Re: Why does this happen?

Your monklynesses

I have a similar problem ....

I get the warning message "Argument "n" isn't numeric in array element at program.pl line 356."

My code looks like this:

foreach $qbase (@query_sequence [$q_start .. $q_end])
    {
        if ($qbase eq ("n"||"N") && $subj_sequence[$qbase] ne ("n"||"N
+"))
        {
            ++$ncount;    
        }
    }

    foreach $sbase (@subj_sequence [$s_start .. $s_end])
    {
        if ($sbase eq ("n"||"N") && $query_sequence[$sbase] ne ("n"||"
+N"))
        {
            ++$ncount;
        }
    }
[download]

My code is intended to mean:
for each position between a start and end position in an array, if the element at that position is an 'n', and the element at the same position in another array is not an n, ++count. $q_start, $q_end, $s_start, $s_end are numbers. @query_sequence and @subj_sequence are arrays of letters. It works ok apart from the warning! Why does this happen and how do I fix it?

Many thanks for your help

Marinegirl x

Comment on Re: Why does this happen? Download Code

Replies are listed 'Best First'.
Re^2: Why does this happen? by poj (Abbot) on Aug 17, 2005 at 20:17 UTC
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; } }` [download] poj	[reply] [d/l]
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 );` [download] 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;` [download]	[reply] [d/l] [select]
Re^4: Why does this happen? by Marinegirl (Initiate) on Aug 17, 2005 at 20:57 UTC
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	[reply]


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