I have a problem with removing columns from a file.
input.tsv:
Otu1 otu2 otu3 otu4 otu5 1 2 5 9 3 8 9 8 4 2 I would like to remove a column if its header is listed in file remove.txt, e.g.:
otu2 otu3 So the result would be:
Otu1 otu4 otu5 1 9 3 8 4 2 How can I do this?
Example using Perl
removeCols.pl:
#!/usr/bin/perl my $file1="input.tsv"; my $file2="remove.txt"; open RFILE, $file2; @cols=<RFILE>; open INPUT, $file1; #read header line, save indicies my @header = split( /\t/, <INPUT> ); for my $i (0..$#header){ if (grep(/$header[$i]/, @cols)){ push @idx,$i; $header[$i] = undef; } } print join("\t",grep(defined,@header)); # loop remaining file while(<INPUT>){ my @line = split(/\t/, $_); $line[$_] = undef for (@idx); print join("\t",grep(defined,@line)); } command-line run as such:
prompt> perl removeCols.pl
