refresh patches
Sascha Steinbiss
5 years ago
| 0 | 0 | Description: Use_both_hmmsets |
| 1 | 1 | --- a/bin/barrnap |
| 2 | 2 | +++ b/bin/barrnap |
| 3 | @@ -4,8 +4,9 @@ | |
| 4 | use Time::Piece; | |
| 3 | @@ -3,6 +3,7 @@ | |
| 4 | use warnings; | |
| 5 | 5 | use List::Util qw(max); |
| 6 | 6 | use FindBin; |
| 7 | 7 | +use File::Temp qw/ tempfile tempdir /; |
| 8 | use File::Temp; | |
| 8 | 9 | |
| 9 | -# . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . | |
| 10 | +# . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . | |
| 11 | # global variables | |
| 12 | ||
| 13 | my $EXE = $FindBin::RealScript; | |
| 14 | @@ -29,13 +30,13 @@ | |
| 15 | ); | |
| 16 | my $MAXLEN = int( 1.2 * max(values %LENG) ); | |
| 17 | ||
| 18 | -# . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . | |
| 19 | +# . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . | |
| 20 | # command line options | |
| 21 | ||
| 22 | my(@Options, $quiet, $kingdom, $threads, $evalue, $lencutoff, $reject, $incseq); | |
| 23 | setOptions(); | |
| 24 | ||
| 25 | -# . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . | |
| 26 | +# . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . | |
| 27 | # check all is well | |
| 28 | ||
| 29 | msg("This is $EXE $VERSION"); | |
| 30 | @@ -64,23 +65,38 @@ | |
| 10 | # . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . | |
| 11 | @@ -64,6 +65,7 @@ | |
| 31 | 12 | my $hmmdb = "$DBDIR/$kdom.hmm"; |
| 32 | 13 | err("Can't find database: $hmmdb") unless -r $hmmdb; |
| 33 | 14 | msg("Using database: $hmmdb"); |
| 34 | 15 | +my $nonfreehmmdb = "$DBDIR/nonfree/$kdom.hmm"; |
| 35 | 16 | |
| 36 | -# . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . | |
| 37 | +# . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . | |
| 17 | # . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . | |
| 18 | # check if user is piping to STDIN | |
| 19 | @@ -84,6 +86,20 @@ | |
| 20 | # . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . | |
| 38 | 21 | # run the external command |
| 39 | ||
| 40 | my $fasta = shift @ARGV; | |
| 41 | $fasta && -r $fasta or err("Usage: $EXE <file.fasta>"); | |
| 42 | 22 | |
| 43 | 23 | +if (-e $nonfreehmmdb) { |
| 44 | 24 | + # prepare full pHMM file (with nonfree if it exists) |
| 55 | 35 | +} |
| 56 | 36 | + |
| 57 | 37 | msg("Scanning $fasta for $kdom rRNA genes... please wait"); |
| 58 | my $cmd = "$NHMMER --cpu $threads -E $evalue --w_length $MAXLEN -o /dev/null --tblout /dev/stdout \Q$hmmdb\E \Q$fasta\E"; | |
| 59 | msg("Command: $cmd"); | |
| 60 | my @hits = qx($cmd 2>&1); | |
| 61 | ||
| 62 | -# . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . | |
| 63 | +# . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . | |
| 64 | # process the output | |
| 65 | ||
| 66 | my @feat; | |
| 67 | -HIT: | |
| 68 | +HIT: | |
| 69 | foreach (@hits) { | |
| 70 | chomp; | |
| 71 | err("nhmmer failed to run - $_") if m/fail|error|core dump|bus error/i; | |
| 72 | @@ -103,7 +119,7 @@ | |
| 38 | my $opts = "--cpu $threads -E $evalue --w_length $MAXLEN -o /dev/null --tblout /dev/stdout"; | |
| 39 | my $cmd = "nhmmer $opts '$hmmdb' '$fasta'"; | |
| 40 | @@ -123,7 +139,7 @@ | |
| 73 | 41 | # check for incomplete alignments |
| 74 | 42 | my $note = ''; |
| 75 | 43 | my $len = $end-$begin+1; |
| 78 | 46 | if ( $len < int($reject * $LENG{$gene}) ) { |
| 79 | 47 | msg("Rejecting short $len nt predicted $gene. Adjust via --reject option."); |
| 80 | 48 | next HIT; |
| 81 | @@ -121,7 +137,7 @@ | |
| 49 | @@ -144,7 +160,7 @@ | |
| 82 | 50 | ]; |
| 83 | 51 | } |
| 84 | 52 | |
| 87 | 55 | # output a sorted GFF3 |
| 88 | 56 | |
| 89 | 57 | sub gff_sort { |
| 90 | @@ -169,13 +185,13 @@ | |
| 91 | ||
| 92 | sub show_citation { | |
| 93 | print STDERR << "EOCITE"; | |
| 94 | - | |
| 95 | + | |
| 96 | If you use Barrnap in your work, please cite: | |
| 97 | ||
| 98 | Seemann T (2013) | |
| 99 | $EXE $VERSION : $DESC | |
| 100 | $URL | |
| 101 | - | |
| 102 | + | |
| 103 | Thank you. | |
| 104 | ||
| 105 | EOCITE | |
| 106 | @@ -194,7 +210,7 @@ | |
| 107 | {OPT=>"help", VAR=>\&usage, DESC=>"This help"}, | |
| 108 | {OPT=>"version", VAR=>\&version, DESC=>"Print version and exit"}, | |
| 109 | {OPT=>"citation",VAR=>\&show_citation, DESC=>"Print citation for referencing $EXE"}, | |
| 110 | - {OPT=>"kingdom=s", VAR=>\$kingdom, DEFAULT=>'bac', | |
| 111 | + {OPT=>"kingdom=s", VAR=>\$kingdom, DEFAULT=>'bac', | |
| 112 | DESC=>"Kingdom: ".join(' ', values %KINGDOM) }, | |
| 113 | {OPT=>"quiet!", VAR=>\$quiet, DEFAULT=>0, DESC=>"No screen output"}, | |
| 114 | {OPT=>"threads=i", VAR=>\$threads, DEFAULT=>8, DESC=>"Number of threads/cores/CPUs to use"}, | |
| 115 | @@ -227,15 +243,15 @@ | |
| 116 | my $def = defined($_->{DEFAULT}) ? " (default '$_->{DEFAULT}')" : ""; | |
| 117 | $def = ($def ? ' (default OFF)' : '(default ON)') if $_->{OPT} =~ m/!$/; | |
| 118 | my $opt = $_->{OPT}; | |
| 119 | - $opt =~ s/!$//; | |
| 120 | - $opt =~ s/=s$/ [X]/; | |
| 121 | + $opt =~ s/!$//; | |
| 122 | + $opt =~ s/=s$/ [X]/; | |
| 123 | $opt =~ s/=i$/ [N]/; | |
| 124 | $opt =~ s/=f$/ [n.n]/; | |
| 125 | printf STDERR " --%-15s %s%s\n", $opt, $_->{DESC}, $def; | |
| 126 | } | |
| 127 | else { | |
| 128 | print STDERR "$_\n"; | |
| 129 | - } | |
| 130 | + } | |
| 131 | } | |
| 132 | exit(1); | |
| 133 | } | |