perl - 如何将 PHYLIP 格式转换为 FASTA

Question

我刚开始使用 perl，我有一个问题。我有 PHYLIP 文件，我需要将其转换为 FASTA。我开始写脚本。首先，我删除了行中的空格，现在我需要对齐每行中应该是 60 个氨基酸的所有行，并且序列标识符应该打印在新行中。也许有人可以给我一些建议？

Answer 1

BioPerl Bio::AlignIO模块可能会有所帮助。它支持PHYLIP序列格式：

phylip2fasta.pl

use strict;
use warnings;
use Bio::AlignIO; 

# http://doc.bioperl.org/bioperl-live/Bio/AlignIO.html
# http://doc.bioperl.org/bioperl-live/Bio/AlignIO/phylip.html
# http://www.bioperl.org/wiki/PHYLIP_multiple_alignment_format

my ($inputfilename) = @ARGV;
die "must provide phylip file as 1st parameter...\n" unless $inputfilename;
my $in  = Bio::AlignIO->new(-file   => $inputfilename ,
                         -format => 'phylip',
                         -interleaved => 1);
my $out = Bio::AlignIO->new(-fh   => \*STDOUT ,
                         -format => 'fasta');

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

$ perl phylip2fasta.pl test.phylip

>Turkey/1-42
AAGCTNGGGCATTTCAGGGTGAGCCCGGGCAATACAGGGTAT
>Salmo_gair/1-42
AAGCCTTGGCAGTGCAGGGTGAGCCGTGGCCGGGCACGGTAT
>H._Sapiens/1-42
ACCGGTTGGCCGTTCAGGGTACAGGTTGGCCGTTCAGGGTAA
>Chimp/1-42
AAACCCTTGCCGTTACGCTTAAACCGAGGCCGGGACACTCAT
>Gorilla/1-42
AAACCCTTGCCGGTACGCTTAAACCATTGCCGGTACGCTTAA

test.phylip http://evolution.genetics.washington.edu/phylip/doc/sequence.html

  5    42
Turkey    AAGCTNGGGC ATTTCAGGGT
Salmo gairAAGCCTTGGC AGTGCAGGGT
H. SapiensACCGGTTGGC CGTTCAGGGT
Chimp     AAACCCTTGC CGTTACGCTT
Gorilla   AAACCCTTGC CGGTACGCTT

GAGCCCGGGC AATACAGGGT AT
GAGCCGTGGC CGGGCACGGT AT
ACAGGTTGGC CGTTCAGGGT AA
AAACCGAGGC CGGGACACTC AT
AAACCATTGC CGGTACGCTT AA

Answer 2

如果您可以访问 BioPerl，我建议使用它（请参阅其他答案）。如果没有，这是我几年前在旧硬件作业中使用的快速脚本。它可能对你有用。

需要注意的一件事：它将整个 fasta 序列打印在一行上，因此您可以在最后编辑 print 语句以每行打印 70 AA。

#!/usr/bin/perl

use warnings;
use strict;

<DATA> =~ /(\d+)/; # first number is number of species

my $num_species = $1;
my $i = 0;
my @species;
my @acids;

# first $num_species rows have the species name
for ($i = 0; $i < $num_species; $i++) {   
    my @line = split /\s+/, <DATA>;
    chomp @line;

    push @species, shift (@line);
    push @acids, join ("", @line);

}

# Get the rest of the AAs
$i = 0;
while (<DATA>) {
    chomp;
    $_ =~ s/\r//g; #remove \r

    next if !$_;

    $_ =~ s/\s+//g; #remove spaces
    $acids[$i] .= $_;
    $i = ++$i % $num_species;

}

# Print them
for ($i = 0; $i < $num_species; $i++) {
    print "> ", $species[$i], "\n";

    # uncomment next line if you want to remove the gaps ("-")
    $acids[$i] =~ s/-//g;
    print $acids[$i], "\n\n";
}

# Simple PHYLIP Amino Acid file
__DATA__
 10 234
Cow          MAYPMQLGFQ DATSPIMEEL LHFHDHTLMI VFLISSLVLY IISLMLTTKL
Carp         MAHPTQLGFK DAAMPVMEEL LHFHDHALMI VLLISTLVLY IITAMVSTKL
Chicken      MANHSQLGFQ DASSPIMEEL VEFHDHALMV ALAICSLVLY LLTLMLMEKL
Human        MAHAAQVGLQ DATSPIMEEL ITFHDHALMI IFLICFLVLY ALFLTLTTKL
Loach        MAHPTQLGFQ DAASPVMEEL LHFHDHALMI VFLISALVLY VIITTVSTKL
Mouse        MAYPFQLGLQ DATSPIMEEL MNFHDHTLMI VFLISSLVLY IISLMLTTKL
Rat          MAYPFQLGLQ DATSPIMEEL TNFHDHTLMI VFLISSLVLY IISLMLTTKL
Seal         MAYPLQMGLQ DATSPIMEEL LHFHDHTLMI VFLISSLVLY IISLMLTTKL
Whale        MAYPFQLGFQ DAASPIMEEL LHFHDHTLMI VFLISSLVLY IITLMLTTKL
Frog         MAHPSQLGFQ DAASPIMEEL LHFHDHTLMA VFLISTLVLY IITIMMTTKL

