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  1. Boa tarde, pessoal! Eu estou tentando usar o script DupGen_finder.pl, disponível em: https://github.com/qiao-xin/DupGen_finder/tree/master Eu organizei todos os dados de entrada necessários, como indica o manual. Entretanto, quando rodo o script: perl DupGen_finder.pl -i /media/dragonstone/dayana/KaKs/data_dir/ -t gma -c pvu -o /media/dragonstone/dayana/KaKs/results Estou tendo o seguinte erro: rm: cannot remove '/media/dragonstone/dayana/KaKs/results/gma_pvu.gff.sorted': No such file or directory Olhei o script, mas como não entendo muita coisa de Perl estou na dúvida se o script tem algum erro ao criar esse arquivo temporário chamado *.gff.sorted Grata se alguém puder me ajudar! Vou deixar o script copiado aqui embaixo. ---------------- #!/usr/bin/perl # Xin Qiao, 15 Nov 2018 # Xin Qiao, 05 Mar 2019, revised # Xin Qiao, 13 Apr 2019, revised # Xin Qiao, 15 Apr 2019, revised # Xin Qiao, 25 Apr 2019, revised use Getopt::Std; %options=(); getopts("i:t:o:c:d:k:g:s:e:m:w:a:x:", \%options); if(!exists $options{i} || !exists $options{t} || !exists $options{o} || !exists $options{c}) { print "Usage: DupGen_finder.pl -i data_directory -t target_species -c outgroup_species -o output_directory\n";#revised on 25 Apr 2019 print "#####################\nOptional:\n"; print "-a 1 or 0(are segmental duplicates ancestral loci or not? default: 1, yes)\n"; print "-d number_of_genes(maximum distance to call proximal, default: 10)\n"; print "#####################\nThe following are optional MCScanX parameters:\n"; print "-k match_score(cutoff score of collinear blocks for MCScanX, default: 50)\n"; print "-g gap_penalty(gap penalty for MCScanX, default: -1)\n"; print "-s match_size(number of genes required to call a collinear block for MCScanX, default: 5)\n"; print "-e e_value(alignment significance for MCScanX, default: 1e-05)\n"; print "-m max_gaps(maximum gaps allowed for MCScanX, default: 25)\n"; print "-w overlap_window(maximum distance in terms of gene number, to collapse BLAST matches for MCScanX, default: 5)\n"; exit; } $options{i}=~s/\/$//; $options{o}=~s/\/$//; $good=1; $t_gff="$options{i}\/$options{t}\.gff"; $t_bla="$options{i}\/$options{t}\.blast"; unless(-e $t_gff) { $good=0; print "Error: Cannot find the gff file for the target species at $t_gff\n"; } unless(-e $t_bla) { $good=0; print "Error: Cannot find the blast file for the target species at $t_bla\n"; } @ogrp=split("\,",$options{c}); ############################ $n_epoch=1; ########################### for($i=0;$i<=$#ogrp;$i++) { $o_gff="$options{i}\/$options{t}_$ogrp[$i]\.gff"; $o_bla="$options{i}\/$options{t}_$ogrp[$i]\.blast"; unless(-e $o_gff) { $good=0; print "Error: Cannot find the gff file between the target species and the outgroup species \"$ogrp[$i]\" at $o_gff\n"; } unless(-e $o_bla) { $good=0; print "Error: Cannot find the blast file between the target species and the outgroup species \"$ogrp[$i]\" at $o_bla\n"; } } if($good==0) { print "##############################################################\n"; print "!!!The execution is terminated due to incorrect input files!!!\n"; print "##############################################################\n"; exit; } unless(-d $options{o}) { mkdir $options{o} or die "Error: Cannot create the output directory\n"; } @para=("k","g","s","e","m","w"); $mcscanx_para=""; for($i=1;$i<6;$i++) { if(exists $options{$para[$i]}) { $mcscanx_para=$mcscanx_para." -$para[$i] $options{$para[$i]}"; } } ######################################################################## $in="$options{i}\/$options{t}"; $out="$options{o}\/$options{t}"; system("MCScanX $in $out $mcscanx_para");#revised on 25 Apr 2019 for($i=0;$i<=$#ogrp;$i++) { $in="$options{i}\/$options{t}_$ogrp[$i]"; $out="$options{o}\/$options{t}_$ogrp[$i]"; system("MCScanX $in $out $mcscanx_para");#revised on 25 Apr 2019 system("rm $out.gff.sorted"); } ######################################################################## $sorted_gff="$options{o}\/$options{t}.gff.sorted"; open(input,$sorted_gff); %gid=(); %gch=(); %glc=(); %anc=(); %gmd=(); %gmd2=(); $i=0; while($line=<input>) { chomp($line); @a=split("\t",$line); $gid{$a[0]}=$i; $gch{$a[0]}=$a[1]; $glc{$a[0]}=$a[2]; $gmd{$a[0]}=0; $gmd2{$a[0]}=0; $anc{$a[0]}=0; $i++; } close(input); $cut=10; if(exists $options{d}) { $cut=$options{d}; } #############Read blastp of target genome######################### %bla1=(); %bla2=(); %bla3=();#added on 05 Mar 2019 %blae=(); %gmd3=(); open(input,$t_bla); while($line=<input>) { @a=split("\t",$line); $bla3{$a[0]}=$a[10];#added on 05 Mar 2019 $bla3{$a[1]}=$a[10];#added on 05 Mar 2019 if($a[0] ne $a[1] && exists $gid{$a[0]} && exists $gid{$a[1]}) { $key="$a[0]\t$a[1]"; if(!exists $bla2{$key}) { $bla2{$key}=$a[11]; $gmd3{$key}=0; } else { if($a[11]>$bla2{$key}) { $bla2{$key}=$a[11]; } } $blae{$key}=$a[10]; if($gid{$a[0]} gt $gid{$a[1]}) { $key="$a[1]\t$a[0]"; } $bla1{$key}=0; } } #######################WGD/segmental############################################# $in="$options{o}\/$options{t}.collinearity"; $out1=">$options{o}\/$options{t}.wgd.pairs"; $out2=">$options{o}\/$options{t}.wgd.genes"; $incl=1; $wp=0; $wg=0; if(exists $options{a}) { $incl=$options{a}; } %h=(); open(input,$in); open(output1,$out1); open(output2,$out2); print output1 "Duplicate 1\tLocation\tDuplicate 2\tLocation\tE-value\n"; print output2 "Duplicate\tLocation\n"; while($line=<input>) { chomp($line); if($line!