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Ubuntu committed Feb 8, 2016
1 parent 68985c0 commit 797aace
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Showing 2 changed files with 39 additions and 12 deletions.
12 changes: 6 additions & 6 deletions mgescan/nonltr/hmm/get_phmm.pl
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Original file line number Diff line number Diff line change
Expand Up @@ -57,9 +57,9 @@
#system("hmmsearch --noali --domtblout ".$phmm_dir."tbl ".$phmm_file."c ".$pep_file." > /dev/null");
my $hmm_command = ("hmmsearch --noali --domtblout ".$tmpfile." ".$phmm_file."3 ".$pep_file." > /dev/null");
print $hmm_command if ($debug);
if ($debug && not prompt_yn("Continue?")) {
exit;
}
#if ($debug && not prompt_yn("Continue?")) {
# exit;
#}
system($hmm_command);
local $/ = undef;
my $hmm_result = <$fh>;
Expand All @@ -81,9 +81,9 @@
}else{
$command = "hmm2search ".$phmm_file." ".$pep_file;
print $command if ($debug);
if ($debug && not prompt_yn("Continue?")) {
exit;
}
#if ($debug && not prompt_yn("Continue?")) {
# exit;
#}
$hmm_result = `$command`;

@hmm_results = split(/\n/, $hmm_result);
Expand Down
39 changes: 33 additions & 6 deletions mgescan/nonltr/post_process2.pl
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Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,11 @@
use Cwd 'abs_path';
use File::Basename;
use File::Temp qw/ tempfile unlink0 /;
use lib (dirname abs_path $0) . '/lib';
use Prompt qw(prompt_yn);

my $debug;
$debug = $ENV{'MGESCAN_DEBUG'};

my $pdir = dirname(abs_path($0))."/";
my $hmm_dir = $pdir."pHMM/";
Expand Down Expand Up @@ -67,8 +72,8 @@
#system("rm ".$seq_dir."*/*.pep");
#system("rm ".$seq_dir."*/*.rt.*");
#system("rm ".$seq_dir."*/*.en.*");
system("rm -r ".$dir."b");
system("rm -r ".$dir."f");
system("rm -r ".$dir."b") if (not $debug);
system("rm -r ".$dir."f") if (not $debug);


sub get_parameter{
Expand Down Expand Up @@ -106,6 +111,8 @@ sub get_domain_for_full_frag{
my ($pep_file, $dna_file);
my ($phmm_file, $result_pep_file, $result_dna_file);

print "get_domain_for_full_frag" if ($debug);

for (my $i=0; $i<=$#all_clade; $i++){

my $clade = $all_clade[$i];
Expand All @@ -125,8 +132,12 @@ sub get_domain_for_full_frag{
get_domain_dna_seq($pep_file, $phmm_file, $result_dna_file, $dna_file, $flag);

my $command = "sed 's/>/>".$clade."_/' ".$result_pep_file." > ".$result_pep_file."p";
print $command if ($debug);
if ($debug && not prompt_yn("Continue?")) {
exit;
}
system($command);
system("rm ".$result_pep_file);
system("rm ".$result_pep_file) if (not $debug);

}
}
Expand All @@ -144,6 +155,7 @@ sub get_full_frag{
my $clade_dir;
my ($dna_file, $pep_file, $file_f, $file_b);

print "get_full_frag" if ($debug);

for (my $i=0; $i<=$#all_clade; $i++){

Expand All @@ -158,12 +170,14 @@ sub get_full_frag{
# copy full length in + strand
if (-e $file_f){
my $command = "cat ".$file_f." > ".$clade_dir.$all_clade[$i].".dna";
print $command if ($debug);
system($command);
}

# copy full length in - strand
if (-e $file_b){
my $command = "cat ".$file_b." >> ".$clade_dir.$all_clade[$i].".dna";
print $command if ($debug);
system($command);
}

Expand All @@ -172,6 +186,7 @@ sub get_full_frag{
$pep_file = $dir."info/full/".$all_clade[$i]."/".$all_clade[$i].".pep";
if (-e $dna_file){
my $command = "transeq -frame=f -sequence=".$dna_file." -outseq=".$pep_file." 2>/dev/null";
print $command if ($debug);
system($command);
}
}
Expand Down Expand Up @@ -199,7 +214,9 @@ sub get_domain_pep_seq{
#system("hmmconvert ".$_[1]." > ".$_[1]."c");
#system("hmmsearch --noali --domtblout ".$hmm_dir."tbl ".$_[1]."c ".$_[0]." > /dev/null");
#system("hmmsearch --noali --domtblout ".$hmm_dir."tbl ".$_[1]."3 ".$_[0]." > /dev/null");
system("hmmsearch --noali --domtblout ".$tmpfile." ".$_[1]."3 ".$_[0]." > /dev/null");
my $command = ("hmmsearch --noali --domtblout ".$tmpfile." ".$_[1]."3 ".$_[0]." > /dev/null");
print $command if ($debug);
system($command);
#my $hmm_command = "cat ".$hmm_dir."tbl";
#my $hmm_result = `$hmm_command`;
local $/ = undef;
Expand Down Expand Up @@ -296,7 +313,12 @@ sub get_domain_dna_seq{
#system("hmmconvert ".$_[1]." > ".$_[1]."c");
#system("hmmsearch --noali --domtblout ".$hmm_dir."tbl ".$_[1]."c ".$_[0]." > /dev/null");
#system("hmmsearch --noali --domtblout ".$hmm_dir."tbl ".$_[1]."3 ".$_[0]." > /dev/null");
system("hmmsearch --noali --domtblout ".$tmpfile." ".$_[1]."3 ".$_[0]." > /dev/null");
my $command = ("hmmsearch --noali --domtblout ".$tmpfile." ".$_[1]."3 ".$_[0]." > /dev/null");
print $command if ($debug);
if ($debug && not prompt_yn("Continue?")) {
exit;
}
system($command);
#my $hmm_command = "cat ".$hmm_dir."tbl";
#my $hmm_result = `$hmm_command`;
local $/ = undef;
Expand Down Expand Up @@ -415,7 +437,12 @@ sub vote_hmmsearch{
if ($hmmerv == 3){
#system("hmmconvert ".$_[1].$line[$i].".".$_[2].".hmm "." > ".$_[1].$line[$i].".".$_[2].".hmmc");
#system("hmmsearch --noali --domtblout ".$hmm_dir."tbl ".$_[1].$line[$i].".".$_[2].".hmmc ".$_[0]." > /dev/null");
system("hmmsearch --noali --domtblout ".$tmpfile." ".$_[1].$line[$i].".".$_[2].".hmm3 ".$_[0]." > /dev/null");
my $command = ("hmmsearch --noali --domtblout ".$tmpfile." ".$_[1].$line[$i].".".$_[2].".hmm3 ".$_[0]." > /dev/null");
system($command);
print $command if ($debug);
if ($debug && not prompt_yn("Continue?")) {
exit;
}
#my $command = "cat ".$hmm_dir."tbl";
#my $hmm_result = `$command`;
local $/ = undef;
Expand Down

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