             THTSTMDAQE VETIWTILPA IILILIALPS LRILYMMDEI NNPSLTVKTM
             TNKYILDSQE IEIVWTILPA VILVLIALPS LRILYLMDEI NDPHLTIKAM
             S-SNTVDAQE VELIWTILPA IVLVLLALPS LQILYMMDEI DEPDLTLKAI
             TNTNISDAQE METVWTILPA IILVLIALPS LRILYMTDEV NDPSLTIKSI
             TNMYILDSQE IEIVWTVLPA LILILIALPS LRILYLMDEI NDPHLTIKAM
             THTSTMDAQE VETIWTILPA VILIMIALPS LRILYMMDEI NNPVLTVKTM
             THTSTMDAQE VETIWTILPA VILILIALPS LRILYMMDEI NNPVLTVKTM
             THTSTMDAQE VETVWTILPA IILILIALPS LRILYMMDEI NNPSLTVKTM
             THTSTMDAQE VETVWTILPA IILILIALPS LRILYMMDEV NNPSLTVKTM
             TNTNLMDAQE IEMVWTIMPA ISLIMIALPS LRILYLMDEV NDPHLTIKAI

             GHQWYWSYEY TDYEDLSFDS YMIPTSELKP GELRLLEVDN RVVLPMEMTI
             GHQWYWSYEY TDYENLGFDS YMVPTQDLAP GQFRLLETDH RMVVPMESPV
             GHQWYWTYEY TDFKDLSFDS YMTPTTDLPL GHFRLLEVDH RIVIPMESPI
             GHQWYWTYEY TDYGGLIFNS YMLPPLFLEP GDLRLLDVDN RVVLPIEAPI
             GHQWYWSYEY TDYENLSFDS YMIPTQDLTP GQFRLLETDH RMVVPMESPI
             GHQWYWSYEY TDYEDLCFDS YMIPTNDLKP GELRLLEVDN RVVLPMELPI
             GHQWYWSYEY TDYEDLCFDS YMIPTNDLKP GELRLLEVDN RVVLPMELPI
             GHQWYWSYEY TDYEDLNFDS YMIPTQELKP GELRLLEVDN RVVLPMEMTI
             GHQWYWSYEY TDYEDLSFDS YMIPTSDLKP GELRLLEVDN RVVLPMEMTI
             GHQWYWSYEY TNYEDLSFDS YMIPTNDLTP GQFRLLEVDN RMVVPMESPT

             RMLVSSEDVL HSWAVPSLGL KTDAIPGRLN QTTLMSSRPG LYYGQCSEIC
             RVLVSAEDVL HSWAVPSLGV KMDAVPGRLN QAAFIASRPG VFYGQCSEIC
             RVIITADDVL HSWAVPALGV KTDAIPGRLN QTSFITTRPG VFYGQCSEIC
             RMMITSQDVL HSWAVPTLGL KTDAIPGRLN QTTFTATRPG VYYGQCSEIC
             RILVSAEDVL HSWALPAMGV KMDAVPGRLN QTAFIASRPG VFYGQCSEIC
             RMLISSEDVL HSWAVPSLGL KTDAIPGRLN QATVTSNRPG LFYGQCSEIC
             RMLISSEDVL HSWAIPSLGL KTDAIPGRLN QATVTSNRPG LFYGQCSEIC
             RMLISSEDVL HSWAVPSLGL KTDAIPGRLN QTTLMTMRPG LYYGQCSEIC
             RMLVSSEDVL HSWAVPSLGL KTDAIPGRLN QTTLMSTRPG LFYGQCSEIC
             RLLVTAEDVL HSWAVPSLGV KTDAIPGRLH QTSFIATRPG VFYGQCSEIC

             GSNHSFMPIV LELVPLKYFE KWSASML--- ----
             GANHSFMPIV VEAVPLEHFE NWSSLMLEDA SLGS
             GANHSYMPIV VESTPLKHFE AWSSL----- -LSS
             GANHSFMPIV LELIPLKIFE M-------GP VFTL
             GANHSFMPIV VEAVPLSHFE NWSTLMLKDA SLGS
             GSNHSFMPIV LEMVPLKYFE NWSASMI--- ----
             GSNHSFMPIV LEMVPLKYFE NWSASMI--- ----
             GSNHSFMPIV LELVPLSHFE KWSTSML--- ----
             GSNHSFMPIV LELVPLEVFE KWSVSML--- ----
             GANHSFMPIV VEAVPLTDFE NWSSSML-EA SL--

输出：

> Cow
MAYPMQLGFQDATSPIMEELLHFHDHTLMIVFLISSLVLYIISLMLTTKLTHTSTMDAQEVETIWTILPAIILILIALPSLRILYMMDEINNPSLTVKTMGHQWYWSYEYTDYEDLSFDSYMIPTSELKPGELRLLEVDNRVVLPMEMTIRMLVSSEDVLHSWAVPSLGLKTDAIPGRLNQTTLMSSRPGLYYGQCSEICGSNHSFMPIVLELVPLKYFEKWSASML

