short script to get predicted sequence being potentially transposons or lying...

short script to get predicted sequence being potentially transposons or lying on bacterial contaminants

misc-scripts/anopheles_scripts/get_transposon_repeats.pl

+#!/usr/local/bin/perl -w
+=head1 NAME
+
+  delete_genes.pl
+
+=head1 SYNOPSIS
+ 
+  delete_genes.pl
+  deletes genes from given database whose ids are passed in through STDIN
+
+=head1 DESCRIPTION
+
+
+=head1 OPTIONS
+
+    -host      host name for database (gets put as host= in locator)
+
+    -port      For RDBs, what port to connect to (port= in locator)
+
+    -dbname    For RDBs, what name to connect to (dbname= in locator)
+
+    -dbuser    For RDBs, what username to connect as (dbuser= in locator)
+
+    -dbpass    For RDBs, what password to use (dbpass= in locator)
+
+    -genefile  File containing list of genes to be deleted
+
+=cut
+
+use strict;
+use Getopt::Long;
+use Bio::EnsEMBL::DBSQL::DBAdaptor;
+
+
+my $host   = 'ecs2d';
+my $port;
+my $dbname = 'anopheles_gambiae_core_13_2';
+my $dbuser = 'ensro';
+my $pass   = undef;
+
+#IPR002104,IPR001584,IPR001037,IPR003308,IPR000477,IPR000123
+
+&GetOptions( 
+	     'host:s'      => \$host,
+	     'port:n'      => \$port,
+	     'dbname:s'    => \$dbname,
+	     'dbuser:s'    => \$dbuser,
+	     'pass:s'      => \$pass,
+	     );
+
+my $db = new Bio::EnsEMBL::DBSQL::DBAdaptor(-host => $host,
+					    -user => $dbuser,
+					    -dbname => $dbname,
+					    -pass  => $pass
+					   );
+
+my $transadaptor = $db->get_TranscriptAdaptor();
+
+my $query = "select distinct(f.translation_id),x.description from protein_feature f, interpro i, xref x where f.hit_id = i.id and i.interpro_ac = x.dbprimary_acc and (x.description like '%transcriptase%' or x.description like '%integrase%' or x.description like '%bact%')";
+
+my $sth = $db->prepare($query);
+$sth->execute();
+
+while (my ($ac,$desc) = $sth->fetchrow()) {
+    my $query1 = "select transcript_id from transcript where translation_id = $ac";
+    my $sth1 = $db->prepare($query1);
+    $sth1->execute();
+    my $translac = $sth1->fetchrow();
+    my $obj = $transadaptor->fetch_by_dbID($translac);
+    my $seq = $obj->seq->seq;
+    print ">$translac#transposon\t$desc\n$seq\n";
+}
+
+
+
+
+
+