Mercurial > repos > fgiacomoni > hmdb_ms_search
diff 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 |
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--- a/lib/hmdb.pm Mon Feb 20 09:55:54 2017 -0500 +++ b/lib/hmdb.pm Fri Jan 19 09:38:17 2018 -0500 @@ -271,23 +271,46 @@ # print Dumper $csv ; foreach my $line (@{$csv}) { - - if ($line !~ /query_mass,compound_id,formula,compound_mass,adduct,adduct_type,adduct_mass,delta/) { - my @entry = split(/,/, $line) ; - - if ( !exists $result_by_entry{$entry[0]} ) { $result_by_entry{$entry[0]} = [] ; } + ## HMDB csv output - [DEPRECATED]... +# if ($line !~ /query_mass,compound_id,formula,compound_mass,adduct,adduct_type,adduct_mass,delta/) { +# my @entry = split(/,/, $line) ; +# +# if ( !exists $result_by_entry{$entry[0]} ) { $result_by_entry{$entry[0]} = [] ; } +# +# $features{ENTRY_ENTRY_ID} = $entry[1] ; +# $features{ENTRY_FORMULA} = $entry[2] ; +# $features{ENTRY_CPD_MZ} = $entry[3] ; +# $features{ENTRY_ADDUCT} = $entry[4] ; +# $features{ENTRY_ADDUCT_TYPE} = $entry[5] ; +# $features{ENTRY_ADDUCT_MZ} = $entry[6] ; +# $features{ENTRY_DELTA} = $entry[7] ; +# +# my %temp = %features ; +# +# push (@{$result_by_entry{$entry[0]} }, \%temp) ; +# } + ## NEW HMDB format V4.0 - dec2017 + if ($line !~ /query_mass,compound_id,compound_name,kegg_id,formula,monoisotopic_mass,adduct,adduct_type,adduct_m\/z,delta\(ppm\)/) { - $features{ENTRY_ENTRY_ID} = $entry[1] ; - $features{ENTRY_FORMULA} = $entry[2] ; - $features{ENTRY_CPD_MZ} = $entry[3] ; - $features{ENTRY_ADDUCT} = $entry[4] ; - $features{ENTRY_ADDUCT_TYPE} = $entry[5] ; - $features{ENTRY_ADDUCT_MZ} = $entry[6] ; - $features{ENTRY_DELTA} = $entry[7] ; - - my %temp = %features ; - - push (@{$result_by_entry{$entry[0]} }, \%temp) ; + if ( $line =~ /(\d+\.\d+),(\w+),(.*),([\w|n\/a]+)\s*,(\w+),(\d+\.\d+),(.*),(\+|\-),(\d+\.\d+),(\d+)/ ) { + my @entry = ("$1","$2","$3","$4","$5","$6","$7","$8","$9","$10") ; + + if ( !exists $result_by_entry{$entry[0]} ) { $result_by_entry{$entry[0]} = [] ; } + + $features{ENTRY_ENTRY_ID} = $entry[1] ; + $features{ENTRY_FORMULA} = $entry[4] ; + $features{ENTRY_CPD_MZ} = $entry[5] ; + $features{ENTRY_ADDUCT} = $entry[6] ; + $features{ENTRY_ADDUCT_TYPE} = $entry[7] ; + $features{ENTRY_ADDUCT_MZ} = $entry[8] ; + $features{ENTRY_DELTA} = $entry[9] ; + + my %temp = %features ; + push (@{$result_by_entry{$entry[0]} }, \%temp) ; + } + else { + warn "The parsed line ($line) does not match your pattern\n " ; + } } else { next ;