Merge pull request nf-core#603 from atrigila/issue_602

Add missing script in local module `GET_RRNA_TRANSCRIPTS`

CHANGELOG.md

@@ -51,6 +51,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Fixed bug in nf-core `RRNATRANSCRIPTS` module [#563](https://github.com/nf-core/rnafusion/issues/563)
 - Fixed bug in `GFFREAD` that caused output `gffread_fasta` not being produced [#565](https://github.com/nf-core/rnafusion/issues/565)
 - Fixed bug in `FUSIONCATCHER_DOWNLOAD` that caused an error when running with singularity profile [#573](https://github.com/nf-core/rnafusion/issues/573)
+- Fixed missing script `gtf2bed` which caused local module `GET_RRNA_TRANSCRIPTS` to fail [#602](https://github.com/nf-core/rnafusion/issues/602)
 
 ### Removed
 

bin/gtf2bed

@@ -0,0 +1,123 @@
+#!/usr/bin/env perl
+
+# Copyright (c) 2011 Erik Aronesty ([email protected])
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+# THE SOFTWARE.
+#
+# ALSO, IT WOULD BE NICE IF YOU LET ME KNOW YOU USED IT.
+
+use Getopt::Long;
+
+my $extended;
+GetOptions("x"=>\$extended);
+
+$in = shift @ARGV;
+
+my $in_cmd =($in =~ /\.gz$/ ? "gunzip -c $in|" : $in =~ /\.zip$/ ? "unzip -p $in|" : "$in") || die "Can't open $in: $!\n";
+open IN, $in_cmd;
+
+while (<IN>) {
+    $gff = 2 if /^##gff-version 2/;
+    $gff = 3 if /^##gff-version 3/;
+    next if /^#/ && $gff;
+
+    s/\s+$//;
+    # 0-chr 1-src 2-feat 3-beg 4-end 5-scor 6-dir 7-fram 8-attr
+    my @f = split /\t/;
+    if ($gff) {
+        # most ver 2's stick gene names in the id field
+        ($id) = $f[8]=~ /\bID="([^"]+)"/;
+        # most ver 3's stick unquoted names in the name field
+        ($id) = $f[8]=~ /\bName=([^";]+)/ if !$id && $gff == 3;
+    } else {
+        ($id) = $f[8]=~ /transcript_id "([^"]+)"/;
+    }
+
+    next unless $id && $f[0];
+
+    if ($f[2] eq 'exon') {
+        die "no position at exon on line $." if ! $f[3];
+        # gff3 puts :\d in exons sometimes
+        $id =~ s/:\d+$// if $gff == 3;
+        push @{$exons{$id}}, \@f;
+        # save lowest start
+        $trans{$id} = \@f if !$trans{$id};
+    } elsif ($f[2] eq 'start_codon') {
+        #optional, output codon start/stop as "thick" region in bed
+        $sc{$id}->[0] = $f[3];
+    } elsif ($f[2] eq 'stop_codon') {
+        $sc{$id}->[1] = $f[4];
+    } elsif ($f[2] eq 'miRNA' ) {
+        $trans{$id} = \@f if !$trans{$id};
+        push @{$exons{$id}}, \@f;
+    }
+}
+
+for $id (
+    # sort by chr then pos
+    sort {
+        $trans{$a}->[0] eq $trans{$b}->[0] ?
+        $trans{$a}->[3] <=> $trans{$b}->[3] :
+        $trans{$a}->[0] cmp $trans{$b}->[0]
+    } (keys(%trans)) ) {
+        my ($chr, undef, undef, undef, undef, undef, $dir, undef, $attr, undef, $cds, $cde) = @{$trans{$id}};
+        my ($cds, $cde);
+        ($cds, $cde) = @{$sc{$id}} if $sc{$id};
+
+        # sort by pos
+        my @ex = sort {
+            $a->[3] <=> $b->[3]
+        } @{$exons{$id}};
+
+        my $beg = $ex[0][3];
+        my $end = $ex[-1][4];
+
+        if ($dir eq '-') {
+        # swap
+        $tmp=$cds;
+        $cds=$cde;
+        $cde=$tmp;
+        $cds -= 2 if $cds;
+        $cde += 2 if $cde;
+    }
+
+    # not specified, just use exons
+    $cds = $beg if !$cds;
+    $cde = $end if !$cde;
+
+    # adjust start for bed
+    --$beg; --$cds;
+
+    my $exn = @ex;												# exon count
+    my $exst = join ",", map {$_->[3]-$beg-1} @ex;				# exon start
+    my $exsz = join ",", map {$_->[4]-$_->[3]+1} @ex;			# exon size
+
+        my $gene_id;
+        my $extend = "";
+        if ($extended) {
+            ($gene_id) = $attr =~ /gene_name "([^"]+)"/;
+            ($gene_id) = $attr =~ /gene_id "([^"]+)"/ unless $gene_id;
+            $extend="\t$gene_id";
+        }
+    # added an extra comma to make it look exactly like ucsc's beds
+    print "$chr\t$beg\t$end\t$id\t0\t$dir\t$cds\t$cde\t0\t$exn\t$exsz,\t$exst,$extend\n";
+}
+
+
+close IN;

modules.json

@@ -20,11 +20,6 @@
                         "git_sha": "467c202a876d26af544fa8c4b22a050a535462a7",
                         "installed_by": ["modules"]
                     },
-                    "bedops/convert2bed": {
-                        "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
-                        "installed_by": ["modules"]
-                    },
                     "cat/cat": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",

modules/local/get_rrna_transcript/main.nf

@@ -20,7 +20,7 @@ process GET_RRNA_TRANSCRIPTS {
 
     script:
     """
-    $baseDir/bin/get_rrna_transcripts.py --gtf ${gtf} --output rrna.gtf
+    $baseDir/bin/get_rrna_transcripts.py ${gtf} rrna.gtf
 
     $baseDir/bin/gtf2bed rrna.gtf > rrna.bed