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Ensembl / WiggleTools

Basic operations on the space of numerical functions defined on the genome using lazy evaluators for flexibility and efficiency
Apache License 2.0
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wiggletools seek combines regions with multiple zero points (undesiderable) #68

Closed SimonaSecomandi closed 3 years ago

SimonaSecomandi commented 3 years ago

Hi,

I'm trying to extract a region from a wiggle file like so:

wiggletools write output.wig seek SUPER_6 53887433 53926022 file.wig

The wig file has base-by-base values and this command tends to combine regions with multiple zero values like so:

.... 0.446000 0.447000 -0.574000 0.447000 0.447000 0.429000 SUPER_6 53889550 53889558 0.000000 fixedStep chrom=SUPER_6 start=53889559 step=1 -0.323000 -0.574000 -1.049000 0.524000 -0.231000 0.447000 0.447000 ...

This is undesideble and the conversion of the wig file in bed format fails due to that lines (e.g. SUPER_6 53889550 53889558 0.000000).

Can this merging be avoided? Many thanks.

dzerbino commented 3 years ago

Dear @SimonaSecomandi ,

I think what you want is the write_bg command that writes straight to bedGraph, as in: 

wiggletools write_bg output.wig seek SUPER_6 53887433 53926022 file.wig

Hope this helps,

Daniel

SimonaSecomandi commented 3 years ago

That worked fine to obtain the bed file!!

I was also wondering if there are ways to obtain a correct wig file with wiggletools seek for visualization.

Many thanks

dzerbino commented 3 years ago

Excellent!

The bedGraph format is a valid subset of the wig specification, therefore this output if both a bed and a wig file.