Im trying to convert a big matrix (a tab separated file with different number of elements in each column) into a hash of arrays. In the first step, I succesful load the file and using Test::CSV convert the columns of the data into lists, but in doing so, I noted that the lengh of each list is the number of elements correspont to the larger column, i.e., for those columns with less elements, a blank space is present. So far, this is my current code:
#!/usr/bin/perl
use warnings;
use strict;
use Text::CSV;
my $csv = Text::CSV->new({
sep_char => "\t",
});
open( LIST, "<", "testfile" ) or die "No esta el archivo\n";
while (<LIST>) {
if ($csv->parse($_)) {
my @columns = $csv->fields();
print "$columns[0]\t$columns[1]\t$columns[2]","\n";
} else {
my $err = $csv->error_input;
}
}
close(LIST);
The input matrix have 20 columns and between 4500-8500 rows plus header row (which ideally I would like to use as keys in the hash). For simplicity I build a "testfile" with three columns, no header and different number of elements (in the same format as the original input file). Here is the content of testfile:
1 1 2
2 2
3 4
5 6
6 7
7 8 8
8 9
This is the output. I presume that the "Use of uninitializated value..." is related to the blank spaces.
1 1 2
Use of uninitialized value in concatenation (.) or string at blast.cruce.especies.pl line 16, <LIST> line 3.
2 2
3 4
Use of uninitialized value in concatenation (.) or string at blast.cruce.especies.pl line 16, <LIST> line 5.
5 6
Use of uninitialized value in concatenation (.) or string at blast.cruce.especies.pl line 16, <LIST> line 6.
6 7
7 8 8
Use of uninitialized value in concatenation (.) or string at blast.cruce.especies.pl line 16, <LIST> line 8.
8 9
Use of uninitialized value in concatenation (.) or string at blast.cruce.especies.pl line 16, <LIST> line 9.
Use of uninitialized value in concatenation (.) or string at blast.cruce.especies.pl line 16, <LIST> line 9.
Any help are welcome.
Christian.
