animalgenomicseth / bovine-graphs Goto Github PK

Hi,

I have used the pipeline and get the multiallelic sequences using the script get_multiseq.py.
However, I find some of the nodes of negative strands are not reverse complemented. This may be due to the codes in line 94-103 in script get_multiseq.py:
if ind == (len(paths) - 1): try: totseq += grseq[path][:100] if chainstrand[2] == "+" else revcomp(grseq[path])[ :100] except: totseq += grseq[path] if chainstrand[2] == "+" else revcomp( grseq[path]) else: totseq += grseq[path] if chainstrand[2] == "+" else revcomp( grseq[path])

All of the chainstrand list are indexed as '2'. I think the index should be corrected as 'ind'.

Please check about it.

Thanks for these useful tools!

Mian

RT

hi, when i used the bovine-graphs, i found that this step (get_multisv.py) have too much memorys. We provide more than 3Tb memory to run this step. But we didn't successfully finish it. Therefore, Could you deal with it ?

Thank you for sharing your code!

I am taking the snakemake pipeline for a spin, and it is not obvious what the "assembly/{refgenome}_full.fa" supposed to be. From scanning the code briefly, I thought this would be something created by the "sv" subworkflow, however, the mash sketch command fails in the dry run because it can't find the "assembly/{refgenome}_full.fa" file.

Thanks again!