tryptic_match.append(part)
5
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galaxyp
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diff changeset
615 temp = {match[dupkey]: match for match in mapping[part]}
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galaxyp
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diff changeset
616 if keyToMatch:
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galaxyp
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diff changeset
617 dkeys = set(keyToMatch.keys()) - set(temp.keys())
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diff changeset
618 for k in dkeys:
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galaxyp
parents: 4
diff changeset
619 del keyToMatch[k]
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galaxyp
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diff changeset
620 else:
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galaxyp
parents: 4
diff changeset
621 keyToMatch = temp
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galaxyp
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diff changeset
622 # keyToMatch = keyToMatch.fromkeys([x for x in keyToMatch if x in temp]) if keyToMatch else temp
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galaxyp
parents: 4
diff changeset
623 if not keyToMatch:
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galaxyp
parents: 4
diff changeset
624 unmatched_peptides.append(peptide)
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galaxyp
parents: 4
diff changeset
625 else:
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galaxyp
parents: 4
diff changeset
626 for key, match in keyToMatch.items():
7
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galaxyp
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diff changeset
627 match['tryptic_match'] = tryptic_match_string(peptide, tryptic_match)
5
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galaxyp
parents: 4
diff changeset
628 match['tryptic_peptide'] = match['peptide']
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galaxyp
parents: 4
diff changeset
629 match['peptide'] = peptide
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galaxyp
parents: 4
diff changeset
630 peptideMatches.append(match)
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galaxyp
parents: 4
diff changeset
631 elif options.unipept in ['pept2lca', 'peptinfo']:
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galaxyp
parents: 4
diff changeset
632 # should be one response per trypticPeptide for pep2lca
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galaxyp
parents: 4
diff changeset
633 respMap = {v['peptide']: v for v in unipept_resp}
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galaxyp
parents: 4
diff changeset
634 # map resp back to peptides
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galaxyp
parents: 4
diff changeset
635 for peptide in peptides:
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galaxyp
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diff changeset
636 matches = list()
7
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galaxyp
parents: 6
diff changeset
637 tryptic_match = []
5
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galaxyp
parents: 4
diff changeset
638 for part in pepToParts[peptide]:
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galaxyp
parents: 4
diff changeset
639 if part in respMap:
7
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galaxyp
parents: 6
diff changeset
640 tryptic_match.append(part)
5
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galaxyp
parents: 4
diff changeset
641 matches.append(respMap[part])
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galaxyp
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diff changeset
642 match = best_match(peptide, matches)
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parents: 4
diff changeset
643 if not match:
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galaxyp
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diff changeset
644 unmatched_peptides.append(peptide)
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parents: 4
diff changeset
645 longest_tryptic_peptide = sorted(pepToParts[peptide], key=lambda x: len(x))[-1]
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diff changeset
646 match = {'peptide': longest_tryptic_peptide}
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diff changeset
647 match['tryptic_match'] = tryptic_match_string(peptide, tryptic_match)
5
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diff changeset
648 match['tryptic_peptide'] = match['peptide']
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diff changeset
649 match['peptide'] = peptide
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diff changeset
650 peptideMatches.append(match)
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diff changeset
651 else:
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diff changeset
652 respMap = {v['peptide']: v for v in unipept_resp}
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diff changeset
653 # map resp back to peptides
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galaxyp
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diff changeset
654 for peptide in peptides:
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diff changeset
655 matches = list()
7
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diff changeset
656 tryptic_match = []
5
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diff changeset
657 for part in pepToParts[peptide]:
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galaxyp
parents: 4
diff changeset
658 if part in respMap and 'total_protein_count' in respMap[part]:
7
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diff changeset
659 tryptic_match.append(part)
5
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diff changeset
660 matches.append(respMap[part])
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diff changeset
