pybedtools.bedtool.Bedtool.sort()

[Accompany0313]

Hi,

First of all - thank you for your amazing work. pybedtools has been super useful for my research so far and I am very grateful.

I have a problem now, when I use pybedtools bedtool. Bedtool. From_dataframe (blacklist_bed_df).sort (), I don't when the incoming parameters g can run normally, but when I passed in parameter g, For example blacklist_bed = pybedtools. Bedtool. Bedtool. From_dataframe (blacklist_bed_df).sort (g = chrom_size_path), will appear unable to run. I haven't thought of a good solution to this problem. I hope to get your help. Thank you very much.

Here is my chrom_size file： hg38.txt

[daler]

@Accompany0313 sorry for such a late reply, but if this is still an issue can you provide the file that you're working with?

For example, the chromsizes file might not have the same chromosomes as your input, or the input might malformed somehow.

You could use Bedtool.from_dataframe(blacklist_bed_df).saveas("example.bed") to get a file I could use for debugging.