http://qs321.pair.com?node_id=484577


in reply to Re: Why does this happen?
in thread Why does this happen?

Because $qbase is a letter, $query_sequence[$qbase] is not valid. To fix it change to this 
foreach $qbase ($q_start .. $q_end)
# qbase is now a number
{
  if ( ($query_sequence[$qbase] =~ /[nN]/) && ($subj_sequence[$qbase] 
+!~ /[nN]/) )
  {
    ++$ncount;    
  }
}

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poj

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Re^3: Why does this happen?
by Transient (Hermit) on Aug 17, 2005 at 20:34 UTC
    I'd keep them separate in case ($#qbase != $#sbase), and since you're not doing anything else with the index, just loop through them all... 
    foreach $qbase ( @qbase ) {
  if ( uc($qbase) eq 'N' ) {
    ++$ncount;
  }
}
foreach $sbase ( @sbase ) {
  if ( uc($sbase) eq 'N' ) {
    ++$ncount;
  }
}

    [download]
    or more concisely... 
      do { $ncount++ if /n/i } foreach ( @qbase, @sbase );

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     Update: disregard, read the OP wrong

    Update: re-read, and the answer doesn't take into account if subj_sequence is n and query is not... 
    foreach my $idx ( 1..$#query_sequence ) {
  if ( $query_sequence[$idx] =~ /n/i && $subj_sequence[$idx] !~ /n/i )
+ {
    $ncount++;
  } elsif ( $subj_sequence[$idx] =~ /n/i && $query_sequence[$idx] !~ /
+n/i ) {
    $ncount++;
  }
}

    [download]
    (Note that it is assumed that $#query_sequence = $#subj_sequence)

    Update: again.. 
    $ncount = grep { ($qbase[$_] =~ /n/i && $sbase[$_] !~ /n/i) || ($qbase
+[$_] !~ /n/i && $sbase[$_] =~ /n/i) } 1..$#qbase;

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[reply]
[d/l]
[select]
      Wow .... I never thought I'd get this much help this fast. Thankyou both very much.

      "(Note that it is assumed that $#query_sequence = $#subj_sequence)"
      The problem is that they aren't equal - it's a bioinformaticological alignment problem - so I have 2 sequences, each with an alignment start and end position, which aren't necessarily at the start and end of the sequence.

      Poj's thing seems to work - thankyou.

      Marinegirl x

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