swissport蛋白数据库拆分成不同的子库

swissport蛋白数据库拆分成不同的子库

首先从数据库下载文件

wget ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/taxonomic_divisions/uniprot_sprot_*.dat.gz
wget ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.fasta.gz

使用写好的脚本进行操作

perl split_swissprot.pl
grep ">" uniprot_sprot.fasta |sed 's/>//'|perl -lane 'print qq{$F[0]\t}.join(" ",@F[1..$#F])' >uniprot_sprot.id.annot.xls

split_swissprot代码如下

!/usr/bin/perl -w

use strict;

my $files = ls taxonomic_divisions/uniprot_sprot_*.dat.gz;
chomp $files;
my %hash;
open OUT,">swissprot_id.xls";
my @tmp = split(/\n/, $files);
for my $id(@tmp){
chomp $id;
if($id =~ /uniprot_sprot_(.*).dat.gz/){
my $class = $1;
open IN,"gzip -dc $id|" || die $!;
$/="//\n";
while(){
chomp;
my @array = split(/\n/);
my @array2 = split(/\s+/, $array[0]);
if($array2[0] eq "ID"){
print OUT "$array2[1]\t$class\n";
}
else{
print "ID error!";
}
$hash{$array2[1]} = $class;
}
close IN;
}
}

open ARCHAEA,">./Archaea.fa";
open BACTERIA,">./Bacteria.fa";
open FUNGI,">./Fungi.fa";
open HUMAN,">./Human.fa";
open INVERTEBRATES,">./Invertebrates.fa";
open MAMMALS,">./Mammals.fa";
open PLANTS,">./Plants.fa";
open RODENTS,">./Rodents.fa";
open VERTEBRATES,">./Vrtebrates.fa";
open VIRUSES,">./Viruses.fa";
open ANIMAL,">./Animal.fa";
open OTHER,">./Other.fa";
open UNKOWN,">./Unkown.fa";

open FASTA,"./uniprot_sprot.fasta";
$/=">";
;
while(){
chomp;
my @tmp2 = split(/\n/, $);
my @tmp3 = split(/\s+/, $tmp2[0]);
if($tmp3[0] =~ /sp|(.)|(.)_(.*)/){
my $cao = $2."_".$3;
unless(exists $hash{$cao}){
print UNKOWN ">$";
print OUT "$cao\tunkown\n";
next;
}
if($hash{$cao} eq "archaea"){
print ARCHAEA ">$";
print OTHER ">$";
}
elsif($hash{$cao} eq "bacteria"){
print BACTERIA ">$";
print OTHER ">$";
}
elsif($hash{$cao} eq "fungi"){
print FUNGI ">$";
print OTHER ">$";
}
elsif($hash{$cao} eq "human"){
print HUMAN ">$";
print ANIMAL ">$";
}
elsif($hash{$cao} eq "invertebrates"){
print INVERTEBRATES ">$";
print ANIMAL ">$";
}
elsif($hash{$cao} eq "mammals"){
print MAMMALS ">$";
print ANIMAL ">$";
}
elsif($hash{$cao} eq "plants"){
print PLANTS ">$";
}
elsif($hash{$cao} eq "rodents"){
print RODENTS ">$";
print ANIMAL ">$";
}
elsif($hash{$cao} eq "vertebrates"){
print VERTEBRATES ">$";
print ANIMAL ">$";
}
elsif($hash{$cao} eq "viruses"){
print VIRUSES ">$";
print OTHER ">$";
}
else{
print UNKOWN ">$";
}
}
}
close FASTA;
close OUT;
my $fas = ls *.fa *.fasta;
chomp $fas;
open FORMAT,">formatdb.sh";
my @fas_arr = split(/\s+/, $fas);
for my $fas_file(@fas_arr){
chomp $fas_file;
print FORMAT "/media/sdb/bio/blast/bin/formatdb -p T -i $fas_file\n";
}
close FORMAT;