Opened 14 years ago

Closed 13 years ago

#800 closed enhancement (fixed)

Make the Illumina importer accept tab as data delimiter and comma as numeric decimal separator

Reported by: base Owned by: Nicklas Nordborg
Priority: minor Milestone: BASE 2.5.1
Component: coreplugins Version:
Keywords: Cc:

Description

My Illumina files are not comma separted but tab separeted. Can you make the Importer accept this as well? Either that that the importer understand wht delimter to use or it could be a parameter for the user. I attach a sample file of my tab separeted Illumina file. The file will work with the current comma based version if I do a search-replace, but some users may use excel and the file might be altered in other ways.

Vegard

Attachments (1)

illumina_tabdelim_example.txt (3.6 KB) - added by base 14 years ago.
Example of a Illumina data file with tab as delimeter.

Download all attachments as: .zip

Change History (5)

Changed 14 years ago by base

Example of a Illumina data file with tab as delimeter.

comment:1 Changed 14 years ago by Nicklas Nordborg

Is this the only thing that can be different in Illumina files? Is that an option in Beadstudio? What do you mean with some users may use Excel and that it may be altered in other ways?

I think BASE will support files exported from BeadStudio? only. If someone edits them, they should make sure to save them in a format that is compatible with how Beadstudio generates them.

comment:2 Changed 13 years ago by base

Sorry I forgot about this post for some time.

I was somewhat unclear in my first description and you misunderstood me. Our Illumina file comes straight out of beadstudion as tab delimited and not comma delimited. This is most likely an option setting in Beadstudio. I also assume that tab-delimited would be more common than comma delimited.

So my reference to excel was just what people have to do now with the current Illumina importer, in order to replace the tab file to a comma file. I tab delimited is an option in the importer they can take the files straight from beadstudio and into BASE2 without using excel (or another tool) first.

Vegard.

comment:3 Changed 13 years ago by Nicklas Nordborg

Milestone: BASE 2.5.1
Owner: changed from everyone to Nicklas Nordborg
Status: newassigned
Summary: Make the Illumina importer accept tab as data delimter.Make the Illumina importer accept tab as data delimiter and comma as numeric decimal separator

Ok, I just got this confirmed by other users. They also report that numeric values use comma and not dot as the decimal separator.

I'll add support for tab-separated columns and decimal commas in 2.5.1.

If anybody knows about other things that may vary, please send us some information about it or it will have to wait until a later release'''

comment:4 Changed 13 years ago by Nicklas Nordborg

Resolution: fixed
Status: assignedclosed

(In [4055]) Fixes #800: Make the Illumina importer accept tab as data delimiter and comma as numeric decimal separator

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