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removed the hashes for the first part of the script

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1 parent 37aea5f commit 39bcdacd03381fbb7981f5034475f843d286dcc9 @fauziharoon committed Apr 7, 2014
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Showing with 113 additions and 113 deletions.
  1. +113 −113 annotateM
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226 annotateM
@@ -60,123 +60,123 @@ my $global_options = checkParams();
# CODE HERE
######################################################################
-# # check that the file exists
-# checkFileExists($global_options->{'in'});
-
-# # run prokka to generate the ORFs and also prokka annotations
-# checkAndRunCommand("prokka", [{
- # "--locustag" => $global_options->{'locustag'},
- # "--outdir" => "prokka_annotation",
- # "--prefix" => $global_options->{'locustag'},
- # "--kingdom" => $global_options->{'kingdom'},
- # "--cpus" => $global_options->{'threads'},
- # "--keep_names",
- # $global_options->{'in'},
- # }], DIE_ON_FAILURE);
+# check that the file exists
+checkFileExists($global_options->{'in'});
+
+# run prokka to generate the ORFs and also prokka annotations
+checkAndRunCommand("prokka", [{
+ "--locustag" => $global_options->{'locustag'},
+ "--outdir" => "prokka_annotation",
+ "--prefix" => $global_options->{'locustag'},
+ "--kingdom" => $global_options->{'kingdom'},
+ "--cpus" => $global_options->{'threads'},
+ "--keep_names",
+ $global_options->{'in'},
+ }], DIE_ON_FAILURE);
# identify the ORF called amino acid fasta file for blast-ing
my $locus = $global_options->{'locustag'};
-# # blast against img
-# if (! -e "./$locus.faaVSimg.blastp")
-# {
-# print "BLASTing against IMG 4.0 database...............\n";
-# checkAndRunCommand("cat",
- # [[
- # "prokka_annotation/$locus.faa |",
- # "parallel",
- # "--block"=> "100k",
- # "--recstart",
- # "'>'",
- # "--pipe",
- # "blastp",
- # -db => "/srv/db/img/4.0/dereplicated/img_dereplicated_species.genes.faa",
- # -outfmt => 6,
- # -max_target_seqs => 1,
- # -evalue => $global_options->{'evalue'},
- # -query => "-",
- # "> $locus.faaVSimg.blastp",
- # ]], DIE_ON_FAILURE);
-# }
-
-# # reciprocal blast of img positive hits against genome ORF
-# if (! -e "./subsetimg.faaVS$locus.faa.blastp")
-# {
-# print "Reciprocal BLASTing positive IMG hits to $locus.faa ...............\n";
-# checkAndRunCommand("contig_extractor.pl",
- # [[
- # -i => "$locus.faaVSimg.blastp",
- # -d => "/srv/db/img/4.0/dereplicated/img_dereplicated_species.genes.faa",
- # -b => '',
- # -S => '',
- # -o => "subsetimg.faa",
- # ]], DIE_ON_FAILURE);
-
-# checkAndRunCommand("makeblastdb",
- # [[
- # -in => "prokka_annotation/$locus.faa",
- # -dbtype => "prot",
- # ]], DIE_ON_FAILURE);
-
-# checkAndRunCommand("blastp",
- # [[
- # -query => "subsetimg.faa",
- # -db => "prokka_annotation/$locus.faa",
- # -outfmt => 6,
- # -max_target_seqs => 1,
- # -evalue => $global_options->{'evalue'},
- # -num_threads => $global_options->{'threads'},
- # -out => "subsetimg.faaVS$locus.faa.blastp",
- # ]], DIE_ON_FAILURE);
-# }
-
-# # blast against uniref
-# if (! -e "./$locus.faaVSuniref90.blastp")
-# {
-# print "BLASTing against Uniref90 database................\n";
-# checkAndRunCommand("cat",[[
- # "prokka_annotation/$locus.faa |",
- # "parallel",
- # "--block"=> "100k",
- # "--recstart",
- # "'>'",
- # "--pipe",
- # "blastp",
- # -db => "/srv/db/uniprot/uniref-20140403/uniref90.fasta",
- # -outfmt => 6,
- # -max_target_seqs => 1,
- # -evalue => $global_options->{'evalue'},
- # -query => "-",
- # "> $locus.faaVSuniref90.blastp",
