Max length of gxf or fasta record filter

examples/gff3_filter_large.conf

@@ -0,0 +1,12 @@
+{  
+  "input_filter" : { "_pre" : "max_length" },
+  "mapping" : {
+    "max_length" : {
+      "_callback" : "run",
+      "_module" : "Bio::FormatTranscriber::Callback::MaxLength",
+      "_init" : {"length" : "100000" },
+      "_parameters" : {"record" : "{{record}}" },
+      "_filter" : 1
+    }
+  }
+}

lib/Bio/FormatTranscriber/Callback/MaxLength.pm

@@ -0,0 +1,108 @@
+=head1 LICENSE
+
+Copyright [1999-2016] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+     http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+
+=cut
+
+
+=head1 CONTACT
+
+  Please email comments or questions to the public Ensembl
+  developers list at <http://lists.ensembl.org/mailman/listinfo/dev>.
+  Questions may also be sent to the Ensembl help desk at
+  <http://www.ensembl.org/Help/Contact>.
+
+=cut
+
+=head1 NAME
+
+Bio::FormatTranscriber::Callback::MaxLength
+
+=head1 SYNOPSIS
+
+  use Bio::FormatTranscriber::Callback::MaxLength;
+
+  $callback_obj = Bio::FormatTranscriber::Callback::MaxLength->new({ length => 100000 });
+
+  $less_than_max_bool = $callback_obj->run({record => $record});
+
+
+=head1 DESCRIPTION
+
+Filter a record based on if the length is greater than the
+given maximum. Throws an error if the object type being filtered
+doesn't support length()
+
+Mapping entry could look like:
+
+
+    "max_length" : {
+      "_callback" : "run",
+      "_module"   : "Bio::FormatTranscriber::Callback::MaxLength",
+      "_init"     : { "length" : 100000 },
+      "_parameters" : { "record" : "{{record}}" } 
+    }
+
+and be called during the _pre or _post field step of a filter, ie.
+
+  "input_filter": { "_pre" : "max_length"
+                  }
+
+=cut
+
+package Bio::FormatTranscriber::Callback::MaxLength;
+
+use strict;
+use warnings;
+use Carp;
+
+use Data::Dumper;
+
+use Bio::EnsEMBL::Utils::Argument qw(rearrange);
+use Bio::EnsEMBL::Utils::Exception qw(throw);
+
+sub new {
+    my $class = shift;
+    my $params = shift;
+
+    my $self = {};
+
+    unless(defined $params->{length}) {
+	throw "You must specify the maximum length, otherwise, what's the point?";
+    }
+
+    $self->{length} = $params->{length};
+
+    return bless $self, $class;
+}
+
+sub run {
+    my $self = shift;
+    my $params = shift;
+
+    # Die if we weren't configured to receive a record
+    unless((ref $params eq 'HASH') &&
+	   $params->{record}) {
+	throw "No record found for sequence";
+    }
+
+    if($params->{record}->length() > $self->{length}) {
+	return 0;
+    }
+
+    return 1;
+}
+
+1;

lib/Bio/FormatTranscriber/Callback/fasta_header.pm

@@ -39,7 +39,7 @@ Bio::FormatTranscriber::Callback::fasta_header
                                                                        parameter_2 => { hash of substitutions },
                                                                       );
 
-  $callback_obj->run({record => $record});
+  $updated_record = $callback_obj->run({record => $record});
 
 =head1 DESCRIPTION
 
@@ -72,7 +72,7 @@ Mapping entry could look like:
 
 and be called during the _pre or _post field step of a filter, ie.
 
-  "input_filter": { "_pre" : "fasta_header"
+  "input_filter": { "_pre" : "fasta_header" 
 		  },
 
