I am using humann version 3.8
I am trying to determine which gene corresponds to each pathway in my pathways.tsv file.
I am running the following command: humann_unpack_pathways --input-genes Name1.genefamilies.tsv --input-pathways Name1.pathabundance.tsv --output Name1_Pathway_genes.tsv
It seems to assign the gene correctly, however, numbers for RPK are only showing up for one of my samples, while the remaining samples are blank.
What can I do to fix this?
Thank you!
I have this same issue - did you ever resolve?
I didn’t, I got distracted by something else. This would be useful though. I wonder if anyone from the Huttenhower lab might know how to trouble shoot this. Eventually I will need to figure it out. @bplet01
Most HUMAnN helper scripts (including this one) are only intended to work on one sample at a time, since that’s how HUMAnN itself works. You would need to use a loop to run this script on each of your samples individually and then merge the results to get the sort of integrated “unpacked” view I think you are trying for?
Running the following command to merge the unpacked data from multiple samples into a single table causes an error:
Command:
humann_join_tables.py
–input humann
–output humann_unpack.tsv
–file_name unpack
Error:
Traceback (most recent call last):
File “/usr/local/bin/humann_join_tables”, line 11, in
load_entry_point(‘humann==3.9’, ‘console_scripts’, ‘humann_join_tables’)()
File “/usr/local/lib/python3.6/dist-packages/humann/tools/join_tables.py”, line 238, in main
join_gene_tables(gene_tables,args.output,verbose=args.verbose)
File “/usr/local/lib/python3.6/dist-packages/humann/tools/join_tables.py”, line 98, in join_gene_tables
sorted_gene_list=util.fsort(list(gene_table_data))
File “/usr/local/lib/python3.6/dist-packages/humann/tools/util.py”, line 403, in fsort
features = sorted( features, key=lambda f: c_topsort.get( fsplit( f )[0], default ) )
File “/usr/local/lib/python3.6/dist-packages/humann/tools/util.py”, line 403, in
features = sorted( features, key=lambda f: c_topsort.get( fsplit( f )[0], default ) )
File “/usr/local/lib/python3.6/dist-packages/humann/tools/util.py”, line 377, in fsplit
sys.exit( “LETHAL ERROR: bad feature name: {}”.format( f ) )
NameError: name ‘f’ is not defined
I suspect that the extra delimiter is causing the problem.
