Mercurial > repos > fgiacomoni > hmdb_ms_search
comparison lib/hmdb.pm @ 4:6091a80df951 draft
planemo upload commit e2dfb6f7afeeb7767ef83e9e2c3a2d3e6a94ae98
| author | fgiacomoni |
|---|---|
| date | Fri, 19 Jan 2018 09:38:17 -0500 |
| parents | 6d0a0f8f672a |
| children | 7ed37640fe2a |
comparison
equal
deleted
inserted
replaced
| 3:505956db90c5 | 4:6091a80df951 |
|---|---|
| 269 my %features = () ; | 269 my %features = () ; |
| 270 | 270 |
| 271 # print Dumper $csv ; | 271 # print Dumper $csv ; |
| 272 | 272 |
| 273 foreach my $line (@{$csv}) { | 273 foreach my $line (@{$csv}) { |
| 274 | 274 ## HMDB csv output - [DEPRECATED]... |
| 275 if ($line !~ /query_mass,compound_id,formula,compound_mass,adduct,adduct_type,adduct_mass,delta/) { | 275 # if ($line !~ /query_mass,compound_id,formula,compound_mass,adduct,adduct_type,adduct_mass,delta/) { |
| 276 my @entry = split(/,/, $line) ; | 276 # my @entry = split(/,/, $line) ; |
| 277 # | |
| 278 # if ( !exists $result_by_entry{$entry[0]} ) { $result_by_entry{$entry[0]} = [] ; } | |
| 279 # | |
| 280 # $features{ENTRY_ENTRY_ID} = $entry[1] ; | |
| 281 # $features{ENTRY_FORMULA} = $entry[2] ; | |
| 282 # $features{ENTRY_CPD_MZ} = $entry[3] ; | |
| 283 # $features{ENTRY_ADDUCT} = $entry[4] ; | |
| 284 # $features{ENTRY_ADDUCT_TYPE} = $entry[5] ; | |
| 285 # $features{ENTRY_ADDUCT_MZ} = $entry[6] ; | |
| 286 # $features{ENTRY_DELTA} = $entry[7] ; | |
| 287 # | |
| 288 # my %temp = %features ; | |
| 289 # | |
| 290 # push (@{$result_by_entry{$entry[0]} }, \%temp) ; | |
| 291 # } | |
| 292 ## NEW HMDB format V4.0 - dec2017 | |
| 293 if ($line !~ /query_mass,compound_id,compound_name,kegg_id,formula,monoisotopic_mass,adduct,adduct_type,adduct_m\/z,delta\(ppm\)/) { | |
| 277 | 294 |
| 278 if ( !exists $result_by_entry{$entry[0]} ) { $result_by_entry{$entry[0]} = [] ; } | 295 if ( $line =~ /(\d+\.\d+),(\w+),(.*),([\w|n\/a]+)\s*,(\w+),(\d+\.\d+),(.*),(\+|\-),(\d+\.\d+),(\d+)/ ) { |
| 279 | 296 my @entry = ("$1","$2","$3","$4","$5","$6","$7","$8","$9","$10") ; |
| 280 $features{ENTRY_ENTRY_ID} = $entry[1] ; | 297 |
| 281 $features{ENTRY_FORMULA} = $entry[2] ; | 298 if ( !exists $result_by_entry{$entry[0]} ) { $result_by_entry{$entry[0]} = [] ; } |
| 282 $features{ENTRY_CPD_MZ} = $entry[3] ; | 299 |
| 283 $features{ENTRY_ADDUCT} = $entry[4] ; | 300 $features{ENTRY_ENTRY_ID} = $entry[1] ; |
| 284 $features{ENTRY_ADDUCT_TYPE} = $entry[5] ; | 301 $features{ENTRY_FORMULA} = $entry[4] ; |
| 285 $features{ENTRY_ADDUCT_MZ} = $entry[6] ; | 302 $features{ENTRY_CPD_MZ} = $entry[5] ; |
| 286 $features{ENTRY_DELTA} = $entry[7] ; | 303 $features{ENTRY_ADDUCT} = $entry[6] ; |
| 287 | 304 $features{ENTRY_ADDUCT_TYPE} = $entry[7] ; |
| 288 my %temp = %features ; | 305 $features{ENTRY_ADDUCT_MZ} = $entry[8] ; |
| 289 | 306 $features{ENTRY_DELTA} = $entry[9] ; |
| 290 push (@{$result_by_entry{$entry[0]} }, \%temp) ; | 307 |
| 308 my %temp = %features ; | |
| 309 push (@{$result_by_entry{$entry[0]} }, \%temp) ; | |
| 310 } | |
| 311 else { | |
| 312 warn "The parsed line ($line) does not match your pattern\n " ; | |
| 313 } | |
| 291 } | 314 } |
| 292 else { | 315 else { |
| 293 next ; | 316 next ; |
| 294 } | 317 } |
| 295 } ## end foreach | 318 } ## end foreach |