Opened 12 years ago

Closed 11 years ago

#93 closed task (fixed)

Illumina SNP validator and meta-data extractor

Reported by: Martin Svensson Owned by: Martin Svensson
Priority: critical Milestone: Illumina package v1.0
Component: net.sf.basedb.illumina Keywords:
Cc:

Description

The data files should be validated automatically and some data such as number of spot should be extracted for display in the GUI.

Change History (10)

comment:1 Changed 12 years ago by Johan Enell

Milestone: Illumina package v1.0

comment:2 Changed 12 years ago by Nicklas Nordborg

Milestone: Illumina package v1.0

comment:3 Changed 12 years ago by Nicklas Nordborg

Milestone: Illumina package v1.x

comment:4 Changed 12 years ago by Nicklas Nordborg

This is for the array design. A BPM file is opened by BeadStudio? and then saved in csv format. The start of that file looks like:

[Heading]
Descriptor File Name(s),HumanCNV370v1_C.bpm
Assay Format,Infinium
SNP Count,370404
[Assay]
IlmnID,Name,IlmnStrand,SNP,AddressA_ID,AlleleA_ProbeSeq,AddressB_ID,AlleleB_ProbeSeq,Chr,MapInfo,Ploidy,Species,CustomerStrand,IlmnStrand,IllumicodeSeq,TopGenomicSeq
rs10000010-126_B_F_IFB1153208421:0,rs10000010,Bot,[T/C],900010475,,0,,4,21227772,2,Homo sapiens,BOT,Bot,,

The "SNP Count" value can be extracted and stored in the array design. No features are imported into the database.

comment:5 Changed 12 years ago by Nicklas Nordborg

Priority: majorcritical

comment:6 Changed 12 years ago by Nicklas Nordborg

Milestone: Illumina package v1.xIllumina package v1.0

comment:7 Changed 12 years ago by Martin Svensson

Owner: changed from Johan Enell to Martin Svensson
Status: newassigned

comment:8 Changed 12 years ago by Martin Svensson

(In [590]) References #93 You can now validate and extract meta-data from SNP-manifest files. The validator class and metadata extractor class is now being set when creating manifest data file-type in the installation plug-in.

comment:9 Changed 12 years ago by Martin Svensson

(In [591]) References #93 Correct some comments and removed debug-code

comment:10 Changed 11 years ago by Martin Svensson

Resolution: fixed
Status: assignedclosed

(In [620]) Fixes #93 Added some more javadoc and improved the code format in a few places.

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