how to convert PHYLIP format to FASTA

Question

I just start working with perl and I have a question. I have PHYLIP file and I need convert it into FASTA. I start writing a script. Firstly, i removed scpaces in lines, now i need to align all lines that in every line should be 60 aminoacids and sequances identificator should be printed in new line. Maybe someone could give me some advice?

Answer 1

If you have access to BioPerl, I suggest using that (see other answer). If not, here is a quick script I used in an old HW assignment a few years ago. It may work for you.

One thing to note: It prints the whole fasta sequences on one line, so you have you edit the print statement at the end to print 70 AA per line.

#!/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--

Output:

> Cow
MAYPMQLGFQDATSPIMEELLHFHDHTLMIVFLISSLVLYIISLMLTTKLTHTSTMDAQEVETIWTILPAIILILIALPSLRILYMMDEINNPSLTVKTMGHQWYWSYEYTDYEDLSFDSYMIPTSELKPGELRLLEVDNRVVLPMEMTIRMLVSSEDVLHSWAVPSLGLKTDAIPGRLNQTTLMSSRPGLYYGQCSEICGSNHSFMPIVLELVPLKYFEKWSASML

> Carp
MAHPTQLGFKDAAMPVMEELLHFHDHALMIVLLISTLVLYIITAMVSTKLTNKYILDSQEIEIVWTILPAVILVLIALPSLRILYLMDEINDPHLTIKAMGHQWYWSYEYTDYENLGFDSYMVPTQDLAPGQFRLLETDHRMVVPMESPVRVLVSAEDVLHSWAVPSLGVKMDAVPGRLNQAAFIASRPGVFYGQCSEICGANHSFMPIVVEAVPLEHFENWSSLMLEDASLGS

> Chicken
MANHSQLGFQDASSPIMEELVEFHDHALMVALAICSLVLYLLTLMLMEKLSSNTVDAQEVELIWTILPAIVLVLLALPSLQILYMMDEIDEPDLTLKAIGHQWYWTYEYTDFKDLSFDSYMTPTTDLPLGHFRLLEVDHRIVIPMESPIRVIITADDVLHSWAVPALGVKTDAIPGRLNQTSFITTRPGVFYGQCSEICGANHSYMPIVVESTPLKHFEAWSSLLSS

> Human
MAHAAQVGLQDATSPIMEELITFHDHALMIIFLICFLVLYALFLTLTTKLTNTNISDAQEMETVWTILPAIILVLIALPSLRILYMTDEVNDPSLTIKSIGHQWYWTYEYTDYGGLIFNSYMLPPLFLEPGDLRLLDVDNRVVLPIEAPIRMMITSQDVLHSWAVPTLGLKTDAIPGRLNQTTFTATRPGVYYGQCSEICGANHSFMPIVLELIPLKIFEMGPVFTL

> Loach
MAHPTQLGFQDAASPVMEELLHFHDHALMIVFLISALVLYVIITTVSTKLTNMYILDSQEIEIVWTVLPALILILIALPSLRILYLMDEINDPHLTIKAMGHQWYWSYEYTDYENLSFDSYMIPTQDLTPGQFRLLETDHRMVVPMESPIRILVSAEDVLHSWALPAMGVKMDAVPGRLNQTAFIASRPGVFYGQCSEICGANHSFMPIVVEAVPLSHFENWSTLMLKDASLGS

> Mouse
MAYPFQLGLQDATSPIMEELMNFHDHTLMIVFLISSLVLYIISLMLTTKLTHTSTMDAQEVETIWTILPAVILIMIALPSLRILYMMDEINNPVLTVKTMGHQWYWSYEYTDYEDLCFDSYMIPTNDLKPGELRLLEVDNRVVLPMELPIRMLISSEDVLHSWAVPSLGLKTDAIPGRLNQATVTSNRPGLFYGQCSEICGSNHSFMPIVLEMVPLKYFENWSASMI

> Rat
MAYPFQLGLQDATSPIMEELTNFHDHTLMIVFLISSLVLYIISLMLTTKLTHTSTMDAQEVETIWTILPAVILILIALPSLRILYMMDEINNPVLTVKTMGHQWYWSYEYTDYEDLCFDSYMIPTNDLKPGELRLLEVDNRVVLPMELPIRMLISSEDVLHSWAIPSLGLKTDAIPGRLNQATVTSNRPGLFYGQCSEICGSNHSFMPIVLEMVPLKYFENWSASMI

> Seal
MAYPLQMGLQDATSPIMEELLHFHDHTLMIVFLISSLVLYIISLMLTTKLTHTSTMDAQEVETVWTILPAIILILIALPSLRILYMMDEINNPSLTVKTMGHQWYWSYEYTDYEDLNFDSYMIPTQELKPGELRLLEVDNRVVLPMEMTIRMLISSEDVLHSWAVPSLGLKTDAIPGRLNQTTLMTMRPGLYYGQCSEICGSNHSFMPIVLELVPLSHFEKWSTSML

> Whale
MAYPFQLGFQDAASPIMEELLHFHDHTLMIVFLISSLVLYIITLMLTTKLTHTSTMDAQEVETVWTILPAIILILIALPSLRILYMMDEVNNPSLTVKTMGHQWYWSYEYTDYEDLSFDSYMIPTSDLKPGELRLLEVDNRVVLPMEMTIRMLVSSEDVLHSWAVPSLGLKTDAIPGRLNQTTLMSTRPGLFYGQCSEICGSNHSFMPIVLELVPLEVFEKWSVSML

> Frog
MAHPSQLGFQDAASPIMEELLHFHDHTLMAVFLISTLVLYIITIMMTTKLTNTNLMDAQEIEMVWTIMPAISLIMIALPSLRILYLMDEVNDPHLTIKAIGHQWYWSYEYTNYEDLSFDSYMIPTNDLTPGQFRLLEVDNRMVVPMESPTRLLVTAEDVLHSWAVPSLGVKTDAIPGRLHQTSFIATRPGVFYGQCSEICGANHSFMPIVVEAVPLTDFENWSSSMLEASL

Answer 2

BioPerl Bio::AlignIO module might help. It support the PHYLIP sequence format :

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