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missing header in output #2

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morien opened this issue Apr 28, 2021 · 0 comments
Open

missing header in output #2

morien opened this issue Apr 28, 2021 · 0 comments

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@morien
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morien commented Apr 28, 2021

I've found that there's no header in the output file, using your blastn_add_taxonomy_lite.py script. This doesn't affect the data, only the ability to use the file in downstream applications. The output of this script can be used downstream with the galaxy-tool-lca repo script "lca.py", but if the header is missing, it throws an error:

python2 ~/programs/galaxy-tool-BLAST/blastn_add_taxonomy_lite.py -i CO1_ASV_sequences.combined.blast.out -t ~/programs/Simple-LCA/rankedlineage.dmp -m ~/programs/Simple-LCA/merged.dmp -o taxonomy_added 
python2 ~/programs/galaxy-tool-lca/lca.py -i taxonomy_CO1_ASV_sequences.combined.blast.out -o test -b 100 -id 80 -cov 80 -t only_lca
Traceback (most recent call last):
  File "programs/galaxy-tool-lca/lca.py", line 303, in <module>
    main()
  File "programs/galaxy-tool-lca/lca.py", line 300, in main
    lca()
  File "programs/galaxy-tool-lca/lca.py", line 290, in lca
    determine_taxonomy(otuLines)#find the lca for the query
  File "
programs/galaxy-tool-lca/lca.py", line 247, in determine_taxonomy
    otu[0][0] + "\tno identification\tno identification\t" + "\t".join(taxonomy).strip() + "\tfiltered out"+endLine)
IndexError: list index out of range

However, manually adding the header back in like so resolves the error:

cat <(head -n 1 ~/programs/galaxy-tool-lca/example/example.tabular) taxonomy_CO1_ASV_sequences.combined.blast.out > tmp
python2 ~/programs/galaxy-tool-lca/lca.py -i tmp -o test -b 100 -id 80 -cov 80 -t only_lca

Here's the input file for reproducing the problem: CO1_ASV_sequences.combined.blast.out.gz

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