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Hello fellow Monks! I need your help to discover the bug in my script... It should something really silly, but I can't seem to be able to detect it..
So, suppose you have a file like the following:

LA5    ATGAAAAAGAC--AGCTATCGCGATTGCAGTGGCACTGGCTGGTTTCGCTAC----CGTAGCG
+----CAGGCCG----------CTCCGAAAGATAACACCTGGTACGCTGGTGCT-----AAACTGGGCTG
+GTCTCAGTACCATGACACCGGCTTCATTCACAATGATGGCCCGACTCATGAAAACCAACTGGGCG-CAG
+GTGCTTTTGGTGGTTACCAGGTTAACCCGTATGTTGGCTTTGAAATGGGCTACGACTGGTTAGGCCGTA
+TGCCGTACAAAGGCGACAACATCAATGGCGCTTATAAAGCTCAGGGCGTTCAGTTGACCGCTAAACTGG
+GTTATCCAATCACTGACGATCTGGACG--TTTATACCCGTCTGGGTGGTATGGTATGGCGTG-CAGACA
+CCAAGTCTAACGTCCCTGGC------GGCCCGTCTACTAAAGACCACGACACCGGCGTTTCCCCGGTAT
+TCGCGGGCGGTATCGAGTATGCCATCACCCCTGAAATCGCAACCCGTCTGGAATACCAGTG----GACT
+AACAACATCGGTGATGCCAACACCATCGGCACCCGTCCGGACAACGGCCTGCTGAGCGTAGGTGTTTCC
+TACCGTTTCGGCCAGCAAGAAGCTGCTC-CGGTAGTAGCTCCGGCACCGGCTCCGGCTCCGGAAGTA--
+CAG---ACCAAGCACTTCACTCT-GAAGTCTGACGTACTGTTCAACTTCAACAAATCTACCCTGAAG--
+CCGGAAGGCCAGCAGGCT-CTGGATCAGCTGTACAGCCAGCTGAGCAACCTGGATCCGAAAGACGGTTC
+CGTTGTCGTTCTGGGCTTCACTGACCGTATCGGTTCTGACGC-TTACAACCAGGGTCTGT-CCGAGAAA
+CGTGCTCAGTCTGTTGTTGATTACCTGATCTCCAAAGGTATTCCGTCTGACAAAATCTCCGCACGTGGT
+ATGGGCGAATCTAACCCGGTTACCGGCAACACCTGTGACAACGTGAAACCTCGCGCTGCCCTG---ATC
+GATTGCCTGGCT-CCGGATCGTCGCGTAGAGATCGAAGTTAAAG--GCGTTAAAGACGTGGTAACTCAG
+CCGCAGGCT-
RKS5078    ATGAAAAAGAC--AGCTATCGCGATTGCAGTGGCACTGGCTGGTTTCGCTAC----CGT
+AGCG----CAGGCCG----------CTCCGAAAGATAACACCTGGTACGCTGGTGCT-----AAACTGG
+GCTGGTCTCAGTACCATGACACCGGCTTCATTCACAATGATGGCCCGACTCATGAAAACCAACTGGGCG
+-CAGGTGCTTTTGGTGGTTACCAGGTTAACCCGTATGTTGGCTTTGAAATGGGCTACGACTGGTTAGGC
+CGTATGCCGTACAAAGGCGACAACATCAATGGCGCTTATAAAGCTCAGGGCGTTCAGTTGACCGCTAAA
+CTGGGTTATCCAATCACTGACGATCTGGACG--TTTATACCCGTCTGGGTGGTATGGTATGGCGTG-CA
+GACACCAAGTCTAATGTCCCTGGC------GGCCCGTCTACTAAAGACCACGACACCGGCGTTTCCCCG
+GTATTCGCGGGCGGTATCGAGTATGCCATCACCCCTGAAATCGCAACCCGTCTGGAATACCAGTG----
+GACTAACAACATCGGTGATGCCAACACCATCGGCACCCGTCCGGACAACGGCCTGCTGAGCGTAGGTGT
+TTCCTACCGTTTCGGCCAGCAAGAAGCTGCTC-CGGTAGTAGCTCCGGCACCGGCTCCGGCTCCGGAAG
+TA--CAG---ACCAAGCACTTCACTCT-GAAGTCTGACGTACTGTTCAACTTCAACAAATCTACCCTGA
+AG--CCGGAAGGCCAGCAGGCT-CTGGATCAGCTGTACAGCCAGCTGAGCAACCTGGATCCGAAAGACG
+GTTCCGTTGTCGTTCTGGGCTTCACTGACCGTATCGGTTCTGACGC-TTACAACCAGGGTCTGT-CCGA
+GAAACGTGCTCAGTCTGTTGTTGATTACCTGATCTCCAAAGGTATTCCGTCTGACAAAATCTCCGCACG
+TGGTATGGGCGAATCTAACCCGGTTACCGGCAACACCTGTGACAACGTGAAACCTCGCGCTGCCCTG--
+-ATCGATTGCCTGGCT-CCGGATCGTCGCGTAGAGATCGAAGTTAAAG--GCGTTAAAGACGTGGTAAC
+TCAGCCGCAGGCT-
06-0676    ATGAAAAAGAC--AGCTATCGCGATTGCAGTGGCACTGGCTGGTTTCGCTAC----CGT
+AGCG----CAGGCCG----------CTCCGAAAGATAACACCTGGTACGCTGGTGCT-----AAACTGG
+GCTGGTCTCAGTACCATGACACCGGCTTCATTCACAATGATGGCCCGACTCATGAAAACCAACTGGGCG