 =cut

t/data/patch_data.gff3

@@ -0,0 +1,28 @@
+##gff-version   3
+##sequence-region   CHR_HG126_PATCH 72325441 72740748
+#!genome-build  GRCh38.p5
+#!genome-version GRCh38
+#!genome-date 2013-12
+#!genome-build-accession NCBI:GCA_000001405.20
+CHR_HG126_PATCH	GRCh38	chromosome	72325441	72740748	.	.	.	ID=chromosome:CHR_HG126_PATCH;Alias=HG126_PATCH
+###
+CHR_HG126_PATCH	ensembl	gene	72374621	72447493	.	-	.	ID=gene:ENSG00000281766;Name=RYBP;biotype=protein_coding;description=RING1 and YY1 binding protein [Source:HGNC Symbol%3BAcc:HGNC:10480];gene_id=ENSG00000281766;logic_name=assembly_patch_ensembl;version=1
+CHR_HG126_PATCH	ensembl	transcript	72374621	72447493	.	-	.	ID=transcript:ENST00000628983;Parent=gene:ENSG00000281766;Name=RYBP-201;biotype=protein_coding;tag=basic;transcript_id=ENST00000628983;version=1
+CHR_HG126_PATCH	ensembl	three_prime_UTR	72374621	72378402	.	-	.	Parent=transcript:ENST00000628983
+CHR_HG126_PATCH	ensembl	exon	72374621	72378655	.	-	.	Parent=transcript:ENST00000628983;Name=ENSE00003764699;constitutive=1;ensembl_end_phase=-1;ensembl_phase=2;exon_id=ENSE00003764699;rank=5;version=1
+CHR_HG126_PATCH	ensembl	CDS	72378403	72378655	.	-	1	ID=CDS:ENSP00000486012;Parent=transcript:ENST00000628983;protein_id=ENSP00000486012
+CHR_HG126_PATCH	ensembl	exon	72379058	72379156	.	-	.	Parent=transcript:ENST00000628983;Name=ENSE00003774199;constitutive=1;ensembl_end_phase=2;ensembl_phase=2;exon_id=ENSE00003774199;rank=4;version=1
+CHR_HG126_PATCH	ensembl	CDS	72379058	72379156	.	-	1	ID=CDS:ENSP00000486012;Parent=transcript:ENST00000628983;protein_id=ENSP00000486012
+CHR_HG126_PATCH	ensembl	exon	72379269	72379445	.	-	.	Parent=transcript:ENST00000628983;Name=ENSE00003765281;constitutive=1;ensembl_end_phase=2;ensembl_phase=2;exon_id=ENSE00003765281;rank=3;version=1
+CHR_HG126_PATCH	ensembl	CDS	72379269	72379445	.	-	1	ID=CDS:ENSP00000486012;Parent=transcript:ENST00000628983;protein_id=ENSP00000486012
+CHR_HG126_PATCH	ensembl	exon	72446378	72446503	.	-	.	Parent=transcript:ENST00000628983;Name=ENSE00003772464;constitutive=1;ensembl_end_phase=2;ensembl_phase=2;exon_id=ENSE00003772464;rank=2;version=1
+CHR_HG126_PATCH	ensembl	CDS	72446378	72446503	.	-	1	ID=CDS:ENSP00000486012;Parent=transcript:ENST00000628983;protein_id=ENSP00000486012
+CHR_HG126_PATCH	ensembl	CDS	72447270	72447295	.	-	0	ID=CDS:ENSP00000486012;Parent=transcript:ENST00000628983;protein_id=ENSP00000486012
+CHR_HG126_PATCH	ensembl	exon	72447270	72447493	.	-	.	Parent=transcript:ENST00000628983;Name=ENSE00003760613;constitutive=1;ensembl_end_phase=2;ensembl_phase=-1;exon_id=ENSE00003760613;rank=1;version=1
+CHR_HG126_PATCH	ensembl	five_prime_UTR	72447296	72447493	.	-	.	Parent=transcript:ENST00000628983
+###
+CHR_HG126_PATCH	havana	lincRNA_gene	72505075	72550889	.	-	.	ID=gene:ENSG00000280864;Name=RP11-654C22.2;biotype=lincRNA;gene_id=ENSG00000280864;havana_gene=OTTHUMG00000159191;havana_version=1;logic_name=proj_havana;version=1
+CHR_HG126_PATCH	havana	lincRNA	72505075	72550889	.	-	.	ID=transcript:ENST00000629165;Parent=gene:ENSG00000280864;Name=RP11-654C22.2-001;biotype=lincRNA;havana_transcript=OTTHUMT00000353763;havana_version=1;tag=basic;transcript_id=ENST00000629165;version=1
+CHR_HG126_PATCH	havana	exon	72505075	72505358	.	-	.	Parent=transcript:ENST00000629165;Name=ENSE00003769648;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=ENSE00003769648;rank=3;version=1
+CHR_HG126_PATCH	havana	exon	72549722	72549841	.	-	.	Parent=transcript:ENST00000629165;Name=ENSE00003773559;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=ENSE00003773559;rank=2;version=1
+CHR_HG126_PATCH	havana	exon	72550428	72550889	.	-	.	Parent=transcript:ENST00000629165;Name=ENSE00003775139;constitutive=1;ensembl_end_phase=-1;ensembl_phase=-1;exon_id=ENSE00003775139;rank=1;version=1