~/\#/ && $line ne "") { @a=split("\t",$line); $t_key="$a[1]\t$a[2]"; $t_key_r="$a[2]\t$a[1]";#revised on 12 Apr 2019 if(exists $blae{$t_key}) { $temp=$blae{$t_key}; $gmd3{$t_key}=1; $gmd3{$t_key_r}=1;#revised on 12 Apr 2019 } else { $t_key="$a[2]\t$a[1]"; $t_key_r="$a[1]\t$a[2]";#revised on 12 Apr 2019 $temp=$blae{$t_key}; $gmd3{$t_key}=1; $gmd3{$t_key_r}=1;#revised on 12 Apr 2019 } print output1 "$a[1]\t$gch{$a[1]}\:$glc{$a[1]}\t$a[2]\t$gch{$a[2]}\:$glc{$a[2]}\t$temp\n"; $wp++; $h{$a[1]}=0; $h{$a[2]}=0; if($incl==1) { $anc{$a[1]}=1; $anc{$a[2]}=1; } $gmd{$a[1]}=1; $gmd{$a[2]}=1; $gmd2{$a[1]}=1; $gmd2{$a[2]}=1; } } foreach $key (sort(keys %h)) { print output2 "$key\t$gch{$key}\:$glc{$key}\n"; $wg++; } ####################Tandem&Proximal##################### $out1=">$options{o}\/$options{t}.tandem.pairs"; $out2=">$options{o}\/$options{t}.tandem.genes"; $out3=">$options{o}\/$options{t}.proximal.pairs"; $out4=">$options{o}\/$options{t}.proximal.genes"; open(output1,$out1); open(output2,$out2); open(output3,$out3); open(output4,$out4); print output1 "Duplicate 1\tLocation\tDuplicate 2\tLocation\tE-value\n"; print output2 "Duplicate\tLocation\n"; print output3 "Duplicate 1\tLocation\tDuplicate 2\tLocation\tE-value\n"; print output4 "Duplicate\tLocation\n"; %tan_p=(); %tan_d=(); $tp=0; $tg=0; $pp=0; $pg=0; foreach $key (keys %bla1) { @a=split("\t",$key); $dis= abs($gid{$a[1]}-$gid{$a[0]}); if($gch{$a[0]} eq $gch{$a[1]} && $dis<$cut) { for($i=0;$i<2;$i++) { if(! exists $tan_p{$a[$i]}) { $tan_p{$a[$i]}=$a[1-$i]; $tan_d{$a[$i]}=$dis; } else { if($dis<$tan_d{$a[$i]}) { $tan_p{$a[$i]}=$a[1-$i]; $tan_d{$a[$i]}=$dis; } elsif($dis==$tan_d{$a[$i]}) { if($gid{$a[1-$i]}>$gid{$a[$i]}) { $tan_p{$a[$i]}=$a[1-$i]; } } else { } } } } } %tan_pairs=(); foreach $key (keys %tan_p) { $newkey=$key."\t".$tan_p{$key}; if($gid{$key} gt $gid{$tan_p{$key}}) { $newkey=$tan_p{$key}."\t".$key; } $tan_pairs{$newkey}=$tan_d{$key}; } %h=(); %k=(); foreach $key (sort(keys %tan_pairs)) { @a=split("\t",$key); if($tan_pairs{$key}==1) { $t_key="$a[0]\t$a[1]"; $t_key_r="$a[1]\t$a[0]"; if($gmd3{$t_key} == 0 && $gmd3{$t_key_r}==0)#revised on 15 Apr 2019 { if(exists $blae{$t_key}) { $temp=$blae{$t_key}; $gmd3{$t_key}=2; $gmd3{$t_key_r}=2; } else { $t_key="$a[1]\t$a[0]"; $t_key_r="$a[0]\t$a[1]"; $temp=$blae{$t_key}; $gmd3{$t_key}=2; $gmd3{$t_key_r}=2; } print output1 "$a[0]\t$gch{$a[0]}\:$glc{$a[0]}\t$a[1]\t$gch{$a[1]}\:$glc{$a[1]}\t$temp\n"; $tp++; for($i=0;$i<2;$i++) { if($gmd{$a[$i]}==0) { $h{$a[$i]}=2; $gmd{$a[$i]}=2; $gmd2{$a[$i]}=2; } } }#revised on 15 Apr 2019 } else { $t_key="$a[0]\t$a[1]"; $t_key_r="$a[1]\t$a[0]"; if($gmd3{$t_key} == 0 && $gmd3{$t_key_r}==0)#revised on 15 Apr 2019 { if(exists $blae{$t_key}) { $temp=$blae{$t_key}; $gmd3{$t_key}=3; $gmd3{$t_key_r}=3; } else { $t_key="$a[1]\t$a[0]"; $t_key_r="$a[0]\t$a[1]"; $temp=$blae{$t_key}; $gmd3{$t_key}=3; $gmd3{$t_key_r}=3; } print output3 "$a[0]\t$gch{$a[0]}\:$glc{$a[0]}\t$a[1]\t$gch{$a[1]}\:$glc{$a[1]}\t$temp\n"; $pp++; for($i=0;$i<2;$i++) { if($gmd{$a[$i]}==0 || $gmd{$a[$i]}==3) { $k{$a[$i]}=3; $gmd{$a[$i]}=3; $gmd2{$a[$i]}=3; } } }#revised on 15 Apr 2019 } } foreach $key (sort(keys %h)) { print output2 "$key\t$gch{$key}\:$glc{$key}\n"; $tg++; } foreach $key (sort(keys %k)) { print output4 "$key\t$gch{$key}\:$glc{$key}\n"; $pg++; } ####################Transposed################ %epoch_pair=(); $trp=0; $trg=0; for($k=$n_epoch;$k>=1;$k--) { for($i=$#ogrp;$i>=$k-1;$i--) { $in="$options{o}\/$options{t}_$ogrp[$i].collinearity"; open(input,$in); while($line=<input>) { chomp($line); if($line!~/\#/ && $line ne "") { @a=split("\t",$line); for($j=1;$j<3;$j++) { if(exists $anc{$a[$j]}) { $anc{$a[$j]}=1; } } } } } %tran_genes=(); %tran_genes2=(); %tran_ident=(); foreach $key (keys %bla2) { $good=0; @a=split("\t",$key); if($gmd{$a[0]}==0) { if($gch{$a[0]} ne $gch{$a[1]}) { $good=1; } else { if(abs($gid{$a[0]}-$gid{$a[1]})>=$cut) { $good=1; } } } if($good==1) { if($anc{$a[0]}==0 && $anc{$a[1]}==1) { if(!exists $tran_genes{$a[0]}) { $tran_genes{$a[0]}=$a[1]; $tran_ident{$a[0]}=$bla2{$key}; } else { if($bla2{$key}>$tran_ident{$a[0]}) { $tran_genes{$a[0]}=$a[1]; $tran_ident{$a[0]}=$bla2{$key}; } } } } } foreach $key (keys %bla2) { $good=0; @a=split("\t",$key); if($gmd{$a[0]}==0) { if($gch{$a[0]} ne $gch{$a[1]}) { $good=1; } else { if(abs($gid{$a[0]}-$gid{$a[1]})>=$cut) { $good=1; } } } if($good==1) { if($anc{$a[0]}==0 && $anc{$a[1]}==1) { if($bla2{$key}==$tran_ident{$a[0]}) { if($tran_genes{$a[0]} ne $a[1]) { $tran_genes2{$key}=$bla2{$key}; } } } } } $out1=">$options{o}\/$options{t}.transposed.pairs"; $out2=">$options{o}\/$options{t}.transposed.genes"; open(output1,$out1); open(output2,$out2); print output1 "Transposed\tLocation\tParental\tLocation\tE-value\n"; print output2 "Duplicate\tLocation\n"; foreach $key (sort(keys %tran_genes)) { print output2 "$key\t$gch{$key}\:$glc{$key}\n"; $trg++; $gmd2{$key}=4; if($gmd2{$tran_genes{$key}}==0) { $gmd2{$tran_genes{$key}}=4; } $temp="$key\t$tran_genes{$key}"; $gmd3{$temp}=4; $rtemp="$tran_genes{$key}\t$key"; $gmd3{$rtemp}=4; print output1 "$key\t$gch{$key}\:$glc{$key}\t$tran_genes{$key}\t$gch{$tran_genes{$key}}\:$glc{$tran_genes{$key}}\t$blae{$temp}\n"; #qx modified $trp++; $epoch_pair{$temp}=$k; } foreach $key (sort(keys %tran_genes2)) { @a=split("\t",$key); $temp="$key"; $rtemp="$a[1]\t$a[0]"; $gmd3{$temp}=4; $gmd3{$rtemp}=4; print output1 "$a[0]\t$gch{$a[0]}\:$glc{$a[0]}\t$a[1]\t$gch{$a[1]}\:$glc{$a[1]}\t$blae{$temp}\n"; $trp++; if($gmd2{$a[1]}==0) { $gmd2{$a[1]}=4; } $epoch_pair{$temp}=$k; } } #############################Dispersed##################################### %disp_genes=(); %hash=(); %hash2=(); %ident=(); %disp_genes2=(); %hash4=(); $mdp=0; $mdg=0; foreach $key (keys %bla2) { @a=split("\t",$key); if($gmd3{$key} == 1) { #$w++; next; } elsif($gmd3{$key} == 2) { #$t++; next; } elsif($gmd3{$key} == 3) { #$pr++; next; } elsif($gmd3{$key} == 4) { #$trp++; next; } elsif($gmd3{$key} == 0) { #$k++; $disp_genes{$key}=$bla2{$key}; $hash{$key}='A'; if(!exists $hash2{$a[0]}{$a[1]}) { $hash2{$a[0]}{$a[1]}=$bla2{$key}; } } else { #$l++; next; } } $out5=">$options{o}\/$options{t}.dispersed.pairs"; $out6=">$options{o}\/$options{t}.dispersed.genes"; open(output5,$out5); open(output6,$out6); print output5 "Duplicate 1\tLocation\tDuplicate 2\tLocation\tE-value\n"; print output6 "Duplicate\tLocation\n"; foreach $key (sort(keys %disp_genes)) { @a=split("\t",$key); if(exists $hash2{$a[0]}{$a[1]}) #remove repetitive lines like ab--ba { delete $hash2{$a[1]}{$a[0]}; } else { next; } } foreach $key1 (sort(keys %hash2)) { foreach $key2 (sort(keys %{$hash2{$key1}})) { $pair="$key1\t$key2"; if(!exists $hash4{$key1}) { $hash4{$key1}=$key2; $ident2{$key1}=$bla2{$pair}; } else { if($bla2{$pair}>$ident2{$key1}) { $hash4{$key1}=$key2; $ident2{$key1}=$bla2{$pair}; } } } } foreach $key (sort(keys %hash4)) { if($gmd2{$key} == 0 && $gmd2{$hash{$key}} == 0) { print output6 "$key\t$gch{$key}\:$glc{$key}\n$hash4{$key}\t$gch{$hash4{$key}}\:$glc{$hash4{$key}}\n"; $mdg++; $mdg++; } elsif($gmd2{$key} == 0 && $gmd2{$hash{$key}} != 0) { print output6 "$key\t$gch{$key}\:$glc{$key}\n"; $mdg++; } elsif($gmd2{$key} != 0 && $gmd2{$hash{$key}} == 0) { print output6 "$hash4{$key}\t$gch{$hash4{$key}}\:$glc{$hash4{$key}}\n"; $mdg++; } $temp="$key\t$hash4{$key}"; print output5 "$key\t$gch{$key}\:$glc{$key}\t$hash4{$key}\t$gch{$hash4{$key}}\:$glc{$hash4{$key}}\t$blae{$temp}\n"; $mdp++; } ###############################Singletons################################ $sg=0; $out=">$options{o}\/$options{t}.singletons"; open(output,$out); print output "GeneID\tLocation\n"; foreach $key (keys %gmd2) { if(!exists $bla3{$key})#revised on 05 Mar 2019 { print output "$key\t$gch{$key}\:$glc{$key}\n"; $sg++; } } #print "$sg\n"; ########################The number of different modes of gene duplications#################### $out1=">$options{o}\/$options{t}.pairs.stats"; open(output1,$out1); print output1 "Types\tNO. of gene pairs\n"; print output1 "WGD-pairs\t$wp\nTD-pairs\t$tp\nPD-pairs\t$pp\nTRD-pairs\t$trp\nDSD-pairs\t$mdp\n"; close output1; __END__
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