Extract reads from a BAM/SAM file of a designated length - perl

Question

I am a bit of new to Perl and wish to use it in order to extract reads of a specific length from my BAM (alignment) file.
The BAM file contains reads, whose length is from 19 to 29 nt.
Here is an example of first 2 reads:
YT:Z:UUA00182:193:HG2NLDMXX:1:1101:29884:1078 0 3R 6234066 42 22M * 0 0 TCACTGGGCTTTGTTTATCTCA FF:FFFF,FFFFFFFF:FFFFF AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:22
YT:Z:UUA00182:193:HG2NLDMXX:1:1101:1777:1094 16 4 1313373 1 24M * 0 0 TCGCATTCTTATTGATTTTCCTTT FFFFFFF,FFFFFFFFFFFFFFFF AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:24
I want to extract only those, which are, let's say, 21 nt in length.
I try to do this with the following code:
my $string = <STDIN>;
$length = samtools view ./file.bam | head | perl -F'\t' -lane'length #F[10]';
if ($length == 21){
print($string)
}
However, the program does not give any result...
Could anyone please suggest the right way of doing this?

Answer 1

Your question is a bit confusing. Is the code snippet supposed to be a Perl script or a shell script that calls a Perl one-liner?
Assuming that you meant to write a Perl script into which you pipe the output of samtools view to:
#!/usr/bin/perl
use strict;
use warnings;
while (<STDIN>) {
my #fields = split("\t", $_);
# debugging, just to see what field is extracted...
print "'$fields[10]' ", length($fields[10]), "\n";
if (length($fields[10]) eq 21) {
print $_;
}
}
exit 0;
With your test data in dummy.txt I get:
# this would be "samtools view ./file.bam | head | perl dummy.pl" in your case?
$ cat dummy.txt | perl dummy.pl
'FF:FFFF,FFFFFFFF:FFFFF' 22
'FFFFFFF,FFFFFFFFFFFFFFFF' 24
Your test data doesn't contain a sample with length 21 though, so the if clause is never executed.

Answer 2

Note that the 10th field in your sample input is having either 22 or 24 in length. Also, the syntax that you use is wrong. Here is the Perl one-liner to match the field with length=22.
$ cat pkom.txt
YT:Z:UUA00182:193:HG2NLDMXX:1:1101:29884:1078 0 3R 6234066 42 22M * 0 0 TCACTGGGCTTTGTTTATCTCA FF:FFFF,FFFFFFFF:FFFFF AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:22
YT:Z:UUA00182:193:HG2NLDMXX:1:1101:1777:1094 16 4 1313373 1 24M * 0 0 TCGCATTCTTATTGATTTTCCTTT FFFFFFF,FFFFFFFFFFFFFFFF AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:24
$ perl -lane ' print if length($F[9])==22 ' pkom.txt
YT:Z:UUA00182:193:HG2NLDMXX:1:1101:29884:1078 0 3R 6234066 42 22M * 0 0 TCACTGGGCTTTGTTTATCTCA FF:FFFF,FFFFFFFF:FFFFF AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:22
$