661 match = best_match(peptide, matches)
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parents: 4
diff changeset
662 if not match:
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diff changeset
663 unmatched_peptides.append(peptide)
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parents: 4
diff changeset
664 longest_tryptic_peptide = sorted(pepToParts[peptide], key=lambda x: len(x))[-1]
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diff changeset
665 match = {'peptide': longest_tryptic_peptide}
7
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diff changeset
666 match['tryptic_match'] = tryptic_match_string(peptide, tryptic_match)
5
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parents: 4
diff changeset
667 match['tryptic_peptide'] = match['peptide']
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parents: 4
diff changeset
668 match['peptide'] = peptide
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galaxyp
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diff changeset
669 peptideMatches.append(match)
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diff changeset
670 resp = peptideMatches
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diff changeset
671 if options.debug:
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parents: 4
diff changeset
672 print("\nmapped response: %s\n" % str(resp), file=sys.stderr)
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parents: 4
diff changeset
673 # output results
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diff changeset
674 if not (options.unmatched or options.json or options.tsv or options.csv):
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parents: 4
diff changeset
675 print(str(resp))
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diff changeset
676 if options.unmatched:
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galaxyp
parents: 4
diff changeset
677 with open(options.unmatched, 'w') as outputFile:
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galaxyp
parents: 4
diff changeset
678 for peptide in peptides:
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galaxyp
parents: 4
diff changeset
679 if peptide in unmatched_peptides:
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galaxyp
parents: 4
diff changeset
680 outputFile.write("%s\n" % peptide)
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galaxyp
parents: 4
diff changeset
681 if options.json:
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galaxyp
parents: 4
diff changeset
682 if options.unipept in ['pept2lca', 'pept2taxa', 'peptinfo']:
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galaxyp
parents: 4
diff changeset
683 root = get_taxon_json(resp)
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parents: 4
diff changeset
684 with open(options.json, 'w') as outputFile:
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galaxyp
parents: 4
diff changeset
685 outputFile.write(json.dumps(root))
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parents: 4
diff changeset
686 elif options.unipept in ['pept2prot', 'pept2ec', 'pept2go', 'pept2interpro', 'pept2funct']:
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
687 with open(options.json, 'w') as outputFile:
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galaxyp
parents: 4
diff changeset
688 outputFile.write(str(resp))
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galaxyp
parents: 4
diff changeset
689 if options.ec_json:
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galaxyp
parents: 4
diff changeset
690 if options.unipept in ['pept2ec', 'pept2funct', 'peptinfo']:
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
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diff changeset
691 root = get_ec_json(resp)
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
692 with open(options.ec_json, 'w') as outputFile:
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
693 outputFile.write(json.dumps(root))
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
694 if options.tsv or options.csv:
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
695 rows = []
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
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diff changeset
696 column_names = None
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
697 if options.unipept in ['pept2ec', 'pept2go', 'pept2interpro', 'pept2funct', 'peptinfo']:
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
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diff changeset
698 taxa = None
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
699 ec_dict = None
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
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diff changeset
700 go_dict = None
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
701 ipr_dict = None
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
702 if options.unipept in ['peptinfo']:
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
703 (taxa, taxon_cols) = get_taxon_dict(resp, column_order, extra=options.extra, names=options.names)
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
704 if options.unipept in ['pept2ec', 'pept2funct', 'peptinfo']:
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
705 (ec_dict, ec_cols) = get_ec_dict(resp, extra=options.extra)
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
706 if options.unipept in ['pept2go', 'pept2funct', 'peptinfo']:
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
707 (go_dict, go_cols) = get_go_dict(resp, extra=options.extra)
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
708 if options.unipept in ['pept2interpro', 'pept2funct', 'peptinfo']:
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
709 (ipr_dict, ipr_cols) = get_ipr_dict(resp, extra=options.extra)
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
710 for i, pdict in enumerate(resp):
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
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diff changeset
