Perl index function to extract a certain substring

Question

Given a certain sequence A stored in an array, I have to find if a larger sequence B contains sequence A.

I am stuck at the index part... and i'm getting an error that argument "TGACCA" isn't numeric in array element in line 69 which is:

if (index($record_r1[1], $r2_seq[$check]) != -1)

The code is:

foreach my $check (@r2_seq)
{
  if (index($record_r1[1], $r2_seq[$check]) != -1)
  {
     $matches= $matches + 1;
     print "Matched";
  }
  else
  {
  }
}

ephemient · Accepted Answer · 2012-06-02 23:39:04Z

3

foreach my $check (@r2_seq)

$check takes on the value of each element in @r2_seq. It is not the index.

$r2_seq[$check]

This is attempting to use an element of @r2_seq as the index into @r2_seq. It is unlikely what you want. More probably, you want to use

$check

as in

if (index($record_r1[1], $check) != -1)

.

answered Jun 2, 2012 at 23:39

ephemient

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Comments

Ωmega · Accepted Answer · 2012-06-02 23:55:07Z

0

I believe you wanted $check to be index, so then use the following code:

foreach my $index (0..$#r2_seq)
{
  if (index($record_r1[1], $r2_seq[$index]) != -1)
  {
     $matches= $matches + 1;
     print "Matched";
  }
  else
  {
  }
}

edited Jun 2, 2012 at 23:55

answered Jun 2, 2012 at 23:49

Ωmega

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1 Comment

A14 Over a year ago

It doesn't go to the match even though the substring is there.

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