> Carp
MAHPTQLGFKDAAMPVMEELLHFHDHALMIVLLISTLVLYIITAMVSTKLTNKYILDSQEIEIVWTILPAVILVLIALPSLRILYLMDEINDPHLTIKAMGHQWYWSYEYTDYENLGFDSYMVPTQDLAPGQFRLLETDHRMVVPMESPVRVLVSAEDVLHSWAVPSLGVKMDAVPGRLNQAAFIASRPGVFYGQCSEICGANHSFMPIVVEAVPLEHFENWSSLMLEDASLGS

> Chicken
MANHSQLGFQDASSPIMEELVEFHDHALMVALAICSLVLYLLTLMLMEKLSSNTVDAQEVELIWTILPAIVLVLLALPSLQILYMMDEIDEPDLTLKAIGHQWYWTYEYTDFKDLSFDSYMTPTTDLPLGHFRLLEVDHRIVIPMESPIRVIITADDVLHSWAVPALGVKTDAIPGRLNQTSFITTRPGVFYGQCSEICGANHSYMPIVVESTPLKHFEAWSSLLSS

> Human
MAHAAQVGLQDATSPIMEELITFHDHALMIIFLICFLVLYALFLTLTTKLTNTNISDAQEMETVWTILPAIILVLIALPSLRILYMTDEVNDPSLTIKSIGHQWYWTYEYTDYGGLIFNSYMLPPLFLEPGDLRLLDVDNRVVLPIEAPIRMMITSQDVLHSWAVPTLGLKTDAIPGRLNQTTFTATRPGVYYGQCSEICGANHSFMPIVLELIPLKIFEMGPVFTL

> Loach
MAHPTQLGFQDAASPVMEELLHFHDHALMIVFLISALVLYVIITTVSTKLTNMYILDSQEIEIVWTVLPALILILIALPSLRILYLMDEINDPHLTIKAMGHQWYWSYEYTDYENLSFDSYMIPTQDLTPGQFRLLETDHRMVVPMESPIRILVSAEDVLHSWALPAMGVKMDAVPGRLNQTAFIASRPGVFYGQCSEICGANHSFMPIVVEAVPLSHFENWSTLMLKDASLGS

> Mouse
MAYPFQLGLQDATSPIMEELMNFHDHTLMIVFLISSLVLYIISLMLTTKLTHTSTMDAQEVETIWTILPAVILIMIALPSLRILYMMDEINNPVLTVKTMGHQWYWSYEYTDYEDLCFDSYMIPTNDLKPGELRLLEVDNRVVLPMELPIRMLISSEDVLHSWAVPSLGLKTDAIPGRLNQATVTSNRPGLFYGQCSEICGSNHSFMPIVLEMVPLKYFENWSASMI

> Rat
MAYPFQLGLQDATSPIMEELTNFHDHTLMIVFLISSLVLYIISLMLTTKLTHTSTMDAQEVETIWTILPAVILILIALPSLRILYMMDEINNPVLTVKTMGHQWYWSYEYTDYEDLCFDSYMIPTNDLKPGELRLLEVDNRVVLPMELPIRMLISSEDVLHSWAIPSLGLKTDAIPGRLNQATVTSNRPGLFYGQCSEICGSNHSFMPIVLEMVPLKYFENWSASMI

> Seal
MAYPLQMGLQDATSPIMEELLHFHDHTLMIVFLISSLVLYIISLMLTTKLTHTSTMDAQEVETVWTILPAIILILIALPSLRILYMMDEINNPSLTVKTMGHQWYWSYEYTDYEDLNFDSYMIPTQELKPGELRLLEVDNRVVLPMEMTIRMLISSEDVLHSWAVPSLGLKTDAIPGRLNQTTLMTMRPGLYYGQCSEICGSNHSFMPIVLELVPLSHFEKWSTSML

> Whale
MAYPFQLGFQDAASPIMEELLHFHDHTLMIVFLISSLVLYIITLMLTTKLTHTSTMDAQEVETVWTILPAIILILIALPSLRILYMMDEVNNPSLTVKTMGHQWYWSYEYTDYEDLSFDSYMIPTSDLKPGELRLLEVDNRVVLPMEMTIRMLVSSEDVLHSWAVPSLGLKTDAIPGRLNQTTLMSTRPGLFYGQCSEICGSNHSFMPIVLELVPLEVFEKWSVSML

> Frog
MAHPSQLGFQDAASPIMEELLHFHDHTLMAVFLISTLVLYIITIMMTTKLTNTNLMDAQEIEMVWTIMPAISLIMIALPSLRILYLMDEVNDPHLTIKAIGHQWYWSYEYTNYEDLSFDSYMIPTNDLTPGQFRLLEVDNRMVVPMESPTRLLVTAEDVLHSWAVPSLGVKTDAIPGRLHQTSFIATRPGVFYGQCSEICGANHSFMPIVVEAVPLTDFENWSSSMLEASL