711 peptide = pdict['peptide']
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
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diff changeset
712 total_protein_count = str(pdict['total_protein_count']) if 'total_protein_count' in pdict else '0'
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
713 column_names = ['peptide', 'total_protein_count']
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
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diff changeset
714 vals = [peptide, total_protein_count]
7
75b3b3d0adbf "planemo upload for repository http://unipept.ugent.be/apidocs commit b6707ea113b2a89b0bb8072dfcc9ceeef4a1b708"
galaxyp
parents: 6
diff changeset
715 if options.peptide_match == 'report':
75b3b3d0adbf "planemo upload for repository http://unipept.ugent.be/apidocs commit b6707ea113b2a89b0bb8072dfcc9ceeef4a1b708"
galaxyp
parents: 6
diff changeset
716 column_names = ['peptide', 'tryptic_match', 'total_protein_count']
75b3b3d0adbf "planemo upload for repository http://unipept.ugent.be/apidocs commit b6707ea113b2a89b0bb8072dfcc9ceeef4a1b708"
galaxyp
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diff changeset
717 tryptic_match = pdict.get('tryptic_match', '')
75b3b3d0adbf "planemo upload for repository http://unipept.ugent.be/apidocs commit b6707ea113b2a89b0bb8072dfcc9ceeef4a1b708"
galaxyp
parents: 6
diff changeset
718 vals = [peptide, tryptic_match, total_protein_count]
5
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
719 if ec_dict:
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
720 vals += ec_dict[peptide]
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
721 column_names += ec_cols
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
722 if go_dict:
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
723 vals += go_dict[peptide]
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
724 column_names += go_cols
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
725 if ipr_dict:
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
726 vals += ipr_dict[peptide]
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
727 column_names += ipr_cols
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
728 if taxa:
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
729 vals += taxa[peptide][1:]
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
730 column_names += taxon_cols[1:]
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
731 rows.append(vals)
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
732 elif options.unipept in ['pept2lca', 'pept2taxa', 'pept2prot']:
7
75b3b3d0adbf "planemo upload for repository http://unipept.ugent.be/apidocs commit b6707ea113b2a89b0bb8072dfcc9ceeef4a1b708"
galaxyp
parents: 6
diff changeset
733 if options.peptide_match == 'report':
75b3b3d0adbf "planemo upload for repository http://unipept.ugent.be/apidocs commit b6707ea113b2a89b0bb8072dfcc9ceeef4a1b708"
galaxyp
parents: 6
diff changeset
734 column_order.insert(1, 'tryptic_match')
5
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
735 (taxa, taxon_cols) = get_taxon_dict(resp, column_order, extra=options.extra, names=options.names)
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
736 column_names = taxon_cols
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
737 rows = list(taxa.values())
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
738 if options.tsv:
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
739 with open(options.tsv, 'w') as outputFile:
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
740 if column_names:
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
741 outputFile.write("#%s\n" % '\t'.join(column_names))
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
742 for vals in rows:
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
743 outputFile.write("%s\n" % '\t'.join(vals))
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
744 if options.csv:
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
745 with open(options.csv, 'w') as outputFile:
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
746 if column_names:
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
747 outputFile.write("%s\n" % ','.join(column_names))
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
748 for vals in rows:
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
749 outputFile.write("%s\n" % ','.join(['"%s"' % (v if v else '') for v in vals]))
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
750 if options.ec_tsv and options.unipept in ['pept2ec', 'pept2funct', 'peptinfo']:
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
751 column_order = pept2ec_extra_column_order if options.extra else pept2ec_column_order
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
752 write_ec_table(options.ec_tsv, resp, column_order)
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
753 if options.go_tsv and options.unipept in ['pept2go', 'pept2funct', 'peptinfo']:
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
754 column_order = pept2go_extra_column_order if options.extra else pept2go_column_order
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
755 write_go_table(options.go_tsv, resp, column_order)
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
756 if options.ipr_tsv and options.unipept in ['pept2interpro', 'pept2funct', 'peptinfo']:
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
757 column_order = pept2interpro_extra_column_order if options.extra else pept2interpro_column_order
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
758 write_ipr_table(options.ipr_tsv, resp, column_order)
0
6430407e5869 Uploaded
galaxyp
parents:
diff changeset
759
5
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
760
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
761 if __name__ == "__main__":
917fd3ebc223 "planemo upload for repository http://unipept.ugent.be/apidocs commit dd464f03c32f657fc555081117da18ba4c091af6-dirty"
galaxyp
parents: 4
diff changeset
762 __main__()