Changeset 248

Timestamp:

08/31/09 08:34:40 (3 months ago)

Author:

cholt

Message:

weird index error and blast merge error

Files:

• lib/GI.pm (modified) (5 diffs)
• lib/Widget/blastn.pm (modified) (1 diff)
• lib/Widget/blastx.pm (modified) (1 diff)
• lib/Widget/tblastx.pm (modified) (1 diff)

lib/GI.pm

@@ -215 +215 @@
-      if (not $fastaObj) {
-         #rebuild index and try again
-
+
+
-         $db_index = Bio::DB::Fasta->new($db_file, '-reindex' => 1);
-         $fastaObj = $db_index->get_Seq_by_id($hit->name);
@@ -256 +257 @@
-         my $keepers = blastn($chunk, 
-                              $t_file,
-                              undef,
-                              $the_void,
-                              $p_safe_id.".".$piece->[0]->{b}.".".$piece->[0]->{e},
@@ -587 +587 @@
-   
-   #write fastas here
+   my %alias;
-   my $FA;
-   open($FA, "> $t_full"); #full file
-   while (my $fasta = $fasta_iterator->nextEntry()) {
-      my $def = Fasta::getDef(\$fasta);
+      my $seq_id = Fasta::def2SeqID($def);
-      my $seq_ref = Fasta::getSeqRef(\$fasta);
-
@@ -601 +603 @@
-      #Skip empty fasta entries
-      next if($$seq_ref eq '');
+
+      #fix weird blast trimming error for long seq IDs by replacing them
+      if(length($seq_id) > 78){
+          my $new_id = substr($seq_id, 0, 78);
+          die "ERROR: The id $seq_id is too long for BLAST, and I can'y uniquely fix it\n"
+              if($alias{$new_id});
+          $alias{$new_id}++;
+          $def =~ s/^>/>$seq_id maker_alias=/;
+      }
-
-      #reformat fasta, just incase
@@ -1020 +1031 @@
-         if (not $fastaObj) {
-            #rebuild index and try again
-
+
+
-            $db_index = Bio::DB::Fasta->new($db_file, '-reindex' => 1);
-            $fastaObj = $db_index->get_Seq_by_id($hit->name);

lib/Widget/blastn.pm

@@ -99 +99 @@
-         $hit->queryLength($result->query_length);
-         $hit->queryName($result->query_name);
-
+
+
+
+
-         my @hsps;
-         while(my $hsp = $hit->next_hsp) {

lib/Widget/blastx.pm

@@ -99 +99 @@
-         $hit->queryLength($result->query_length);
-         $hit->queryName($result->query_name);
-
+
+
+
-         my @hsps;
-         while(my $hsp = $hit->next_hsp) {

lib/Widget/tblastx.pm

@@ -99 +99 @@
-         $hit->queryLength($result->query_length);
-         $hit->queryName($result->query_name);
+         if($hit->description() =~ /maker_alias=(\S+)/){
+             $hit->name($1);
+         }
-         
-         my @hsps;