amadeo: Tools/CREF/shorten-headers-galaxy.pl comparison

Uploaded

comparison

equal deleted inserted replaced

--1:000000000000
+:229d36377838
+#!/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);

Mercurial > repos > amadeo > amadeo