Setting start and end regions position for wig files

[felipealbrecht]

Hello, in the line 85 of the file parser/wig.py:

feature = [params['start'], params['start'] + params['span'], line]
params['start'] += params['span'] + params['step'] - 1

I think that it is wrong. Because it is using the span to set the starting position.
The right code is:

feature = [params['start'], params['start'] + params['span'] - 1, line]
params['start'] += params['step']

The explanation is here (taken from http://genome.ucsc.edu/goldenPath/help/wiggle.html)

fixedStep chrom=chr3 start=400601 step=100 span=5
11
22
33
causes the values 11, 22, and 33 to be displayed as 5-base regions on chromosome 3 at positions 400601-400605, 400701-400705, and 400801-400805, respectively.

(If we use the actual code from parser/wig.py, the positions will be 400601-400606, 400705-400709, 400809-400814, and so on...)

[xapple]

Hi !

Yeah that looks like an error indeed. One should add a test case with a WIG file that uses the step and span instructions at the same. I don't think there is one at the moment. One should also add to the WIG parser a line that checks that the step is equal or smaller than the span.

However considering the numbering convention used throughout the package (it's the same as UCSC) I would say the right code is:

feature = [params['start'], params['start'] + params['span'], line]
params['start'] += params['step']

I corrected it in 84ec769! Would you like to add a test case and the sanity check ?

[felipealbrecht]

Hi! Thank you for the very fast feedback.

Unhappily I cant change the code right now, I am working in a project in my work and I do not have time.
If you are not in rush, I can do it latter.

Another question: Which test does use the files in the samples/wig/ ?

[xapple]

Yeah I don't have time either. But the parser should be fixed now !

The tests for the wig format are in https://github.com/xapple/track/blob/master/track/test/format_wig.py

[felipealbrecht]

Okay, thank you.
I will do and commit latter.

[felipealbrecht]

Hello,

Using part of the scores4.wig file as an example:

fixedStep chrom=chr1 start=10 span=5
10.0
20.0

In this case, the step value will be 1, the default value.
So, it will trigger to this features:

chr1 10 15
chr1 11 20

That is invalid because the overlapping.

By the UCSC definition:

  fixedStep  chrom=chrN  start=position  step=stepInterval  [span=windowSize]
  dataValue1
  dataValue2
  ... etc ...

all fixedStep data should contain the step value, but in the line 68, the code attributes a default value:

params['step'] = int(params.get('step',1))

I believe that the code should throws an exception in case that the step value is not found.

[xapple]

Yeah you're right. I don't know what I was thinking when writing that code. Feel free to change it, I'm giving you commit access.