Opened 11 years ago

Closed 11 years ago

Last modified 11 years ago

#237 closed Request (fixed)

Add support for MicroRNA BGX files to reporter importer

Reported by: Nicklas Nordborg Owned by: Nicklas Nordborg
Priority: major Milestone: Illumina package v1.4
Component: net.sf.basedb.illumina Keywords:
Cc:

Description

See #215 and #236 for some background info.

Change History (3)

comment:1 Changed 11 years ago by Nicklas Nordborg

Milestone: Illumina package v1.xIllumina package v1.4
Status: newassigned
Summary: Add support for MicroRNA BGX files to reporter and feature importerAdd support for MicroRNA BGX files to reporter importer

The feature importer should already be able to handle the MicroRNA BGX files. It only cares about the Probe_ID and Array_Address_Id columns and ignores all other columns.

The problem with the BGX reporter importer stems from the BgxMergeControlsInputStream class which merges reporter information for rows that have duplicated the Probe_Id from another row. I think this code could be generalized a bit:

  • The Probe_Id is used as the key. Duplicate rows should be merged.
  • The Array_Address_Id column is always ignored since it is only relevant for features
  • All remaining columns are merged no matter how few or many they are.

The first two points are more or less the same as in the current code. The third point is currently hardcoded to require 4 additional columns (Reporter_Group_Name, Reporter_Group_Id, Reporter_Composite_Map and Probe_Sequence).

comment:2 Changed 11 years ago by Nicklas Nordborg

Resolution: fixed
Status: assignedclosed

(In [1147]) Fixes #237: Add support for MicroRNA BGX files to reporter importer

comment:3 Changed 11 years ago by Nicklas Nordborg

The importer imports data from the [Probes] and [Controls] section. The other sections, [ControlGraphs?] and [ControlBars?], doesn't seem to have reporter data and are ignored.

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