0.6.3

Fixes for pubMLST db XML changes

0.6.1

Adds the enhancement from #46 .

Now stringMLST directly parses the PubMLST databases XML instead of performing a table-based lookup. This should work much better and is flexible to PubMLST changing their scheme names and adding/removing schemes

0.5.2

Fix for Issue #40, I missed escaping the "*" in the re.sub statement on line 790 while refactoring code .

python2 --version;python2 ./stringMLST.py --predict -d tests/fastqs -P neisseria/nmb --coverage --config neisseria/nmb_config.txt; python3 --version; python3 ./stringMLST.py --predict -d tests/fastqs -P neisseria/nmb --coverage --config neisseria/nmb_config.txt

Python 2.7.11
Sample  abcZ    adk     aroE    fumC    gdh     pdhC    pgm  ST
ERR027250       581 (100.00)    408 (99.35)     655 (91.63)  602 (92.47)        633 (99.60)     612 (100.00)    632 (97.33)     10252
ERR026529       231 (100.00)    180 (100.00)    306 (100.00) 612 (100.00)       269 (100.00)    277 (100.00)    260 (99.78)     10174
ERR036104       2 (100.00)      3 (100.00)      4 (100.00)   3 (100.00) 8 (100.00)      4 (100.00)      6 (100.00)      11

Python 3.6.3 :: Anaconda custom (64-bit)
Sample  abcZ    adk     aroE    fumC    gdh     pdhC    pgm  ST
ERR026529       231 (100.00)    180 (100.00)    306 (100.00) 612 (100.00)       269 (100.00)    277 (100.00)    260 (99.78)     10174
ERR027250       581 (100.00)    408 (99.35)     655 (91.63)  602 (92.47)        633 (99.60)     612 (100.00)    632 (97.33)     10252
ERR036104       2 (100.00)      3 (100.00)      4 (100.00)   3 (100.00) 8 (100.00)      4 (100.00)      6 (100.00)      11

0.5.1

This update brings a new output format to stringMLST and fixes float comparisons in Py<3.4.

Notably, versions prior would return no output (columns omitted)
for alleles which had 0 kmer hits. stringMLST will now return
"NA" values for alleles with no hits. This should hopefully
make the output more obvious in cases such as #35

0.5

This update brings a new output format to stringMLST.
Notably, versions prior would return no output (columns omitted)
for alleles which had 0 kmer hits. stringMLST will now return
"NA" values for alleles with no hits. This should hopefully
make the output more obvious in cases such as #35

0.4.2

Small fixes for UTF8 + Python2

0.4

Fixes for badly behaving databases and color support

0.3.7

stringMLST is licensed and distributed under CC Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) and is free for academic users and requires permission before any commercial use for any version of this code/algorithm.

If you are a commercial user, please contact "king.jordan biology.gatech.edu" for permissions

v0.3.6.1

Fix for weighted dictionaries when alleles are dash ('-') delimited instead of underscore ('_')

v0.3.6

This version fixes several cosmetic issues with v0.3.4 and brings stringMLST to the masses via PyPI