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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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"fastaFromBed" error #396

Closed franjmt closed 3 months ago

franjmt commented 8 months ago

Hi, I am trying to implement getfasta from bedtools in my python script. but keep getting an error:

coordinates_bed = BedTool(os.path.join(bed_file_dir,'AAMDC_transcript_1.bed')) sequence = coordinates_bed.sequence(fi=genome_fasta, name=True)

I get the error: NotImplementedError: "fastaFromBed" does not appear to be installed or on the path, so this method is disabled. Please install a more recent version of BEDTools and re-import to use this method.

daler commented 8 months ago

As the error suggests, bedtools is not found on the path. Have you installed bedtools and is it on your path?

daler commented 3 months ago

@franjmt please reopen if this is still an issue.