The line sorts both the .genepred and the temporary .bed files and collates them in a single, final, .bed file. This causes issues when calling intersect_flank in https://github.com/wyang17/SQuIRE/blob/7c4c79a0d2882d8b72a5c28c44313b97183b7983/squire/Count.py#L275 in particular, bedtools does not recognize the .bed file as a proper .bed file due to the upper half of the collated file generated by Fetch.py
I do not know if this is intended behavior but I would recommend to change L75 in Fetch.py with:
https://github.com/wyang17/SQuIRE/blob/7c4c79a0d2882d8b72a5c28c44313b97183b7983/squire/Fetch.py#L75
The line sorts both the .genepred and the temporary .bed files and collates them in a single, final, .bed file. This causes issues when calling intersect_flank in https://github.com/wyang17/SQuIRE/blob/7c4c79a0d2882d8b72a5c28c44313b97183b7983/squire/Count.py#L275 in particular, bedtools does not recognize the .bed file as a proper .bed file due to the upper half of the collated file generated by Fetch.py
I do not know if this is intended behavior but I would recommend to change L75 in Fetch.py with:
sort_commandlist = ["sort","-k2,2n",refGene_temp, ">", bed]
and keep the file a .bed file at 100%