Question

#!/usr/bin/perl -w
use strict;
use Bio::AlignIO;

# Creating a new AlignIO object
my $in = Bio::AlignIO->new( '-file' => "seq.fas" , '-format' => "fasta" );

# And another one for output
my $out = Bio::AlignIO->new( '-file' => ">seq.nxs", '-format' => "nexus" );

while ( my $aln = $in->next_aln() ) {
 $out->write_aln($aln);
}

我想重写此脚本，以便可以从命令行指定文件名以及格式。

输入文件是Fasta，我想将其转换为Phylip。

到目前为止，我已经做到了：

#!/usr/bin/perl -w
use strict;
use Bio::AlignIO; #this is how you include a perl module in your program


# read from standard input
my $str = $ARGV[0];
my $for = $ARGV[1];
my $in = Bio::AlignIO->new( '-file' => $str, '-format' => $for);

my $out = Bio::AlignIO->new( '-file' => ">output.phy", '-format' => "phylip" );

# Write to $out while there's still stuff at $in
while ( my $aln = $in->next_aln() ) {
    $out->write_aln($aln);   
}

这是输出的一部分：

 16 1582
gi|4559793   GCAAATATTT AGCCCAACAT GAATCCAAAA AAAAATATTA AACAAATAAA ACCAAAACAT 
gi|9448114   GCCAAATAAA GCCCTCTTAC CCCAAAAATC TTAACTATTC AAATTTTCCT ACAAAACATT 
gi|8330908   GCTAAYCTAA GCCCCGCTAA TTATTTATAY AACTAATTAA CTAAATCAAA AAAAAACATT 
gi|1087933   GCCAATATAA GCCCATCCAC TAACTAATAC AACTATATTA AATTTCTACC AAAACATTCA 
gi|1155320   GCTAACCTAA GCCCGCACAA CTATTAAATT AACTATTTTC ATTACTAATC TAAACCATTT 
gi|1087932   GCCAATCAAA AGCCTCCCCA CCTCAAGAAT CAATTATTTA AATTATTCAC CAAAACATTT 
gi|1087935   GCCAATAATA GCCCCAACAC CCACCAAAAA CAATTATTAC AAATAACCAA ACAAAACATT 
gi|1087933   GCCAATATAA GCCCATCCAC TAACTAATAC AACTATATTA AATTTCTACC AAAACATTCA 
gi|8330902   GCGAGACTTA GTCCTAGCAC ACAACTATTT AACTATTTTA CCTAATCTTC AAAACATTAA 
gi|1807789   GCCAATAAAA GCCCATCCAC CCACCAACAC AATTATATCA AATCTTAACG AAAACATTAA 
gi|4559822   GCTAATATTA GCCCTACATG AATCCAAAAA AAAATATTTA ATAATCAATC TCAAAACATT 
gi|1367680   GCCAATTTTA GCCCTACCAA TATCTCACAA AACTAACTTA CCTGTTTTTT AAAAAACATT 
gi|9448117   GCCAATATAA AGCTCCATTC ATACAAAAAT AAAATATTAT TACTAATCAA TCAAATCATT 
gi|5639854   GCTAATTTAA AGCCCCAACA ACTATTCATA AAATTAATTT ATCTACTAAA AAAACATTAA 
gi|4559833   CAATCATAGC CCTAACTATC CCCAACTAAA CTAATCATAA CTCTAACTAA AACATTTTCT 
gi|5835470   TCCAATAGAT CGTTTATTTA TTTACCCTCT TGTTATTTCG AAACATCCAC CACCCTTAAT 

     TTAATCATTT AAGTATAGGT GATAGAAAAT TTTATACGGG CGCTATAACG TAAGTACCGC 
     TCTCCTCCTA GTATAGGTGA TAGAACAGAC AAACAGGAGC AATAACGCTA GTACCGCAAG 
     CATTTATCAT AGTATAGGTG ATAGAAAAGA TTAATWGGGA GCCATAACRA AAGTACCGYA 
     ATTCATCCTA GTATAGGAGA TAGAACAGAT AAAAAGGCGC ATTAATGATA GTACCGCAAG 
     ACCCTATCAT AGTATAGGCG ATAGAACAGA TACCCAGGCG CAATAACGCA CAGTACCGTA 
     ACAAATCCAA GTATAGGTGA TAGAAAAGAT CACATGAGCG CAATAGCTAT AAGTACCGCA 
     TATTCATCCA AGTATAGGTG ATAGAACAGA CACACAGGAG CAATATATAC TAGTACCGTA 
     ATTCATCCTA GTATAGGAGA TAGAACAGAT AAAAAGGCGC ATTAATGATA GTACCGCAAG 
     CCTTTATCCT AGTATAGGTG ATAGAACAGA TACTTATAGG CACAATAACG AAAGTACCGT 
     TTTAATCACA GTATAGGTGA TAGAACAGAT AAATAGGCGC ATTAATGTAA GTACCGCAAG 
     TAATTAATCA AGTATAGGTG ATAGAAAGAT TTGTACAGGC GCTATAATGT AAGTACCGTA 
     TTACTTATCA TAGTATAGGT GATAGAAAAG ATACTTAAGG AGCCATAACG AAAGTACCGC 
     TACCCAAATC TTAGTATAGG TGATAGAAAA GATTACTAGG ACGCTATAAT GTAAGTACCG 
     CTAATCATAG TATAGGTGAT AGAAAAGATA CTAATGGAGC TATAACGAAG AGTACCGTAA 
     TGATCTTAGT ATAGGAGATA GAAAAGATAA CCTAGGCGCC ATAACATTAG TACCGCAAGG 
     CCCCTGAAAG TAAAGGCGAT TGAACCCAGT AAAACTGCAA GTACCGTAAG GGAACTATGA