+-CAGGTGCTTTTGGTGGTTACCAGGTTAACCCGTATGTTGGCTTTGAAATGGGCTACGACTGGTTAGGC
+CGTATGCCGTACAAAGGCGACAACATCAATGGCGCTTATAAAGCTCAGGGCGTTCAGTTGACCGCTAAA
+CTGGGTTATCCAATCACTGACGATCTGGACG--TTTATACCCGTCTGGGTGGTATGGTATGGCGTG-CA
+GACACCAAGTCTAACGTCCCTGGC------GGCCCGTCTACTAAAGACCACGACACCGGCGTTTCCCCG
+GTATTCGCGGGCGGTATCGAGTATGCCATCACCCCTGAAATCGCAACCCGTCTGGAATACCAGTG----
+GACTAACAACATCGGTGATGCCAACACCATCGGCACCCGTCCGGACAACGGCCTGCTGAGCGTAGGTGT
+TTCCTACCGTTTCGGCCAGCAAGAAGCTGCTC-CGGTAGTAGCTCCGGCACCGGCTCCGGCTCCGGAAG
+TA--CAG---ACCAAGCACTTCACTCT-GAAGTCTGACGTACTGTTCAACTTCAACAAATCTACCCTGA
+AG--CCGGAAGGCCAGCAGGCT-CTGGATCAGCTGTACAGCCAGCTGAGCAACCTGGATCCGAAAGACG
+GTTCCGTTGTCGTTCTGGGCTTCACTGACCGTATCGGTTCTGACGC-TTACAACCAGGGTCTGT-CCGA
+GAAACGTGCTCAGTCTGTTGTTGATTACCTGATCTCCAAAGGTATTCCGTCTGACAAAATCTCCGCACG
+TGGTATGGGCGAATCTAACCCGGTTACCGGCAACACCTGTGACAACGTGAAACCTCGCGCTGCCCTG--
+-ATCGATTGCCTGGCT-CCGGATCGTCGCGTAGAGATCGAAGTTAAAG--GCGTTAAAGACGTGGTAAC
+TCAGCCGCAGGCT-
58-6482    ATGAAAAAGAC--AGCTATCGCGATTGCAGTGGCACTGGCTGGTTTCGCTAC----CGT
+AGCG----CAGGCCG----------CTCCGAAAGATAACACCTGGTACGCTGGTGCT-----AAACTGG
+GCTGGTCTCAGTACCATGACACCGGCTTCATTCACAATGATGGCCCGACTCATGAAAACCAACTGGGCG
+-CAGGTGCTTTTGGTGGTTACCAGGTTAACCCGTATGTTGGCTTTGAAATGGGCTACGACTGGTTAGGC
+CGTATGCCGTACAAAGGCGACAACATCAATGGCGCTTATAAAGCTCAGGGCGTTCAGTTGACCGCTAAA
+CTGGGTTATCCAATCACTGACGATCTGGACG--TTTATACCCGTCTGGGTGGTATGGTATGGCGTG-CA
+GACACCAAGTCTAACGTCCCTGGC------GGCCCGTCTACTAAAGACCACGACACCGGCGTTTCCCCG
+GTATTCGCGGGCGGTATCGAGTATGCCATCACCCCTGAAATCGCAACCCGTCTGGAATACCAGTG----
+GACTAACAACATCGGTGATGCCAACACCATCGGCACCCGTCCGGACAACGGCCTGCTGAGCGTAGGTGT
+TTCCTACCGTTTCGGCCAGCAAGAAGCTGCTC-CGGTAGTAGCTCCGGCACCGGCTCCGGCTCCGGAAG
+TA--CAG---ACCAAGCACTTCACTCT-GAAGTCTGACGTACTGTTCAACTTCAACAAATCTACCCTGA
+AG--CCGGAAGGCCAGCAGGCT-CTGGATCAGCTGTACAGCCAGCTGAGCAACCTGGATCCGAAAGACG
+GTTCCGTTGTCGTTCTGGGCTTCACTGACCGTATCGGTTCTGACGC-TTACAACCAGGGTCTGT-CCGA
+GAAACGTGCTCAGTCTGTTGTTGATTACCTGATCTCCAAAGGTATTCCGTCTGACAAAATCTCCGCACG
+TGGTATGGGCGAATCTAACCCGGTTACCGGCAACACCTGTGACAACGTGAAACCTCGCGCTGCCCTG--
+-ATCGATTGCCTGGCT-CCGGATCGTCGCGTAGAGATCGAAGTTAAAG--GCGTTAAAGACGTGGTAAC
+TCAGCCGCAGGCT-
648905    ATGAAAAAGAC--AGCTATCGCGATTGCAGTGGCACTGGCTGGTTTCGCTAC----CGTA
+GCG----CAGGCCG----------CTCCGAAAGATAACACCTGGTACGCTGGTGCT-----AAACTGGG
+CTGGTCTCAGTACCATGACACCGGCTTCATTCACAATGATGGCCCGACTCATGAAAACCAACTGGGCG-
+CAGGTGCTTTTGGTGGTTACCAGGTTAACCCGTATGTTGGCTTTGAAATGGGCTACGACTGGTTAGGCC
+GTATGCCGTACAAAGGCGACAACATCAATGGCGCTTATAAAGCTCAGGGCGTTCAGTTGACCGCTAAAC
+TGGGTTATCCAATCACTGACGATCTGGACG--TTTATACCCGTCTGGGTGGTATGGTATGGCGTG-CAG
+ACACCAAGTCTAACGTCCCTGGC------GGCCCGTCTACTAAAGACCACGACACCGGCGTTTCCCCGG
+TATTCGCGGGCGGTATCGAGTATGCCATCACCCCTGAAATCGCAACCCGTCTGGAATACCAGTG----G
+ACTAACAACATCGGTGATGCCAACACCATCGGCACCCGTCCGGACAACGGCCTGCTGAGCGTAGGTGTT
+TCCTACCGTTTCGGCCAGCAAGAAGCTGCTC-CGGTAGTAGCTCCGGCACCGGCTCCGGCTCCGGAAGT
