I have a text file formatted like BED and I want to add the sequences as a column on to it. Bedtools getfasta should be doing that with -bedOut option but as explained in this post (https://github.com/arq5x/bedtools2/issues/571), it doesn't work as it is supposed to. I also tried to download the sequences using UCSC's REST API with requests in Python but it is too slow for the number of lines in my file. My last resort will be to download the whole genome as a FASTA file and try to parse that but it tedious to do and introduces extra steps, files and scripts to my pipeline.
Does anybody know an alternative to bedtools getfasta -bedOut or any suggestions to speed up the downloads from UCSC's REST API?
Thanks in advance.