Bioperl printing part of sequence using subseq()

Question

[riaasuddin]

Hello, I want to apply following function on a file which has thousands of sequences. I want to print 192 residues after it finds a motif at position $pos.

print $seq_obj->subseq($pos+1,$pos+192), "\n";

Now problem is that sometimes sequence length is short than 192 residues and it resulted in error. Can anybody help me to find the possible solution? I like the sequence to be printed even if it is shorter than 192 residues. Thanks. Reaz

[riaasuddin]

Hi Chris, Thanks. Actually I need to print only 192 residues after motif not the complete sequence. I will be OK if my subseq ignores those sequences which are shorter than 192 residues.

[Chris Fields]

See modified answer below.

Answer 1

[Chris Fields]

You need to extract up to 192 bases after the motif without going outside the bounds. You would still need to use the length() method, but to clarify the code a bit break out the coordinates into specific variables and basically do a ternary check to pick the right end, something like:

my $len = $seq->length;
my $start = $pos + 1;
my $end = ($pos + 192) < $len ? $pos + 192 : $len;
print $seq_obj->subseq($start,$end), "\n";

I assign the length to a variable to avoid running two method calls, which can add up depending on how many times you will run this.

Original Reply:

Check the length of the sequence, and if it's shorter than 192 residues then simply print it and not the subseq.

EDIT: clarified a tad bit more.

EDIT2: Modified answer to address respondent's question after they clarified the intent.

Answer 2

[Eric Lim]

Use List::Util qw(min) and replace 192 with min($seq_obj->length, 192).

Answer 3

[riaasuddin]

Hello Chris, This ternary check seems to solve my problem. Thanks I appreciate.

[Chris Fields]

Hi riaasuddin , just to make sure it's clear, you should then accept that answer as correct for others to note.

Answer 4

[riaasuddin]

Yes I confirm that the ternary check solved my problem.