+A--CAG---ACCAAGCACTTCACTCT-GAAGTCTGACGTACTGTTCAACTTCAACAAATCTACCCTGAA
+G--CCGGAAGGCCAGCAGGCT-CTGGATCAGCTGTACAGCCAGCTGAGCAACCTGGATCCGAAAGACGG
+TTCCGTTGTCGTTCTGGGCTTCACTGACCGTATCGGTTCTGACGC-TTACAACCAGGGTCTGT-CCGAG
+AAACGTGCTCAGTCTGTTGTTGATTACCTGATCTCCAAAGGTATTCCGTCTGACAAAATCTCCGCACGT
+GGTATGGGCGAATCTAACCCGGTTACCGGCAACACCTGTGACAACGTGAAACCTCGCGCTGCCCTG---
+ATCGATTGCCTGGCT-CCGGATCGTCGCGTAGAGATCGAAGTTAAAG--GCGTTAAAGACGTGGTAACT
+CAGCCGCAGGCT-
8b-1    ATGAAAAAGAC--AGCTATCGCGATTGCAGTGGCACTGGCTGGTTTCGCTAC----CGTAGC
+G----CAGGCCG----------CTCCGAAAGATAACACCTGGTACGCTGGTGCT-----AAACTGGGCT
+GGTCTCAGTACCATGACACCGGCTTCATTCACAATGATGGCCCGACTCATGAAAACCAACTGGGCG-CA
+GGTGCTTTTGGTGGTTACCAGGTTAACCCGTATGTTGGCTTTGAAATGGGCTACGACTGGTTAGGCCGT
+ATGCCGTACAAAGGCGACAACATCAATGGCGCTTATAAAGCTCAGGGCGTTCAGTTGACCGCTAAACTG
+GGTTATCCAATCACTGACGATCTGGACG--TTTATACCCGTCTGGGTGGTATGGTATGGCGTG-CAGAC
+ACCAAGTCTAACGTCCCTGGC------GGCCCGTCTACTAAAGACCACGACACCGGCGTTTCCCCGGTA
+TTCGCGGGCGGTATCGAGTATGCCATCACCCCTGAAATCGCAACCCGTCTGGAATACCAGTG----GAC
+TAACAACATCGGTGATGCCAACACCATCGGCACCCGTCCGGACAACGGCCTGCTGAGCGTAGGTGTTTC
+CTACCGTTTCGGCCAGCAAGAAGCTGCTC-CGGTAGTAGCTCCGGCACCGGCTCCGGCTCCGGAAGTA-
+-CAG---ACCAAGCACTTCACTCT-GAAGTCTGACGTACTGTTCAACTTCAACAAATCTACCCTGAAG-
+-CCGGAAGGCCAGCAGGCT-CTGGATCAGCTGTACAGCCAGCTGAGCAACCTGGATCCGAAAGACGGTT
+CCGTTGTCGTTCTGGGCTTCACTGACCGTATCGGTTCTGACGC-TTACAACCAGGGTCTGT-CCGAGAA
+ACGTGCTCAGTCTGTTGTTGATTACCTGATCTCCAAAGGTATTCCGTCTGACAAAATCTCCGCACGTGG
+TATGGGCGAATCTAACCCGGTTACCGGCAACACCTGTGACAACGTGAAACCTCGCGCTGCCCTG---AT
+CGATTGCCTGGCT-CCGGATCGTCGCGTAGAGATCGAAGTTAAAG--GCGTTAAAGACGTGGTAACTCA
+GCCGCAGGCT-
22510-1    ATGAAAAAGAC--AGCTATCGCGATTGCAGTGGCACTGGCTGGTTTCGCTAC----CGT
+AGCG----CAGGCCG----------CTCCGAAAGATAACACCTGGTACGCTGGTGCT-----AAACTGG
+GCTGGTCTCAGTACCATGACACCGGCTTCATTCACAATGATGGCCCGACTCATGAAAACCAACTGGGCG
+-CAGGTGCTTTTGGTGGTTACCAGGTTAACCCGTATGTTGGCTTTGAAATGGGCTACGACTGGTTAGGC
+CGTATGCCGTACAAAGGCGACAACATCAATGGCGCTTATAAAGCTCAGGGCGTTCAGTTGACCGCTAAA
+CTGGGTTATCCAATCACTGACGATCTGGACG--TTTATACCCGTCTGGGTGGTATGGTATGGCGTG-CA
+GACACCAAGTCTAACGTCCCTGGC------GGCCCGTCTACTAAAGACCACGACACCGGCGTTTCCCCG
+GTATTCGCGGGCGGTATCGAGTATGCCATCACCCCTGAAATCGCAACCCGTCTGGAATACCAGTG----
+GACTAACAACATCGGTGATGCCAACACCATCGGCACCCGTCCGGACAACGGCCTGCTGAGCGTAGGTGT
+TTCCTACCGTTTCGGCCAGCAAGAAGCTGCTC-CGGTAGTAGCTCCGGCACCGGCTCCGGCTCCGGAAG
+TA--CAG---ACCAAGCACTTCACTCT-GAAGTCTGACGTACTGTTCAACTTCAACAAATCTACCCTGA
+AG--CCGGAAGGCCAGCAGGCT-CTGGATCAGCTGTACAGCCAGCTGAGCAACCTGGATCCGAAAGACG
+GTTCCGTTGTCGTTCTGGGCTTCACTGACCGTATCGGTTCTGACGC-TTACAACCAGGGTCTGT-CCGA
+GAAACGTGCTCAGTCTGTTGTTGATTACCTGATCTCCAAAGGTATTCCGTCTGACAAAATCTCCGCACG
+TGGTATGGGCGAATCTAACCCGGTTACCGGCAACACCTGTGACAACGTGAAACCTCGCGCTGCCCTG--
+-ATCGATTGCCTGGCT-CCGGATCGTCGCGTAGAGATCGAAGTTAAAG--GCGTTAAAGACGTGGTAAC
+TCAGCCGCAGGCT-
[download]

