Stringmlst

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

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

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

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

Small fixes for UTF8 + Python2

Fixes for badly behaving databases and color support