Perl script to join Tab Delimitted File elements

[hansoffate]

Hi,

The first part of my script works fine. Basically, the script reads a file with IDs that I want to search from a Flatdatabase and pull information. I setup the a TILDA Delimitted File and then I setup the two Tab Delimitted Files.
Located Here:
ftp://genome-ftp.stanford.edu/pub/yeast/data_download/chromosomal_feature/SGD_features.tab

ftp://genome-ftp.stanford.edu/pub/yeast/data_download/literature_curation/go_slim_mapping.tab

The SGD_features.tab part of the script works great and it does everything that I need it to. However, the go_slim_mapping.tab part of the script is where I am having some trouble. If you check out the link, you can see that there are multiple rows of the same SGDID.

What I need to do is lookup sgdid's and reference the go_aspect term (three choices: F,C,P) and the associated description under go_slim. If there are multiple entries of $sgdids with multiple F,C,P entries, join the specific entries (let's say C) together with a | delimmiter.

If you lookup S000004664 in the linked file, you can see about 8 rows with the same SGDID but each row has 1 associated go_aspect letter, with 1 definition for go_slim. So for this example, lets say it takes the C values and combines them so it looks like this

cytoplasm|membrane|mitochondrial envelope|mitochondrion

which will then be placed in the csv file for that particular SGDID under the Cellular Component column. I would need this same process to be done for the F, and P values and their respective columns Molecular Function and Biological Process.

If you don't understand what I am talking about, please ask and I'll try to explain it again.

Thanks for the help,
Hans

#!/usr/bin/perl
use strict;
use warnings;
 
 
open IDS, "<partsgdids.txt";
chomp (my @ids = <IDS> );
close(IDS);
 
##Tilda Delimitted File
open (MYFILE, '>data.csv');
print MYFILE "SGDID~ORF~Standard_Name~Alias~Description~Name_Description~Molecular_Function~Biological_Process~Cellular_Component~Define~Mutant_Phenotype\n";
 
open (SGDFEAT, "SGD_features.tab") || die "File not found\n";
chomp (my @sgdfeats=<SGDFEAT>);
close (SGDFEAT);
 
open (SLIMMAP, "go_slim_mapping.tab") || die "File not found\n";
chomp (my @slim=<SLIMMAP>);
close (SLIMMAP);
 
 
##List of columns $sgdid, $feat_type, $feat_qual, $feat_name, $stnd_name, $alias, 
##$parent, $sec_sgdid, $chrom, $start_coord, $stop_coord, $strand, $genetic_pos, 
##$coord_ver, $seq_vers, $desc
 
my %feat_type = ();
my %feat_qual = ();
my %feat_name = ();
my %stnd_name = ();
my %desc = ();
my %alias = ();
my %parent = ();
my %sec_sgdid = ();
my %chrom = ();
my %start_coord = ();
my %stop_coord = ();
my %strand = ();
my %genetic_pos = ();
my %coord_ver = ();
my %seq_vers = ();
 
foreach my $i (@sgdfeats) {
    my ($sgdid, $feat_type, $feat_qual, $feat_name, $stnd_name, $alias, $parent, $sec_sgdid, $chrom, $start_coord, $stop_coord, $strand, $genetic_pos, $coord_ver, $seq_vers, $desc) = split(/\t/, $i);
    $feat_type{$sgdid} = $feat_type;
    $feat_qual{$sgdid} = $feat_qual;
    $feat_name{$sgdid} = $feat_name;
    $stnd_name{$sgdid} = $stnd_name;
    $desc{$sgdid} = $desc;
    $alias{$sgdid} = $alias;
    $parent{$sgdid} = $parent;
    $sec_sgdid{$sgdid} = $sec_sgdid;
    $chrom{$sgdid} = $chrom;
    $start_coord{$sgdid} = $start_coord;
    $stop_coord{$sgdid} = $stop_coord;
    $strand{$sgdid} = $strand;
    $genetic_pos{$sgdid} = $genetic_pos;
    $coord_ver{$sgdid} = $coord_ver;
    $seq_vers{$sgdid} = $seq_vers;
}
 
 
 
##List of Columns for go_slim: $orf, $gene, $sgdid, $go_aspect, $go_slim, $goid, $feature_type
 
##NEED HELP HERE
my %orf = ();
my %gene = ();
#my %sgdid = ();
my %go_aspect = ();
my %go_slim = ();
my %goid = ();
my %feature_type = ();
 
foreach my $p (@slim) 
    {
    my ($orf, $gene, $sgdid, $go_aspect, $go_slim, $goid, $feature_type) = split(/\t/, $p);
      #$orf{$sgdid} = $orf;
    #$gene{$sgdid} = $gene;
    #$go_aspect{$sgdid} = $go_aspect;
    #$go_slim{$sgdid} = $go_slim;
    #$goid{$sgdid} = $goid;
    #$feature_type{$sgdid} = $feature_type;
 
}
 
 
foreach my $ids (@ids) {
    print MYFILE "$ids~$feat_name{$ids}~$stnd_name{$ids}~$alias{$ids}~$desc{$ids}~\n"
}
 
 

[KevinADC]

Looking at the lines you mentioned:

YMR060C    SAM37    S000004664    C    cytoplasm    GO:0005737    ORF|Verified
YMR060C    SAM37    S000004664    C    membrane    GO:0016020    ORF|Verified
YMR060C    SAM37    S000004664    C    mitochondrial envelope    GO:0005740    ORF|Verified
YMR060C    SAM37    S000004664    C    mitochondrion    GO:0005739    ORF|Verified
YMR060C    SAM37    S000004664    F    protein binding    GO:0005515    ORF|Verified
YMR060C    SAM37    S000004664    P    anatomical structure morphogenesis    GO:0009653    ORF|Verified
YMR060C    SAM37    S000004664    P    membrane organization    GO:0016044    ORF|Verified
YMR060C    SAM37    S000004664    P    organelle organization    GO:0006996    ORF|Verified
 

From the code you posted, I take it that the SGDID is the third field: S000004664

And the lines appear to have 7 fields of data but the fifth field can have spaces in the data, for example: "mitochondrial envelope".

Is what I have said correct?