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IndexError: child index out of range #55
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Pubmlst appears to have changed their XML schema, so just pushed a small point update to stringMLST. Also, do note that you should use quotes around your species to make sure you're getting the scheme you think you are;
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How can I update the version? in my computer!
regards
…________________________________
From: Aroon Chande <notifications@github.com>
Sent: Wednesday, September 2, 2020 5:06 PM
To: jordanlab/stringMLST <stringMLST@noreply.github.com>
Cc: AbatwahelQuitol <christhian091089@outlook.com>; Author <author@noreply.github.com>
Subject: Re: [jordanlab/stringMLST] IndexError: child index out of range (#55)
Pubmlst appears to have changed their XML schema, so just pushed a small point update to stringMLST. Also, do note that you should use quotes around your species to make sure you're getting the scheme you think you are; stringMLST.py --getMLST -P Listeria --species "Listeria monocytogenes"
$ ./stringMLST.py -v
stringMLST v0.6.3 (updated : September 02, 2020)
$ ./stringMLST.py --getMLST -P Listeria --species "Listeria monocytogenes"
Preparing: Listeria monocytogenes
INFO: normalizing name to: Listeria_monocytogenes
Database ready for Listeria monocytogenes
Listeria/Listeria_monocytogenes
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Either by pip or cloning the repo and installing from there. I still need to submit an updated conda package and that'll take some time to process on their side. |
The new conda package should be available shortly |
If I use the next line:
stringMLST.py --getMLST -P Listeria --species Listeria monocytogenes
I get the following error:
Preparing: Listeria
Traceback (most recent call last):
File "/mnt/disk1/bin/miniconda3/bin/stringMLST.py", line 1562, in
profileURL, loci = get_links(dbRoot, filePrefix, species)
File "/mnt/disk1/bin/miniconda3/bin/stringMLST.py", line 268, in get_links
profileURL = child[1].text
IndexError: child index out of range
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