Opened 10 years ago

Closed 10 years ago

Last modified 10 years ago

#1624 closed task (fixed)

Create array design (feature) importer for GTF files

Reported by: Nicklas Nordborg Owned by: Nicklas Nordborg
Priority: critical Milestone: BASE 3.0
Component: coreplugins Version:
Keywords: Cc:

Description

A description of the GTF file format can be found at: http://www.ensembl.org/info/website/upload/gff.html

The importer should use "transcript_id" as the feature id. Reporter id is either the "gene_id" or "transcript_id" with an optional prefix (eg. hg19).

Change History (5)

comment:1 Changed 10 years ago by Nicklas Nordborg

Owner: changed from everyone to Nicklas Nordborg
Status: newassigned

comment:2 Changed 10 years ago by Nicklas Nordborg

Resolution: fixed
Status: assignedclosed

(In [5764]) Fixes #1624: Create array design (feature) importer for GTF files

  • Created GtfReporterMapImporter and two configurations that uses transcript_id/gene_id for reporter ids. The GTF importer builds on the ReporterMapFlatFileImporter but has less configuration options. Eg. it is locked to use FEATURE_ID for identifying features.
  • Added a new parameter to the regular ReporterMapFlatFileImporter that makes it possible to limit a configuration to certain platforms. This is used to hide genepix, illumina, etc. when using the sequencing platform.
  • Added SEQUENCING platform and SEQUENCING_EXPRESSION variant.
  • Created a GTF validator that hooks into the fileset validation extension point for array designs and extracts the number of unique transcript_id:s from the GTF file.

comment:3 Changed 10 years ago by Nicklas Nordborg

(In [5771]) References #1624: Create array design (feature) importer for GTF files

The default configuration now uses transcript_id@seqname as the reporter and feature id. We discovered that this is needed to make up a unique id for all entries that we want to track in array design features and raw data.

comment:4 Changed 10 years ago by Nicklas Nordborg

(In [5772]) References #1624: Create array design (feature) importer for GTF files

Fixed incorrect mapping for reporter id.

comment:5 Changed 10 years ago by Nicklas Nordborg

(In [5787]) References #1624: Create array design (feature) importer for GTF files

The importer should not be shared to everyone, since the other array design importers are not.

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