[Bio] / FigKernelPackages / ProtSims.pm Repository:
ViewVC logotype

Diff of /FigKernelPackages/ProtSims.pm

Parent Directory Parent Directory | Revision Log Revision Log | View Patch Patch

revision 1.12, Sat Mar 6 23:54:11 2010 UTC revision 1.13, Mon Aug 30 16:09:00 2010 UTC
# Line 25  Line 25 
25  use Carp;  use Carp;
26  use gjoseqlib;  use gjoseqlib;
27    
28  my $blat_cmd = "blat";  use SeedAware;
29  my $blastall_cmd = "blastall";  
30  my $formatdb_cmd = "formatdb";  my $blat_cmd = SeedAware::executable_for("blat");
31    my $blastall_cmd = SeedAware::executable_for("blastall");
32  BEGIN {  my $formatdb_cmd = SeedAware::executable_for("formatdb");
     eval {  
         require FIG_Config;  
         if (defined $FIG_Config::ext_bin) {  
             $blat_cmd = "$FIG_Config::ext_bin/blat";  
             $blastall_cmd = "$FIG_Config::ext_bin/blastall";  
             $formatdb_cmd = "$FIG_Config::ext_bin/formatdb";  
         }  
     };  
 }  
33    
34  sub blastP {  sub blastP {
35      my($q,$db,$min_hits,$use_blast) = @_;      my($q,$db,$min_hits,$use_blast) = @_;
36    
37      my(@q,@db);      my(@q,@db);
38    
39        my $tmp_dir = SeedAware::location_of_tmp();
40    
41      my $qF;      my $qF;
42      if (ref $q)      if (ref $q)
43      {      {
44          $qF = "/tmp/query.$$";          $qF = "$tmp_dir/query.$$";
45          &gjoseqlib::print_alignment_as_fasta($qF,$q);          &gjoseqlib::print_alignment_as_fasta($qF,$q);
46      }      }
47      else      else
# Line 68  Line 61 
61      my $dbF;      my $dbF;
62      if (ref $db)      if (ref $db)
63      {      {
64          $dbF = "/tmp/db.$$";          $dbF = "$tmp_dir/db.$$";
65          &gjoseqlib::print_alignment_as_fasta($dbF,$db);          &gjoseqlib::print_alignment_as_fasta($dbF,$db);
66          system "$formatdb_cmd -i $dbF";          system($formatdb_cmd, '-i', $dbF);
67      }      }
68      else      else
69      {      {
# Line 79  Line 72 
72          {          {
73              if (! ((-e "$dbF.psq") && ((-M "$dbF.psq") < (-M $dbF))))              if (! ((-e "$dbF.psq") && ((-M "$dbF.psq") < (-M $dbF))))
74              {              {
75                  system "formatdb_cmd -i $dbF";                  system($formatdb_cmd, '-i', $dbF);;
76              }              }
77              @db = &gjoseqlib::read_fasta($dbF);              @db = &gjoseqlib::read_fasta($dbF);
78              $db = \@db;              $db = \@db;
# Line 90  Line 83 
83          }          }
84      }      }
85    
86      my $tmpF = "/tmp/sim.out.$$";      my $tmpF = "$tmp_dir/sim.out.$$";
87      my $cmd = $use_blast ? "touch $tmpF" : "$blat_cmd $dbF $qF -prot -out=blast8 $tmpF > /dev/null";  
88      #print STDERR "$cmd\n";      if ($use_blast)
89      my $rc = system $cmd;      {
90            open(my $fh, ">", $tmpF);
91            close($fh);
92        }
93        else
94        {
95            my @cmd = ($blat_cmd, $dbF, $qF, "-prot", "-out=blast8", $tmpF);
96    
97            my $rc = system_with_redirect(\@cmd, { stdout => '/dev/null' } );
