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What is wrong in this code???

by Anonymous Monk
on Dec 07, 2012 at 20:40 UTC ( #1007821=perlquestion: print w/ replies, xml ) Need Help??

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  1. or download this
    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-
    ...
    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-
    
  2. or download this
    @all_seqs = ();
    while(<>)
    ...
        print $j."\t".$count_A."\t".$count_T."\t".$count_C."\t".$count_G."
    +\n";
        }
    }
    

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