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daler / pybedtools

Python wrapper -- and more -- for BEDTools (bioinformatics tools for "genome arithmetic")
http://daler.github.io/pybedtools
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Recent issue with input bed that only have 3 columns #410

Open xuebingjie1990 opened 4 months ago

xuebingjie1990 commented 4 months ago

Hi....

I recently start to have prolem with pybedtools.BedTool() when the input bed file only have the first 3 columns like 

chr1    3012568 3012773
chr1    3094410 3095612
chr1    3113593 3113955
chr1    3119518 3120728
chr1    3121390 3121765
chr1    3121835 3122127
chr1    3181166 3181337
chr1    3204856 3205092
chr1    3210229 3210709
chr1    3235436 3235734

It gave me the warning WARNING: File universe.bed has inconsistent naming convention for record: chr1 3012568 3012773 and resulted in no bedtool obj.

I just started to have this problem about a month ago. I used the same file before with no problem. I tried to update pybedtools to the leatest version but no help.

Can you please explain if I am missing something?

Many thanks

Bing

daler commented 3 weeks ago

Are you able to attach the problematic file? It could be that there is a space instead of tab or something like that. And what specific command did you use to trigger that error?