98            print STDERR "Blat returns $rc: @cmd\n";
99      if ($rc != 0)      if ($rc != 0)
100      {      {
101          die "ProtSims::blastP: blat run failed with rc=$rc: $cmd\n";              warn "Blat run failed with rc=$rc\n";
102                open(my $fh, ">", $tmpF);
103                close($fh);
104            }
105      }      }
106    
107    #     my $cmd = $use_blast ? "touch $tmpF" : "$blat_cmd $dbF $qF -prot -out=blast8 $tmpF > /dev/null";
108    #     #print STDERR "$cmd\n";
109    #     my $rc = system $cmd;
110    #     if ($rc != 0)
111    #     {
112    #       die "ProtSims::blastP: blat run failed with rc=$rc: $cmd\n";
113    #     }
114    
115      my @sims1 = ();      my @sims1 = ();
116      open(BLAT,"<$tmpF") || die "could not open $tmpF";      open(BLAT,"<$tmpF") || die "could not open $tmpF";
117      my $sim = <BLAT>;      my $sim = <BLAT>;
# Line 151  Line 164 
164    
165      if (@rerun > 0)      if (@rerun > 0)
166      {      {
167          my $tmpQ = "/tmp/tmpQ.$$";          my $tmpQ = "$tmp_dir/tmpQ.$$";
168          &gjoseqlib::print_alignment_as_fasta($tmpQ,\@rerun);          &gjoseqlib::print_alignment_as_fasta($tmpQ,\@rerun);
169          my $cmd = "$blastall_cmd -m 8 -i $tmpQ -d $dbF -FF -p blastp -e 1e-5";          # my $cmd = "$blastall_cmd -m 8 -i $tmpQ -d $dbF -FF -p blastp -e 1e-5";
170            my @cmd = ($blastall_cmd,  '-m', 8, '-i', $tmpQ, '-d', $dbF, '-FF', '-p', 'blastp', '-e', '1e-5');
171            print STDERR "@cmd\n";
172          #print STDERR "$cmd\n";          #print STDERR "$cmd\n";
173          open(BL, "$cmd|") or die "ProtSims::blastP: pipe to blast failed with $!: $cmd\n";          #open(BL, "$cmd|") or die "ProtSims::blastP: pipe to blast failed with $!: $cmd\n";
174    
175            open(BL, "-|", @cmd) or die "ProtSims::blastP: pipe to blast failed with $!: @cmd\n";
176    
177          my @blastout = map { chomp; [split(/\s+/,$_)] } <BL>;          my @blastout = map { chomp; [split(/\s+/,$_)] } <BL>;
178          close(BL);          close(BL);
179          push(@sims,@blastout);          push(@sims,@blastout);
# Line 166  Line 184 
184      my %lnDB  = map { $_->[0] => length($_->[2]) } @$db;      my %lnDB  = map { $_->[0] => length($_->[2]) } @$db;
185      @sims = map { push(@$_,$lnQ{$_->[0]},$lnDB{$_->[1]}); bless($_,'Sim') } @sims;      @sims = map { push(@$_,$lnQ{$_->[0]},$lnDB{$_->[1]}); bless($_,'Sim') } @sims;
186    
187      if ($qF      eq "/tmp/query.$$")   { unlink $qF  }      if ($qF      eq "$tmp_dir/query.$$")   { unlink $qF  }
188      if ($dbF     eq "/tmp/db.$$")      { unlink($dbF,"$dbF.psq","$dbF.pin","$dbF.phr") }      if ($dbF     eq "$tmp_dir/db.$$")      { unlink($dbF,"$dbF.psq","$dbF.pin","$dbF.phr") }
189      return sort { ($a->id1 cmp $b->id1) or ($a->psc <=> $b->psc) or ($a->id2 cmp $b->id2) } @sims;      return sort { ($a->id1 cmp $b->id1) or ($a->psc <=> $b->psc) or ($a->id2 cmp $b->id2) } @sims;
190  }  }
191    

Legend:
Removed from v.1.12  
changed lines
  Added in v.1.13

MCS Webmaster
ViewVC Help
Powered by ViewVC 1.0.3