- # #-num_threads => $global_options->{'threads'},
- # ]], DIE_ON_FAILURE);
-# }
-
-# # reciprocal blast of Uniref positive hits against genome ORF
-# if (! -e "./subsetuniref.faaVS$locus.faa.blastp")
-# {
-# print "Reciprocal BLASTing positive Uniref hits to $locus.faa ...............\n";
-
-# checkAndRunCommand("contig_extractor.pl",
- # [[
- # -i => "$locus.faaVSuniref90.blastp",
- # -d => "/srv/db/uniprot/uniref-20140403/uniref90.fasta",
- # -b => '',
- # -S => '',
- # -o => "subsetuniref.faa",
- # ]], DIE_ON_FAILURE);
-
-# checkAndRunCommand("blastp",
- # [[
- # -query => "subsetuniref.faa",
- # -db => "prokka_annotation/$locus.faa",
- # -outfmt => 6,
- # -max_target_seqs => 1,
- # -evalue => $global_options->{'evalue'},
- # -num_threads => $global_options->{'threads'},
- # -out => "subsetuniref.faaVS$locus.faa.blastp",
- # ]], DIE_ON_FAILURE);
-# }
+# blast against img
+if (! -e "./$locus.faaVSimg.blastp")
+{
+print "BLASTing against IMG 4.0 database...............\n";
+checkAndRunCommand("cat",
+ [[
+ "prokka_annotation/$locus.faa |",
+ "parallel",
+ "--block"=> "100k",
+ "--recstart",
+ "'>'",
+ "--pipe",
+ "blastp",
+ -db => "/srv/db/img/4.0/dereplicated/img_dereplicated_species.genes.faa",
+ -outfmt => 6,
+ -max_target_seqs => 1,
+ -evalue => $global_options->{'evalue'},
+ -query => "-",
+ "> $locus.faaVSimg.blastp",
+ ]], DIE_ON_FAILURE);
+}
+
+# reciprocal blast of img positive hits against genome ORF
+if (! -e "./subsetimg.faaVS$locus.faa.blastp")
+{
+print "Reciprocal BLASTing positive IMG hits to $locus.faa ...............\n";
+checkAndRunCommand("contig_extractor.pl",
+ [[
+ -i => "$locus.faaVSimg.blastp",
+ -d => "/srv/db/img/4.0/dereplicated/img_dereplicated_species.genes.faa",
+ -b => '',
+ -S => '',
+ -o => "subsetimg.faa",
+ ]], DIE_ON_FAILURE);
+
+checkAndRunCommand("makeblastdb",
+ [[
+ -in => "prokka_annotation/$locus.faa",
+ -dbtype => "prot",
+ ]], DIE_ON_FAILURE);
+
+checkAndRunCommand("blastp",
+ [[
+ -query => "subsetimg.faa",
+ -db => "prokka_annotation/$locus.faa",
+ -outfmt => 6,
+ -max_target_seqs => 1,
+ -evalue => $global_options->{'evalue'},
+ -num_threads => $global_options->{'threads'},
+ -out => "subsetimg.faaVS$locus.faa.blastp",
+ ]], DIE_ON_FAILURE);
+}
+
+# blast against uniref
+if (! -e "./$locus.faaVSuniref90.blastp")
+{
+print "BLASTing against Uniref90 database................\n";
+checkAndRunCommand("cat",[[
+ "prokka_annotation/$locus.faa |",
+ "parallel",
+ "--block"=> "100k",
+ "--recstart",
+ "'>'",
+ "--pipe",
+ "blastp",
+ -db => "/srv/db/uniprot/uniref-20140403/uniref90.fasta",
+ -outfmt => 6,
+ -max_target_seqs => 1,
+ -evalue => $global_options->{'evalue'},
+ -query => "-",
+ "> $locus.faaVSuniref90.blastp",
+ #-num_threads => $global_options->{'threads'},
+ ]], DIE_ON_FAILURE);
+}
+
+# reciprocal blast of Uniref positive hits against genome ORF
+if (! -e "./subsetuniref.faaVS$locus.faa.blastp")
+{
+print "Reciprocal BLASTing positive Uniref hits to $locus.faa ...............\n";
+
+checkAndRunCommand("contig_extractor.pl",
+ [[
+ -i => "$locus.faaVSuniref90.blastp",
+ -d => "/srv/db/uniprot/uniref-20140403/uniref90.fasta",
+ -b => '',
+ -S => '',
+ -o => "subsetuniref.faa",
+ ]], DIE_ON_FAILURE);
+
+checkAndRunCommand("blastp",
+ [[
+ -query => "subsetuniref.faa",
+ -db => "prokka_annotation/$locus.faa",
+ -outfmt => 6,
+ -max_target_seqs => 1,
+ -evalue => $global_options->{'evalue'},
+ -num_threads => $global_options->{'threads'},
+ -out => "subsetuniref.faaVS$locus.faa.blastp",
+ ]], DIE_ON_FAILURE);
+}
# hashes for img
my %hash = ();

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