Recent issue with input bed that only have 3 columns
Opened this issue · 1 comments
xuebingjie1990 commented
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
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?