10000 Recent issue with input bed that only have 3 columns · Issue #410 · daler/pybedtools · GitHub
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Recent issue with input bed that only have 3 columns #410

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xuebingjie1990 opened this issue Jul 31, 2024 · 1 comment
Open

Recent issue with input bed that only have 3 columns #410

xuebingjie1990 opened this issue Jul 31, 2024 · 1 comment

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@xuebingjie1990
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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
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daler commented Nov 5, 2024

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?

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