为什么要获得这些列？看起来部分序列会跳下来并变得混乱。输出文件应如下所示：

gi|4559793GCAAATATTTAGCCCAACATGAATCCAAAAAAAAATATTAAACAAATAAA 
gi|9448114GCCAAATAAAGCCCTCTTACCCCAAAAATCTTAACTATTCAAATTTTCCT 
gi|8330908GCTAAYCTAAGCCCCGCTAATTATTTATAYAACTAATTAACTAAATCAAA 
gi|1087933GCCAATATTAGCCCATTCAACTATTAAACCAAATATCACAATCACTTAAT 
gi|1155320GCTAACCTAAGCCCGCACAACTATTAAATTAACTATTTTCATTACTAATC 
gi|1087932GCCAATCAAAAGCCTCCCCACCTCAAGAATCAATTATTTAAATTATTCAC 
gi|1087935GCCAATAATAGCCCCAACACCCACCAAAAACAATTATTACAAATAACCAA 
gi|1087933GCCAATATAAGCCCATCCACTAACTAATACAACTATATTAAATTTCTACC 
gi|8330902GCGAGACTTAGTCCTAGCACACAACTATTTAACTATTTTACCTAATCTTC 
gi|1807789GCCAATAAAAGCCCATCCACCCACCAACACAATTATATCAAATCTTAACG 
gi|4559822GCTAATATTAGCCCTACATGAATCCAAAAAAAAATATTTAATAATCAATC 
gi|1367680GCCAATTTTAGCCCTACCAATATCTCACAAAACTAACTTACCTGTTTTTT 
gi|9448117GCCAATATAAAGCTCCATTCATACAAAAATAAAATATTATTACTAATCAA 
gi|5639854GCTAATTTAAAGCCCCAACAACTATTCATAAAATTAATTTATCTACTAAA 
gi|4559833CAATCATAGCCCTAACTATCCCCAACTAAACTAATCATAACTCTAACTAA 
gi|5835470TCCAATAGATCGTTTATTTATTTACCCTCTTGTTATTTCGAAACATCCAC 

          ACCAAAACATTTAATCATTTAAGTATAGGTGATAGAAAATTTTATACGGG
          ACAAAACATTTCTCCTCCTAGTATAGGTGATAGAACAGACAAACAGGAGC
          AAAAAACATTCATTTATCATAGTATAGGTGATAGAAAAGATTAATWGGGA
          CTAAACCATTTACTCTGTCCAAGTATAGGTGATAGAAAAGACTAATCCAG
          TAAACCATTTACCCTATCATAGTATAGGCGATAGAACAGATACCCAGGCG
          CAAAACATTTACAAATCCAAGTATAGGTGATAGAAAAGATCACATGAGCG
          ACAAAACATTTATTCATCCAAGTATAGGTGATAGAACAGACACACAGGAG
          AAAACATTCAATTCATCCTAGTATAGGAGATAGAACAGATAAAAAGGCGC
          AAAACATTAACCTTTATCCTAGTATAGGTGATAGAACAGATACTTATAGG
          AAAACATTAATTTAATCACAGTATAGGTGATAGAACAGATAAATAGGCGC
          TCAAAACATTTAATTAATCAAGTATAGGTGATAGAAAGATTTGTACAGGC
          AAAAAACATTTTACTTATCATAGTATAGGTGATAGAAAAGATACTTAAGG
          TCAAATCATTTACCCAAATCTTAGTATAGGTGATAGAAAAGATTACTAGG
          AAAACATTAACTAATCATAGTATAGGTGATAGAAAAGATACTAATGGAGC
          AACATTTTCTTGATCTTAGTATAGGAGATAGAAAAGATAACCTAGGCGCC
          CACCCTTAATCCCCTGAAAGTAAAGGCGATTGAACCCAGTAAAACTGCAA

来自Bio :: AlignIO脚本的奇怪输出

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