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SysBioChalmers / HGTphyloDetect

HGTphyloDetect is a versatile toolbox to identify horizontal gene transfer (HGT) events combined with phylogenetic analysis.
MIT License
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Is that a Bug? #17

Open wsh-1046 opened 2 weeks ago

wsh-1046 commented 2 weeks ago

Hi le-yuan: When I was operating the step "python HGT_workflow_distant.py Nanorana_parkeri_SimID.faa", I got a problem,which show below: Taxid by BLAST: 7917 Taxid by BLAST: 13616 Alien index: 299.19 This is a HGT event Accession_id: AAP36269.1 Evalue: 1.16e-130 Traceback (most recent call last): File "~/HGT/HGTphyloDetect/main/HGT_workflow_distant.py", line 222, in main() File "~/HGT/HGTphyloDetect/main/HGT_workflow_distant.py", line 196, in main taxid2name = ncbi.get_taxid_translator([ranks2lineage['phylum'], ranks2lineage['class'], ranks2lineage['superkingdom']])


Traceback (most recent call last):
  File "~/HGT/HGTphyloDetect/main/HGT_workflow_distant.py", line 222, in <module>
    main()
  File "~/HGT/HGTphyloDetect/main/HGT_workflow_distant.py", line 196, in main
    taxid2name = ncbi.get_taxid_translator([ranks2lineage['phylum'], ranks2lineage['class'], ranks2lineage['superkingdom']])
                                            ~~~~~~~~~~~~~^^^^^^^^^^
KeyError: 'phylum'
-----------------------------------------------------------------------------------------
Please tell me how to deal this problem. THANK YOU VERY MUCH!
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wsh-1046 commented 3 days ago

After I changed the script in HGT_workflow_distant.py in order to ignore the problem "KeyError:'phylum'",I have found that when I got into the next step,it would be interrupted often by the problem like this"This is gene 3------------------ XP_018426332.1 Yes, blast file already exists, nice! Attention: please check the gene accession id!" Please tell me how to deal with it.Thanks!