Open deppworld opened 6 months ago
qiyunzhu
commented
6 months ago @deppworld I checked this file: http://ftp.microbio.me/pub/wol-20April2021/function/metacyc/reaction-to-pathway.txt . There seems to be some duplicates in the placement of RXN-13667. You may try removing all lines that have RXN-13667, and see if the program works. If so, this entry might be a special case that we need to deal with.
deppworld
commented
6 months ago @qiyunzhu Hi thanks for your prompt response. I removed this Id and tried but there are so many IDs duplicated in two reference files (reaction-to-pathway.txt and pathway-to-super_pathway.txt ). I am trying to remove them and update them here if it will work.
qiyunzhu
commented
6 months ago @deppworld In your situation, I think classifying to just genes (ORFs) followed by multiple collapses is more appropriate. See here for an example.
deppworld
commented
6 months ago @qiyunzhu
Hi, I run the following command:
woltka collapse -i C003.sam -m protein-to-enzrxn.txt -n enzrxn_name.txt -m enzrxn-to-reaction.txt -n reaction_name.txt -m reaction-to-pathway.txt -n pathway_name.txt -m pathway-to-super_pathway.txt -n pathway_name.txt -m pathway_type.txt -n all_class_name.txt -m protein-to-gene.map -n gene_name.txt -m protein-to-go.map -m enzrxn-to-regulation.map -m regulation-to-regulator.map -n compound_name.txt -o ./test
and I am getting the following error:
Traceback (most recent call last):
File "/home/dverma2/miniforge3/bin/woltka", line 8, in
in addition to this, the reference folder is missing some files (protein.map.xz, gene-to-protein.map.xz )
qiyunzhu
commented
6 months ago Which reference folder are you referring to? WoL1 or WoL2?
deppworld
commented
6 months ago Wol2
deppworld
commented
6 months ago Hi
I tried with the collapse command but I could not get gene-to-protein.biome because of no reference file in the folder( https://ftp.microbio.me/pub/wol-20April2021/function/metacyc/ ) then I directly tried gene-to-pathway but I am getting following error:
(base) dverma2@EB-ONC-J8Q3FF3:/mnt/f/woltka$ woltka collapse -i gene.biom -m gene-to-pathway.txt -o pathway.biom
Number of features before collapsing: 435442.
Reading mapping file: gene-to-pathway.txt... Done.
Collapsing profile...Traceback (most recent call last):
File "/home/dverma2/miniforge3/bin/woltka", line 8, in vectorize on size 0 inputs '
ValueError: cannot call vectorize on size 0 inputs unless otypes is set
I also tried with classify but getting different error:
(base) dverma2@EB-ONC-J8Q3FF3:/mnt/f/woltka$ woltka classify -i gene.biom -m gene-to-pathway.txt -o pathway.biom
Traceback (most recent call last):
File "/home/dverma2/miniforge3/bin/woltka", line 8, in
I think IDs are not matching due to one-step escaping (Gene to protein). I am hoping you can help me with this.
jolespin
commented
3 months ago @qiyunzhu It looks like the FTP might be down right now.
Hi I am getting this error when I am running the following :
woltka classify \ --input indir \ --coords coords.txt \ --map gene-to-protein.map \ --map protein-to-enzrxn.map \ --map enzrxn-to-reaction.map \ --map reaction-to-pathway.map \ --map pathway-to-super.map \ --rank gene,protein,enzrxn,reaction,pathway,super \ --output outdir
Constructing classification system... Will extract rank name from map filename. Parsing simple map file: gene-to-protein.txt... Done. Parsing simple map file: protein-to-enzrxn.txt... Done. Parsing simple map file: enzrxn-to-reaction.txt... Done. Parsing simple map file: reaction-to-pathway.txt...Traceback (most recent call last): File "/home/dverma2/miniforge3/bin/woltka", line 8, in
sys.exit(cli())
File "/home/dverma2/miniforge3/lib/python3.10/site-packages/click/core.py", line 1157, in call
return self.main(args, kwargs)
File "/home/dverma2/miniforge3/lib/python3.10/site-packages/click/core.py", line 1078, in main
rv = self.invoke(ctx)
File "/home/dverma2/miniforge3/lib/python3.10/site-packages/click/core.py", line 1688, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/home/dverma2/miniforge3/lib/python3.10/site-packages/click/core.py", line 1434, in invoke
return ctx.invoke(self.callback, ctx.params)
File "/home/dverma2/miniforge3/lib/python3.10/site-packages/click/core.py", line 783, in invoke
return __callback(args, kwargs)
File "/home/dverma2/miniforge3/lib/python3.10/site-packages/woltka/cli.py", line 195, in classify_cmd
workflow(kwargs)
File "/home/dverma2/miniforge3/lib/python3.10/site-packages/woltka/workflow.py", line 122, in workflow
tree, rankdic, namedic, root = build_hierarchy(
File "/home/dverma2/miniforge3/lib/python3.10/site-packages/woltka/workflow.py", line 801, in build_hierarchy
updatedict(rankdic, {k: rank for k in set(map.values())})
File "/home/dverma2/miniforge3/lib/python3.10/site-packages/woltka/util.py", line 75, in update_dict
add_dict(dic, key, value)
File "/home/dverma2/miniforge3/lib/python3.10/site-packages/woltka/util.py", line 44, in add_dict
assert dic[key] == value, f'Conflicting values found for "{key}".'
AssertionError: Conflicting values found for "RXN-13667".
Kindly help me to resolve this.