"Michael S. Robeson II" <[EMAIL PROTECTED]> wrote in message ...
> open(DNA_SEQ, $dna_seq)
Due to precedence, the parens are optional here.
> open(OUTFILE, ">indel_list_"."$dna_seq")
^^^^^^^^^^^^^^^^^^^^^^^^^
">indel_list_$dna_seq" or ">indel_list_".$dna_seq
> foreach (keys %sequences) {
> print "\t\t\>\>\>\>\>\> $_ \<\<\<\<\<\<\n";
> print OUTFILE "\>\>\>\>\>\> $_ \<\<\<\<\<\<\n";
The > and < do not need to be escaped.
> $position{$gap_length} .= "$gap_pos"." \n";
"$gap_pos \n" or "$gap_pos\n"
> foreach my $key (@keys) {
> print "Indel size:\t$key\tTimes found:\t$gap_data{$key}\n";
> print OUTFILE "Indel size:\t$key\tTimes found:\t$gap_data{$key}\n";
> print "Positions:\n";
> print OUTFILE "Positions:\n";
> print "$position{$key}";
> print OUTFILE "$position{$key}";
> print "\n";
> print OUTFILE "\n";
> }
As a general rule, whenever you keep doing the same thing in multiple
places, think sub {}. See alternative below.
------------------
#!/usr/bin/perl
use warnings;
use strict;
# By pre-declaring print2mfh, you can call it without parentheses!
sub print2mfh;
my($animal, %gap);
# my $data = '/path/to/data.txt';
# open DATA, $data or die "Could not open $data: $!\n";
while (<DATA>) {
/>(\w+)/ and $animal=$1 and next;
while ( /(-+)/g ) {
push @{ $gap{$animal}{length $1} }, $-[1]+1;
}
}
die "No gaps found!" unless scalar keys %gap;
# if you are on unix or linux, use tee to print to multiple outputs
# See Perl Cookbook 7.18
# open TEE, "| tee outfile.txt" or die "Could not tee off!: $!\n";
# instead of print2mfh and OUT, you would do: print TEE "text to print";
open OUT, ">output.txt" or die "Could not open output file: $!\n";
print "***Discovered the following DNA sequences:***\n";
print "$_ found!\n" for sort keys %gap;
foreach my $animal(sort keys %gap) {
print2mfh "\t\t>>>>>> $animal <<<<<<\n";
foreach my $length(sort {$a <=> $b} keys %{ $gap{$animal} }) {
my $pos = [EMAIL PROTECTED] $gap{$animal}{$length} };
print2mfh "Indel size:\t$length\tTimes found:\t", scalar @$pos, "\n";
print2mfh join("\n", "Positions:", @$pos, "\n");
}
}
sub print2mfh {
# print to multiple file handles
foreach my $fh(*STDOUT, *OUT) { print $fh @_ }
}
__DATA__
>dog
atcg--acgat---act-ca----
>cat
acgt-acgt----acgt-gt-agct-
>mouse
---acgtacg-atcg---actgac-
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