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Description: Use_both_hmmsets
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--- a/bin/barrnap
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+++ b/bin/barrnap
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@@ -3,6 +3,7 @@
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Index: barrnap.git/bin/barrnap
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===================================================================
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--- barrnap.git.orig/bin/barrnap
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+++ barrnap.git/bin/barrnap
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@@ -3,6 +3,7 @@ use strict;
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use warnings;
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use List::Util qw(max);
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use FindBin;
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use File::Temp;
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# . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
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@@ -64,6 +65,7 @@
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@@ -64,6 +65,7 @@ my $kdom = $KINGDOM{ lc substr($kingdom,
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my $hmmdb = "$DBDIR/$kdom.hmm";
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err("Can't find database: $hmmdb") unless -r $hmmdb;
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msg("Using database: $hmmdb");
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# . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
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# check if user is piping to STDIN
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@@ -84,6 +86,20 @@
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@@ -84,6 +86,20 @@ $fasta && -r $fasta or err("No input fil
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# . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
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# run the external command
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msg("Scanning $fasta for $kdom rRNA genes... please wait");
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my $opts = "--cpu $threads -E $evalue --w_length $MAXLEN -o /dev/null --tblout /dev/stdout";
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my $cmd = "nhmmer $opts '$hmmdb' '$fasta'";
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@@ -123,7 +139,7 @@
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@@ -123,7 +139,7 @@ foreach (@hits) {
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# check for incomplete alignments
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my $note = '';
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my $len = $end-$begin+1;
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if ( $len < int($reject * $LENG{$gene}) ) {
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msg("Rejecting short $len nt predicted $gene. Adjust via --reject option.");
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next HIT;
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@@ -144,7 +160,7 @@
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@@ -144,7 +160,7 @@ foreach (@hits) {
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];
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}
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