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tseemann / mlst

:id: Scan contig files against PubMLST typing schemes
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Latest mlst database includes a new column #8

Closed kimleeng closed 9 years ago

kimleeng commented 9 years ago

The latest mlst database includes a new column for species which if not removed will cause the type to not be identified properly and will search for a nonexistant species.tsv.

tseemann commented 9 years ago

@kimleeng i'm not sure what you mean? can you point to a URL of a file you have?

kimleeng commented 9 years ago

So using mlst v1.2 / sbin / run_me to obtain the mlst public db (on oct 26, 2015) the abaumannii scheme there is a column called "species" and running /mlst/bin/mlst --scheme abaumannii *.fasta gives many of these errors "Use of uninitialized value in join or string at /software/mlst-1.2/bin/mlst line 162, line 2." I can get rid of this error by removing the extra "species" column.

Here's the head of the file abaumannii.txt:

ST Oxf_gltA Oxf_gyrB Oxf_gdhB Oxf_recA Oxf_cpn60 Oxf_gpi Oxf_rpoD clonal_complex species 1 1 1 1 1 1 1 6
2 2 2 2 1 1 2 7
3 1 1 1 1 2 1 4
4 1 12 3 2 2 7 3
5 1 3 3 2 2 3 1
6 1 4 3 2 2 3 3
7 3 3 3 2 3 3 8
8 4 4 4 4 4 5 9
9 1 3 3 2 2 6 8

Hope the information helps.

tseemann commented 9 years ago

@kimleeng - that helped a lot! I have fixed the bug. I will make a new release. Thank you for your patience.