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comparison PGAP-1.2.1/PGAP.pl @ 5:d8c5bea1cce2 draft

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author dereeper
date Thu, 24 Jun 2021 17:56:22 +0000
parents 70b7a5270968
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4:70b7a5270968 5:d8c5bea1cce2
1802 &PrepareFasta(\@species,$inputDIR,".pep"); ###prepare pep file 1802 &PrepareFasta(\@species,$inputDIR,".pep"); ###prepare pep file
1803 system("cat ".join(".pep ",@species).".pep > All.pep"); 1803 system("cat ".join(".pep ",@species).".pep > All.pep");
1804 system("grep '>' All.pep > genelist"); 1804 system("grep '>' All.pep > genelist");
1805 system("$formatdb -p T -i All.pep"); 1805 system("$formatdb -p T -i All.pep");
1806 system("$blastall -p blastp -i All.pep -d All.pep -M BLOSUM45 -m9 -e $evalue -o All.blastp -a $thread"); 1806 system("$blastall -p blastp -i All.pep -d All.pep -M BLOSUM45 -m9 -e $evalue -o All.blastp -a $thread");
1807 system("perl ./Blast_Filter.pl All.blastp All.pep $coverage $identity $score | $mcl - --abc -I 2.0 -o All.cluster"); 1807 my $dircur = dirname(__FILE__);
1808 system("perl $dircur/Blast_Filter.pl All.blastp All.pep $coverage $identity $score | $mcl - --abc -I 2.0 -o All.cluster");
1808 &FormatCluster("All.cluster","genelist",$spnum,\@clusters); 1809 &FormatCluster("All.cluster","genelist",$spnum,\@clusters);
1809 #system("rm -rf *.pep* All.blastp All.cluster genelist"); 1810 #system("rm -rf *.pep* All.blastp All.cluster genelist");
1810 } 1811 }
1811 1812
1812 sub MP() 1813 sub MP()