Merge pull request #689 from nuno-agostinho/update/GeneSplicer

GeneSplicer: improve argument processing

GeneSplicer.pm

@@ -28,7 +28,12 @@ limitations under the License.
 =head1 SYNOPSIS
 
  mv GeneSplicer.pm ~/.vep/Plugins
- ./vep -i variants.vcf --plugin GeneSplicer,[path_to_genesplicer_bin],[path_to_training_dir],[option1=value],[option2=value]
+ ./vep -i variants.vcf --plugin GeneSplicer,binary=$GS/bin/linux/genesplicer,training=$GS/human
+ ./vep -i variants.vcf --plugin GeneSplicer,binary=$GS/bin/linux/genesplicer,training=$GS/human,context=200,tmpdir=/mytmp
+
+ # VEP Docker/Singularity: if 'genesplicer' is a command available in $PATH,
+ # there is no need to specify the location of the binary
+ ./vep -i variants.vcf --plugin GeneSplicer,training=$GS/human
 
 =head1 DESCRIPTION
 
@@ -41,49 +46,58 @@ limitations under the License.
  sequence included either side defaults to 100bp, but can be modified
  by passing e.g. "context=50" as a parameter to the plugin.
 
- Any predicted splicing regions that overlap the variant are reported
- in the output with one of four states: no_change, diff, gain, loss
+ You will need to download the GeneSplicer binary and data from
+ ftp://ftp.ccb.jhu.edu/pub/software/genesplicer/GeneSplicer.tar.gz. Extract the
+ folder using:
+
+ tar -xzf GeneSplicer.tar.gz
 
- There follows a "/"-separated string consisting of the following data:
+ GeneSplicer comes with precompiled binaries for multiple systems. If the
+ provided binaries do not run, compile `genesplicer` from source:
 
- 1) type (donor, acceptor)
- 2) coordinates (start-end)
- 3) confidence (Low, Medium, High)
- 4) score
+ ```
+ cd $GS/sources
+ # if macOS, run this step
+ [[ $(uname -s) == "Darwin" ]] && perl -pi -e "s/^main  /int main  /" genesplicer.cpp
+ make
+ cd -
+ ./vep [options] --plugin GeneSplicer,$GS/sources/genesplicer,$GS/human
+ ```
 
- Example: loss/acceptor/727006-727007/High/16.231924
+ Predicted splicing regions that overlap the variant are reported in the output
+ with a '/'-separated string (e.g., 'loss/acceptor/727006-727007/High/16.231924')
+ consisting of the following data by this order:
+
+ 1) state (no_change, diff, gain, loss)
+ 2) type (donor, acceptor)
+ 3) coordinates (start-end)
+ 4) confidence (Low, Medium, High)
+ 5) score
 
  If multiple sites are predicted, their reports are separated by ",".
 
  For diff, the confidence and score for both the reference and alternate
- sequences is reported as REF-ALT.
-
- Example: diff/donor/621915-621914/Medium-Medium/7.020731-6.988368
+ sequences is reported as REF-ALT, such as
+ 'diff/donor/621915-621914/Medium-Medium/7.020731-6.988368'.
 
  Several key=value parameters can be modified in the the plugin string:
 
+ training   : (mandatory) directory to species-specific training data, such as
+              `GeneSplicer/human`
+ binary     : path to `genesplicer` binary (default: `genesplicer`)
  context    : change the amount of sequence added either side of
               the variant (default: 100bp)
- tmpdir     : change the temporary directory used (default: /tmp)
+ tmpdir     : change the temporary directory used (default: `/tmp`)
  cache_size : change how many sequences' scores are cached in memory
               (default: 50)
 
  Example:
-   --plugin GeneSplicer,$GS/bin/linux/genesplicer,$GS/human,context=200,tmpdir=/mytmp
-
- On some systems the binaries provided will not execute, but can be compiled from source:
-
-   cd $GS/sources
-   make
-   cd -
-   ./vep [options] --plugin GeneSplicer,$GS/sources/genesplicer,$GS/human
-
- On Mac OSX the make step is known to fail; the genesplicer.cpp file requires modification:
+   --plugin GeneSplicer,binary=$GS/bin/linux/genesplicer,training=$GS/human,context=200,tmpdir=/mytmp
 
-   cd $GS/sources
-   perl -pi -e "s/^main  /int main  /" genesplicer.cpp
-   make
- 
+ When using VEP Docker/Singularity, the `binary` argument can be ommitted, as
+ the `genesplicer` command is exported in the $PATH variable and is thus
+ automatically detected by the plugin:
+   --plugin GeneSplicer,training=$GS/human,context=200,tmpdir=/mytmp
 
 =cut
 
@@ -106,6 +120,23 @@ our %DEFAULTS = (
   cache_size => 50,
 );
 
+sub _check_binary {
+  my $binary_file = shift;
+  # if $binary_file is the genesplicer command, try to get its path to check if it exists
+  $binary_file = (`which $binary_file 2>&1` || '') unless -e $binary_file;
+  chomp $binary_file;
+  die("ERROR: genesplicer binary not found\n") unless -e $binary_file;
+
+  my $test = `$binary_file 2>&1` || '';
+  die("ERROR: failed to run genesplicer binary:\n$test\n") unless $test =~ /^USAGE/;
+}
+
+sub _check_training_dir {
+  my $training_dir = shift;
+  die("ERROR: training directory not specified\n") unless $training_dir;
+  die("ERROR: training directory not found\n") unless -d $training_dir;
+}
+
 sub new {
   my $class = shift;
 
@@ -116,32 +147,39 @@ sub new {
 
   my $params = $self->params;
 
-  my $bin = shift @$params;
-  die("ERROR: genesplicer binary not specified\n") unless $bin;
-  die("ERROR: genesplicer binary not found\n") unless -e $bin;
-  my $test = `$bin 2>&1`;
-  die("ERROR: failed to run genesplicer binary:\n$test\n") unless $test =~ /^USAGE/;
-  $self->{_bin} = $bin;
-
-  my $training_dir = shift @$params;
-  die("ERROR: training directory not specified\n") unless $training_dir;
-  die("ERROR: training directory not found\n") unless -d $training_dir;
-  $self->{_training_dir} = $training_dir;
-
   # defaults
   $self->{'_param_'.$_} = $DEFAULTS{$_} for keys %DEFAULTS;
 
-  # REST API passes 1 as first param
-  shift @$params if $params->[0] && $params->[0] eq '1';
-
   # set/override with user params
   foreach my $param(@$params) {
+    next if $param eq '1'; # REST API passes 1 as a param
+
     my ($key, $val) = split('=', $param);
-    die("ERROR: Failed to parse parameter $param\n") unless defined($key) && defined($val);
 
-    $self->{'_param_'.$key} = $val;
+    if (!defined $val) {
+      # for positional arguments, set 'binary' and 'training data'
+      if (!defined $self->{_bin}) {
+        $self->{_bin} = $param;
+        next;
+      } elsif (!defined $self->{_training_dir}) {
+        $self->{_training_dir} = $param;
+        next;
+      }
+      die("ERROR: Failed to parse parameter $param\n") unless defined($key);
+    }
+
+    if ($key eq 'binary') {
+      $self->{_bin} = $val;
+    } elsif ($key eq 'training') {
+      $self->{_training_dir} = $val;
+    } else {
+      $self->{'_param_'.$key} = $val;
+    }
   }
 
+  $self->{_bin} ||= 'genesplicer';
+  _check_binary($self->{_bin});
+  _check_training_dir($self->{_training_dir});
   return $self;
 }