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Import data with TabLoader and skipping first N lines

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Import data with TabLoader and skipping first N lines

Anthony Corbett

2013-04-22 12:16

Status: Closed

I have a file format from a Nanodrop instrument which looks like this:

Module: Nucleic Acid
Path: 10 mm
Software: 3.7.1
Firmware:
Sample ID User ID Date Time ng/ul A260 A280 260/280 260/230
Z109 Default 2/12/2013 2:31 PM 12.78 0.320 0.127
Z110 Default 2/12/2013 2:31 PM 8.88 0.222 0.065
Z111 Default 2/12/2013 2:32 PM 16.65 0.416 0.118

I am planning on creating a Java based assay module to import this data. I'm wondering if the TabLoader class has a way to skip the first 4 lines of this file or if I'll have to write my own parser.

It looks like the parent class DataLoader has a _skipLines member variable but its usage looks to be very specific and not generic enough for my use case. Am I correct in this?

Thanks,

Anthony

kevink responded:	2013-04-22 14:25
I think you can use _skipLines if you set it before .inferColumnInfo() is called by .initialize(). You may have to subclass TabLoader in order to set _skipLines. Maybe we need to expose a setter for _skipLines. Another option would be to do something similar to TabLoader.getComments() in your subclass. The TabLoaderIterator will position the reader past the comments and header in it's constructor.