Package list barrnap / dacdd2b9-f84b-477d-8e9f-19614858fb2b/main
Refresh patches. Debian Janitor a month ago
2 changed file(s) with 14 addition(s) and 10 deletion(s). Raw diff Collapse all Expand all
00 Description: Use_both_hmmsets
1 --- a/bin/barrnap
2 +++ b/bin/barrnap
3 @@ -3,6 +3,7 @@
1 Index: barrnap/bin/barrnap
2 ===================================================================
3 --- barrnap.orig/bin/barrnap
4 +++ barrnap/bin/barrnap
5 @@ -3,6 +3,7 @@ use strict;
46 use warnings;
57 use List::Util qw(max);
68 use FindBin;
810 use File::Temp;
911
1012 # . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
11 @@ -64,6 +65,7 @@
13 @@ -64,6 +65,7 @@ my $kdom = $KINGDOM{ lc substr($kingdom,
1214 my $hmmdb = "$DBDIR/$kdom.hmm";
1315 err("Can't find database: $hmmdb") unless -r $hmmdb;
1416 msg("Using database: $hmmdb");
1618
1719 # . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
1820 # check if user is piping to STDIN
19 @@ -84,6 +86,20 @@
21 @@ -84,6 +86,20 @@ $fasta && -r $fasta or err("No input fil
2022 # . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
2123 # run the external command
2224
3739 msg("Scanning $fasta for $kdom rRNA genes... please wait");
3840 my $opts = "--cpu $threads -E $evalue --w_length $MAXLEN -o /dev/null --tblout /dev/stdout";
3941 my $cmd = "nhmmer $opts '$hmmdb' '$fasta'";
40 @@ -123,7 +139,7 @@
42 @@ -123,7 +139,7 @@ foreach (@hits) {
4143 # check for incomplete alignments
4244 my $note = '';
4345 my $len = $end-$begin+1;
4648 if ( $len < int($reject * $LENG{$gene}) ) {
4749 msg("Rejecting short $len nt predicted $gene. Adjust via --reject option.");
4850 next HIT;
49 @@ -144,7 +160,7 @@
51 @@ -144,7 +160,7 @@ foreach (@hits) {
5052 ];
5153 }
5254
00 Description: Make sure we use correct paths for Debian policy
1 --- a/bin/barrnap
2 +++ b/bin/barrnap
1 Index: barrnap/bin/barrnap
2 ===================================================================
3 --- barrnap.orig/bin/barrnap
4 +++ barrnap/bin/barrnap
35 @@ -1,4 +1,4 @@
46 -#!/usr/bin/env perl
57 +#!/usr/bin/perl
68 use strict;
79 use warnings;
810 use List::Util qw(max);
9 @@ -14,6 +14,9 @@
11 @@ -14,6 +14,9 @@ my $DESC = "rapid ribosomal RNA predicti
1012 my $AUTHOR = 'Torsten Seemann';
1113 my $URL = 'https://github.com/tseemann/barrnap';
1214 my $DBDIR = "$FindBin::RealBin/../db";