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Seeking further help from Grand Father and other Perl Monks for pattern matching and counting lengths

by supriyoch_2008 (Scribe)
on Feb 02, 2012 at 05:52 UTC ( #951360=perlquestion: print w/ replies, xml ) Need Help??
supriyoch_2008 has asked for the wisdom of the Perl Monks concerning the following question:

Hi Grand Father and other Perl Monks,

Thank you Grand Father. Your program has worked for basecount in 299 MB file. But when I have tried to add a do-until  loop to the end of this program to find the number of motifs and to find lengths between motifs with a <STDIN> input for motif (with 2- 100 letters), I am not getting correct results in either cmd or output text file. I have initialized several variables. But I am confused about how to correct the cmd warning i.e."my" variable $motif masks earlier declaration in same scope at C:\Documents and Settings\user\Desktop\basecount.pl line 58 so that I get correct results of inter-motif lengths vertically in text output page.

I have given the program below along with the cmd and text output results. I shall appreciate if you kindly help in this matter.

#!usr/bin/perl use strict; use warnings; if (! @ARGV) { print <<HELP; # Line 5 Usage: > basecount.pl <bases file> HELP exit; } # Line 10 open my $dnaIn, '<', $ARGV[0] or die "Can't open bases file $ARGV[0]: ++$!\n"; my %counts; my @baseList = qw(A T G C); while (defined (my $line = <$dnaIn>)) { chomp $line; # Line 15 ++$counts{$_} for grep {/\S/} split '', $line; } my $bases; my $errors; $bases += $_ for @counts{@baseList}; # Line 20 $errors += $_ for map {$counts{$_}} grep {! /[ATGC]/} keys %counts; print "\n\n Total bases: $bases\n\n"; print join (', ', map {"$_= $counts{$_}"} @baseList), "\n"; print "Errors (N)= $errors\n" if $errors; # Line 24 # In a loop, ask the user for a motif, search for the motif, and r +eport if it was found.Exit if no motif is entered.Line 25 my $DNA=join('',@ARGV); my $motif=''; # Line 26 do { print "\n\nEnter a motif to count its number and lengths between motif +s:\n";# Line 28 $motif = <STDIN>;# Line 29 # Remove the newline at the end of $motif chomp $motif; # Look for the motif Line 32 if ( $DNA=~ / $motif/ ) { print "I found the motif!\n\n"; # Line 34 } else { print"I couldn\'t find it.\n\n"; } #Line 37 # Count number of motifs and Count number of nt between two motifs use 5.010; # Line 39 my $string ="@ARGV"; # Remove whitespace Line 41 $string=~ s/\s//g; my $count= () =$string=~ /$motif/g; # Line 43 print "Number of motifs: $count.\n\n"; say "The inter-motif nt Lengths are:\n"; # Line 45 say length for split/$motif/,$string; my @a=map length,split/$motif/,$string; # exit on an empty user input Line 48 my $output="result .txt"; unless (open(RESULT,"> $output")){ print"Cannot open file\"$output\".\n\n";# Line 51 exit; } # Line 53 print RESULT"\n\n Number of bases: $bases. Errors(N)=$errors.\n Motif: $motif. Number of motifs: $count.\n\n The inter-motif nt Lengt +hs are:\n\n @a"; close(RESULT);# Line 56 } until (my $motif =~ /^\s*$/ );# Line 58 exit;

Cmd output as follows:

Microsoft Windows XP [Version 5.1.2600] (C) Copyright 1985-2001 Microsoft Corp. C:\Documents and Settings\user>cd d* C:\Documents and Settings\user\Desktop>basecount.pl t.txt "my" variable $motif masks earlier declaration in same scope at C:\Doc +uments and Settings\user\Desktop\basecount.pl line 58. Total bases: 36 A= 9, T= 11, G= 6, C= 10 Errors (N)= 3 Enter a motif to count its number and lengths between motifs: AT I couldn't find it. Number of motifs: 0. The inter-motif nt Lengths are: 5 Use of uninitialized value $motif in pattern match (m//) at C:\Documen +ts and Set tings\user\Desktop\basecount.pl line 27, <STDIN> line 1. C:\Documents and Settings\user\Desktop>

Text Output as follows:

Number of bases: 36. Errors(N)=3. Motif: AT. Number of motifs: 0. The inter-motif nt Lengths are: 5

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Re: Seeking further help from Grand Father and other Perl Monks for pattern matching and counting lengths
by choroba (Abbot) on Feb 02, 2012 at 08:56 UTC
    It would be convenient if you added a link to the previous thread you are continuing here.

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