Extracting values from columns in tab delim text file [closed] - regex

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perlI have tab delimited text file with 3 columns like following
Name Description Ontology
dda1 box1_homodomain gn=box1 os=homo C:Cell;C:surface;F:binding;P:toy
dda2 sox2_plurinet gn=plu os=mouse C:Organ;F:transport;P:carrier;P:avi
dd13 klf4_iPSC gn=klf os=Bos C:Cell;F:tiad;P:abs;P:digestion
Now I would like to split the values (gn=xxx and os=xxx) in column Description and values in Ontology column(C:xxx;F=xxx;P=xxx;) into seperate columns like following:
Name Description gn os C F P
dda1 box1_homodomain box1 homo Cell;surface binding toy
dda2 sox2_plurinet plu mouse Organ; transport carrier;avi
dd13 klf4_iPSC klf Bos Cell; tiad abs;digestion
I want this has to export as tab delim file or excel file.I would be really great if someone can guide how can I achieve that in perl. Please help me.
Thanks in advance

Answer 1

I saw perl question after 5 years of my Java. I was excited and i want to do this exercise. Now, that i remember things i did and pasted the code below. Just enrich the same code for last column 'Ontology' with regexp and same hash concept you are done. You can do multiple ways in perl. It could be more code. But, i remember below way.
#!/usr/bin/perl
use Data::Dumper;
my %output;
open(IN, "stack.txt");
while(<IN>) {
my #nameColumns, #descriptionColumns;
if ($_ =~ /Name/) {
$ouput{'Name'} = #nameColumns;
$ouput{'Description'} = #descriptionColumns;
next;
}
my ($group1, $group2, $group3, $group4, $group5, $group6, $group7) = ($_ =~ m/(\w+)\s+(\w+)\s+(\w+)\=(\w+)\s+(\w+)\=(\w+)\s+(.*)/gi);
# Column 1
#nameColumns = #{$output{'Name'}};
push(#nameColumns, $group1);
$output{'Name'} = [#nameColumns];
# Column 2
#print "$group2, $group3, $group4, $group5, $group6, $group7";
#descriptionColumns = #{$output{'Description'}};
push(#descriptionColumns, $group2);
$output{'Description'} = [#descriptionColumns];
# column 3
#column3 = #{$output{$group3}};
push(#column3, $group4);
$output{$group3} = [#column3];
# column 4
#column4 = #{$output{$group5}};
push(#column4, $group6);
$output{$group5} = [#column4];
#Column ...
}
close(IN);
print Dumper(\%output);
$VAR1 = {
'gn' => [
'box1',
'plu',
'klf'
],
'os' => [
'homo',
'mouse',
'Bos'
],
'Name' => [
'dda1',
'dda2',
'dd13'
],
'Description' => [
'box1_homodomain',
'sox2_plurinet',
'klf4_iPSC'
]
};
Note : Output above. If you still didn't figure out, how to finish this program let me know to spend more time