and you want to count, per position, how many A, T, G, C or - you have.
I have written this:

@all_seqs = ();
while(<>)
{
    if($_=~/(.*)\t(.*)/)
    {
        $id=$1;
        $seq=$2;

        push @all_seqs, $seq;
    }
}

for ($i=0; $i<=$#all_seqs; $i++)
{
    $seq_to_examine=$all_seqs[$i];
    @split_seq_to_examine=split(//, $seq_to_examine);    

    for($j=0; $j<=1108; $j++)
    {
        if ($split_seq_to_examine[$j] eq 'A') {$count_A++;}
        elsif ($split_seq_to_examine[$j] eq 'T') {$count_T++;}
        elsif ($split_seq_to_examine[$j] eq 'C') {$count_C++;}
        elsif ($split_seq_to_examine[$j] eq 'G') {$count_G++;}
        elsif ($split_seq_to_examine[$j] eq '-') {$count_non++;}

    print $j."\t".$count_A."\t".$count_T."\t".$count_C."\t".$count_G."
+\n";
    }
}
[download]

but it keeps increasing the counters, and not reporting position-by-position. I think I must somewhere set the counters to 0, but the positions I tried just made the script worse...

In reply to What is wrong in this code??? by Anonymous Monk

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The best material for plates (tableware) is: