perlquestion Anonymous Monk 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..<br> So, suppose you have a file like the following:<br> <code> LA5 ATGAAAAAGAC--AGCTATCGCGATTGCAGTGGCACTGGCTGGTTTCGCTAC----CGTAGCG----CAGGCCG----------CTCCGAAAGATAACACCTGGTACGCTGGTGCT-----AAACTGGGCTGGTCTCAGTACCATGACACCGGCTTCATTCACAATGATGGCCCGACTCATGAAAACCAACTGGGCG-CAGGTGCTTTTGGTGGTTACCAGGTTAACCCGTATGTTGGCTTTGAAATGGGCTACGACTGGTTAGGCCGTATGCCGTACAAAGGCGACAACATCAATGGCGCTTATAAAGCTCAGGGCGTTCAGTTGACCGCTAAACTGGGTTATCCAATCACTGACGATCTGGACG--TTTATACCCGTCTGGGTGGTATGGTATGGCGTG-CAGACACCAAGTCTAACGTCCCTGGC------GGCCCGTCTACTAAAGACCACGACACCGGCGTTTCCCCGGTATTCGCGGGCGGTATCGAGTATGCCATCACCCCTGAAATCGCAACCCGTCTGGAATACCAGTG----GACTAACAACATCGGTGATGCCAACACCATCGGCACCCGTCCGGACAACGGCCTGCTGAGCGTAGGTGTTTCCTACCGTTTCGGCCAGCAAGAAGCTGCTC-CGGTAGTAGCTCCGGCACCGGCTCCGGCTCCGGAAGTA--CAG---ACCAAGCACTTCACTCT-GAAGTCTGACGTACTGTTCAACTTCAACAAATCTACCCTGAAG--CCGGAAGGCCAGCAGGCT-CTGGATCAGCTGTACAGCCAGCTGAGCAACCTGGATCCGAAAGACGGTTCCGTTGTCGTTCTGGGCTTCACTGACCGTATCGGTTCTGACGC-TTACAACCAGGGTCTGT-CCGAGAAACGTGCTCAGTCTGTTGTTGATTACCTGATCTCCAAAGGTATTCCGTCTGACAAAATCTCCGCACGTGGTATGGGCGAATCTAACCCGGTTACCGGCAACACCTGTGACAACGTGAAACCTCGCGCTGCCCTG---ATCGATTGCCTGGCT-CCGGATCGTCGCGTAGAGATCGAAGTTAAAG--GCGTTAAAGACGTGGTAACTCAGCCGCAGGCT- RKS5078 ATGAAAAAGAC--AGCTATCGCGATTGCAGTGGCACTGGCTGGTTTCGCTAC----CGTAGCG----CAGGCCG----------CTCCGAAAGATAACACCTGGTACGCTGGTGCT-----AAACTGGGCTGGTCTCAGTACCATGACACCGGCTTCATTCACAATGATGGCCCGACTCATGAAAACCAACTGGGCG-CAGGTGCTTTTGGTGGTTACCAGGTTAACCCGTATGTTGGCTTTGAAATGGGCTACGACTGGTTAGGCCGTATGCCGTACAAAGGCGACAACATCAATGGCGCTTATAAAGCTCAGGGCGTTCAGTTGACCGCTAAACTGGGTTATCCAATCACTGACGATCTGGACG--TTTATACCCGTCTGGGTGGTATGGTATGGCGTG-CAGACACCAAGTCTAATGTCCCTGGC------GGCCCGTCTACTAAAGACCACGACACCGGCGTTTCCCCGGTATTCGCGGGCGGTATCGAGTATGCCATCACCCCTGAAATCGCAACCCGTCTGGAATACCAGTG----GACTAACAACATCGGTGATGCCAACACCATCGGCACCCGTCCGGACAACGGCCTGCTGAGCGTAGGTGTTTCCTACCGTTTCGGCCAGCAAGAAGCTGCTC-CGGTAGTAGCTCCGGCACCGGCTCCGGCTCCGGAAGTA--CAG---ACCAAGCACTTCACTCT-GAAGTCTGACGTACTGTTCAACTTCAACAAATCTACCCTGAAG--CCGGAAGGCCAGCAGGCT-CTGGATCAGCTGTACAGCCAGCTGAGCAACCTGGATCCGAAAGACGGTTCCGTTGTCGTTCTGGGCTTCACTGACCGTATCGGTTCTGACGC-TTACAACCAGGGTCTGT-CCGAGAAACGTGCTCAGTCTGTTGTTGATTACCTGATCTCCAAAGGTATTCCGTCTGACAAAATCTCCGCACGTGGTATGGGCGAATCTAACCCGGTTACCGGCAACACCTGTGACAACGTGAAACCTCGCGCTGCCCTG---ATCGATTGCCTGGCT-CCGGATCGTCGCGTAGAGATCGAAGTTAAAG--GCGTTAAAGACGTGGTAACTCAGCCGCAGGCT- 06-0676 ATGAAAAAGAC--AGCTATCGCGATTGCAGTGGCACTGGCTGGTTTCGCTAC----CGTAGCG----CAGGCCG----------CTCCGAAAGATAACACCTGGTACGCTGGTGCT-----AAACTGGGCTGGTCTCAGTACCATGACACCGGCTTCATTCACAATGATGGCCCGACTCATGAAAACCAACTGGGCG-CAGGTGCTTTTGGTGGTTACCAGGTTAACCCGTATGTTGGCTTTGAAATGGGCTACGACTGGTTAGGCCGTATGCCGTACAAAGGCGACAACATCAATGGCGCTTATAAAGCTCAGGGCGTTCAGTTGACCGCTAAACTGGGTTATCCAATCACTGACGATCTGGACG--TTTATACCCGTCTGGGTGGTATGGTATGGCGTG-CAGACACCAAGTCTAACGTCCCTGGC------GGCCCGTCTACTAAAGACCACGACACCGGCGTTTCCCCGGTATTCGCGGGCGGTATCGAGTATGCCATCACCCCTGAAATCGCAACCCGTCTGGAATACCAGTG----GACTAACAACATCGGTGATGCCAACACCATCGGCACCCGTCCGGACAACGGCCTGCTGAGCGTAGGTGTTTCCTACCGTTTCGGCCAGCAAGAAGCTGCTC-CGGTAGTAGCTCCGGCACCGGCTCCGGCTCCGGAAGTA--CAG---ACCAAGCACTTCACTCT-GAAGTCTGACGTACTGTTCAACTTCAACAAATCTACCCTGAAG--CCGGAAGGCCAGCAGGCT-CTGGATCAGCTGTACAGCCAGCTGAGCAACCTGGATCCGAAAGACGGTTCCGTTGTCGTTCTGGGCTTCACTGACCGTATCGGTTCTGACGC-TTACAACCAGGGTCTGT-CCGAGAAACGTGCTCAGTCTGTTGTTGATTACCTGATCTCCAAAGGTATTCCGTCTGACAAAATCTCCGCACGTGGTATGGGCGAATCTAACCCGGTTACCGGCAACACCTGTGACAACGTGAAACCTCGCGCTGCCCTG---ATCGATTGCCTGGCT-CCGGATCGTCGCGTAGAGATCGAAGTTAAAG--GCGTTAAAGACGTGGTAACTCAGCCGCAGGCT- 58-6482 ATGAAAAAGAC--AGCTATCGCGATTGCAGTGGCACTGGCTGGTTTCGCTAC----CGTAGCG----CAGGCCG----------CTCCGAAAGATAACACCTGGTACGCTGGTGCT-----AAACTGGGCTGGTCTCAGTACCATGACACCGGCTTCATTCACAATGATGGCCCGACTCATGAAAACCAACTGGGCG-CAGGTGCTTTTGGTGGTTACCAGGTTAACCCGTATGTTGGCTTTGAAATGGGCTACGACTGGTTAGGCCGTATGCCGTACAAAGGCGACAACATCAATGGCGCTTATAAAGCTCAGGGCGTTCAGTTGACCGCTAAACTGGGTTATCCAATCACTGACGATCTGGACG--TTTATACCCGTCTGGGTGGTATGGTATGGCGTG-CAGACACCAAGTCTAACGTCCCTGGC------GGCCCGTCTACTAAAGACCACGACACCGGCGTTTCCCCGGTATTCGCGGGCGGTATCGAGTATGCCATCACCCCTGAAATCGCAACCCGTCTGGAATACCAGTG----GACTAACAACATCGGTGATGCCAACACCATCGGCACCCGTCCGGACAACGGCCTGCTGAGCGTAGGTGTTTCCTACCGTTTCGGCCAGCAAGAAGCTGCTC-CGGTAGTAGCTCCGGCACCGGCTCCGGCTCCGGAAGTA--CAG---ACCAAGCACTTCACTCT-GAAGTCTGACGTACTGTTCAACTTCAACAAATCTACCCTGAAG--CCGGAAGGCCAGCAGGCT-CTGGATCAGCTGTACAGCCAGCTGAGCAACCTGGATCCGAAAGACGGTTCCGTTGTCGTTCTGGGCTTCACTGACCGTATCGGTTCTGACGC-TTACAACCAGGGTCTGT-CCGAGAAACGTGCTCAGTCTGTTGTTGATTACCTGATCTCCAAAGGTATTCCGTCTGACAAAATCTCCGCACGTGGTATGGGCGAATCTAACCCGGTTACCGGCAACACCTGTGACAACGTGAAACCTCGCGCTGCCCTG---ATCGATTGCCTGGCT-CCGGATCGTCGCGTAGAGATCGAAGTTAAAG--GCGTTAAAGACGTGGTAACTCAGCCGCAGGCT- 648905 ATGAAAAAGAC--AGCTATCGCGATTGCAGTGGCACTGGCTGGTTTCGCTAC----CGTAGCG----CAGGCCG----------CTCCGAAAGATAACACCTGGTACGCTGGTGCT-----AAACTGGGCTGGTCTCAGTACCATGACACCGGCTTCATTCACAATGATGGCCCGACTCATGAAAACCAACTGGGCG-CAGGTGCTTTTGGTGGTTACCAGGTTAACCCGTATGTTGGCTTTGAAATGGGCTACGACTGGTTAGGCCGTATGCCGTACAAAGGCGACAACATCAATGGCGCTTATAAAGCTCAGGGCGTTCAGTTGACCGCTAAACTGGGTTATCCAATCACTGACGATCTGGACG--TTTATACCCGTCTGGGTGGTATGGTATGGCGTG-CAGACACCAAGTCTAACGTCCCTGGC------GGCCCGTCTACTAAAGACCACGACACCGGCGTTTCCCCGGTATTCGCGGGCGGTATCGAGTATGCCATCACCCCTGAAATCGCAACCCGTCTGGAATACCAGTG----GACTAACAACATCGGTGATGCCAACACCATCGGCACCCGTCCGGACAACGGCCTGCTGAGCGTAGGTGTTTCCTACCGTTTCGGCCAGCAAGAAGCTGCTC-CGGTAGTAGCTCCGGCACCGGCTCCGGCTCCGGAAGTA--CAG---ACCAAGCACTTCACTCT-GAAGTCTGACGTACTGTTCAACTTCAACAAATCTACCCTGAAG--CCGGAAGGCCAGCAGGCT-CTGGATCAGCTGTACAGCCAGCTGAGCAACCTGGATCCGAAAGACGGTTCCGTTGTCGTTCTGGGCTTCACTGACCGTATCGGTTCTGACGC-TTACAACCAGGGTCTGT-CCGAGAAACGTGCTCAGTCTGTTGTTGATTACCTGATCTCCAAAGGTATTCCGTCTGACAAAATCTCCGCACGTGGTATGGGCGAATCTAACCCGGTTACCGGCAACACCTGTGACAACGTGAAACCTCGCGCTGCCCTG---ATCGATTGCCTGGCT-CCGGATCGTCGCGTAGAGATCGAAGTTAAAG--GCGTTAAAGACGTGGTAACTCAGCCGCAGGCT- 8b-1 ATGAAAAAGAC--AGCTATCGCGATTGCAGTGGCACTGGCTGGTTTCGCTAC----CGTAGCG----CAGGCCG----------CTCCGAAAGATAACACCTGGTACGCTGGTGCT-----AAACTGGGCTGGTCTCAGTACCATGACACCGGCTTCATTCACAATGATGGCCCGACTCATGAAAACCAACTGGGCG-CAGGTGCTTTTGGTGGTTACCAGGTTAACCCGTATGTTGGCTTTGAAATGGGCTACGACTGGTTAGGCCGTATGCCGTACAAAGGCGACAACATCAATGGCGCTTATAAAGCTCAGGGCGTTCAGTTGACCGCTAAACTGGGTTATCCAATCACTGACGATCTGGACG--TTTATACCCGTCTGGGTGGTATGGTATGGCGTG-CAGACACCAAGTCTAACGTCCCTGGC------GGCCCGTCTACTAAAGACCACGACACCGGCGTTTCCCCGGTATTCGCGGGCGGTATCGAGTATGCCATCACCCCTGAAATCGCAACCCGTCTGGAATACCAGTG----GACTAACAACATCGGTGATGCCAACACCATCGGCACCCGTCCGGACAACGGCCTGCTGAGCGTAGGTGTTTCCTACCGTTTCGGCCAGCAAGAAGCTGCTC-CGGTAGTAGCTCCGGCACCGGCTCCGGCTCCGGAAGTA--CAG---ACCAAGCACTTCACTCT-GAAGTCTGACGTACTGTTCAACTTCAACAAATCTACCCTGAAG--CCGGAAGGCCAGCAGGCT-CTGGATCAGCTGTACAGCCAGCTGAGCAACCTGGATCCGAAAGACGGTTCCGTTGTCGTTCTGGGCTTCACTGACCGTATCGGTTCTGACGC-TTACAACCAGGGTCTGT-CCGAGAAACGTGCTCAGTCTGTTGTTGATTACCTGATCTCCAAAGGTATTCCGTCTGACAAAATCTCCGCACGTGGTATGGGCGAATCTAACCCGGTTACCGGCAACACCTGTGACAACGTGAAACCTCGCGCTGCCCTG---ATCGATTGCCTGGCT-CCGGATCGTCGCGTAGAGATCGAAGTTAAAG--GCGTTAAAGACGTGGTAACTCAGCCGCAGGCT- 22510-1 ATGAAAAAGAC--AGCTATCGCGATTGCAGTGGCACTGGCTGGTTTCGCTAC----CGTAGCG----CAGGCCG----------CTCCGAAAGATAACACCTGGTACGCTGGTGCT-----AAACTGGGCTGGTCTCAGTACCATGACACCGGCTTCATTCACAATGATGGCCCGACTCATGAAAACCAACTGGGCG-CAGGTGCTTTTGGTGGTTACCAGGTTAACCCGTATGTTGGCTTTGAAATGGGCTACGACTGGTTAGGCCGTATGCCGTACAAAGGCGACAACATCAATGGCGCTTATAAAGCTCAGGGCGTTCAGTTGACCGCTAAACTGGGTTATCCAATCACTGACGATCTGGACG--TTTATACCCGTCTGGGTGGTATGGTATGGCGTG-CAGACACCAAGTCTAACGTCCCTGGC------GGCCCGTCTACTAAAGACCACGACACCGGCGTTTCCCCGGTATTCGCGGGCGGTATCGAGTATGCCATCACCCCTGAAATCGCAACCCGTCTGGAATACCAGTG----GACTAACAACATCGGTGATGCCAACACCATCGGCACCCGTCCGGACAACGGCCTGCTGAGCGTAGGTGTTTCCTACCGTTTCGGCCAGCAAGAAGCTGCTC-CGGTAGTAGCTCCGGCACCGGCTCCGGCTCCGGAAGTA--CAG---ACCAAGCACTTCACTCT-GAAGTCTGACGTACTGTTCAACTTCAACAAATCTACCCTGAAG--CCGGAAGGCCAGCAGGCT-CTGGATCAGCTGTACAGCCAGCTGAGCAACCTGGATCCGAAAGACGGTTCCGTTGTCGTTCTGGGCTTCACTGACCGTATCGGTTCTGACGC-TTACAACCAGGGTCTGT-CCGAGAAACGTGCTCAGTCTGTTGTTGATTACCTGATCTCCAAAGGTATTCCGTCTGACAAAATCTCCGCACGTGGTATGGGCGAATCTAACCCGGTTACCGGCAACACCTGTGACAACGTGAAACCTCGCGCTGCCCTG---ATCGATTGCCTGGCT-CCGGATCGTCGCGTAGAGATCGAAGTTAAAG--GCGTTAAAGACGTGGTAACTCAGCCGCAGGCT- </code> <br> and you want to count, per position, how many A, T, G, C or - you have.<br> I have written this:<br> <code> @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"; } } </code><br> 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... 9