Mercurial > repos > amadeo > amadeo
view Tools/CREF/shorten-headers-galaxy.pl @ 3:b30ba2b06326 draft
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author | amadeo |
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date | Mon, 05 Sep 2016 06:01:48 -0400 |
parents | 229d36377838 |
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#!/usr/bin/perl -w $|=1; use strict; #using this makes debugging your code much easier use warnings; #Script to take a multiple fasta file and truncate the header lines to #GeneIDs so the fasta file can be used as input to AME #Checking to see if the user has provided 2 arguments - which is the #name of the promoter sequence file and an output file name if(@ARGV < 2){ print "\nUsage:shorten-headers.pl promoters.fasta promoters-sh.fasta\n\n"; exit(0); } #Declaring variables my $line; # a scalar varaible #Using a FIELHANDLE to open the input file open (INPUT, "<$ARGV[0]") || die "File '$ARGV[0]' not found\n" ; #Using a FIELHANDLE to open the input file open (OUTPUT, ">$ARGV[1]") || die "File '>$ARGV[1]' not found\n" ; #looping through each line of the file while (<INPUT>){ #assigning line to variable $line #$_ is a special default variable that here holds the line contents $line = $_; #match lines header lines if ($line =~ /^>/){ #printing header lines to file as a substring of x charaters printf OUTPUT "%s\n", substr($line,0,21); #the third number is the x characters of the name of the header } else{ #printing out sequence lines just as they are in the orginal file. printf OUTPUT "$line"; } } close (INPUT); close(OUTPUT);