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comparison lib/hmdb_api.pm @ 2:be504ccbc41c draft default tip

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master branch Updating with tag :CI_COMMIT_TAG - - Fxx
author fgiacomoni
date Wed, 30 Nov 2022 16:14:27 +0000
parents 7c9269bded0e
children
comparison
equal deleted inserted replaced
1:4373f936111d 2:be504ccbc41c
212 my $tmp_mass = $metabolites->{$id}{'monisotopic_molecular_weight'} ; 212 my $tmp_mass = $metabolites->{$id}{'monisotopic_molecular_weight'} ;
213 $metabolites->{$id}{'[M+H]+'} = ( $tmp_mass + $proton_mass - $electron_mass) * $charge ; 213 $metabolites->{$id}{'[M+H]+'} = ( $tmp_mass + $proton_mass - $electron_mass) * $charge ;
214 $metabolites->{$id}{'[M-H]-'} = ( $tmp_mass - $proton_mass + $electron_mass) * $charge ; 214 $metabolites->{$id}{'[M-H]-'} = ( $tmp_mass - $proton_mass + $electron_mass) * $charge ;
215 } 215 }
216 else { 216 else {
217 warn "No monisotopic_molecular_weight field exists with metabolite $id\n " ; 217 warn "No monoisotopic_molecular_weight field exists with metabolite $id - this entry is not added in dumped file\n " ;
218 } 218 }
219 } 219 }
220 } 220 }
221 elsif ( ($format eq 'CARD') ) { 221 elsif ( ($format eq 'CARD') ) {
222 foreach my $entry (@$metabolites) { 222 foreach my $entry (@$metabolites) {
224 my $tmp_mass = $entry->{'MZ_MONO'} ; 224 my $tmp_mass = $entry->{'MZ_MONO'} ;
225 $entry->{'MZ_[M+H]+'} = ( $tmp_mass + $proton_mass - $electron_mass) * $charge ; 225 $entry->{'MZ_[M+H]+'} = ( $tmp_mass + $proton_mass - $electron_mass) * $charge ;
226 $entry->{'MZ_[M-H]-'} = ( $tmp_mass - $proton_mass + $electron_mass) * $charge ; 226 $entry->{'MZ_[M-H]-'} = ( $tmp_mass - $proton_mass + $electron_mass) * $charge ;
227 } 227 }
228 else { 228 else {
229 warn "No MZ_MONO field exists with metabolite $entry->{'HMDB_ID'}\n " ; 229 warn "No MZ_MONO field exists with metabolite $entry->{'HMDB_ID'} - this entry is not added in dumped file\n " ;
230 } 230 }
231 } 231 }
232 } 232 }
233 233
234 234
268 push (@tmp, $metabolites->{$id}{'metabolite_name'}) ; 268 push (@tmp, $metabolites->{$id}{'metabolite_name'}) ;
269 push (@tmp, $metabolites->{$id}{'chemical_formula'}) ; 269 push (@tmp, $metabolites->{$id}{'chemical_formula'}) ;
270 push (@tmp, $metabolites->{$id}{'inchikey'}) ; 270 push (@tmp, $metabolites->{$id}{'inchikey'}) ;
271 271
272 # merge 272 # merge
273 push (@metabolitesSorted, \@tmp) ; 273
274 ## filter entry if no monisotopic_molecular_weight is present
275 if ($metabolites->{$id}{'monisotopic_molecular_weight'} ne '') {
276 push (@metabolitesSorted, \@tmp) ;
277 }
274 } 278 }
275 279
276 return (\@metabolitesSorted) ; 280 return (\@metabolitesSorted) ;
277 } 281 }
278 ### END of SUB 282 ### END of SUB