Package: lissero
LisSeroIn silicoserogroup typing prediction forListeria monocytogenesAuthorsJason Kwong (@kwongjc) - GitHub:kwongjJosh Zhang (@abcdtree)  - GitHub:abcdtreeTorsten Seemann (@torstenseemann) - GitHub:tseemannMaintainersMDU PHL - Josh Zhang, Kristy Horan, and Anders Gonçalves da SilvaDependenciesPython 3.6+BLAST 2.10.0Installationpip3 install lisseroInstalling BLAST 2.10.0Brew:brew install blastConda:conda install -c bioconda blastIn silicoserogrouping forListeria monocytogenesLisSero is based on a method of predicting serogroup forListeria monocytogenesusing PCR, as described by Doumithet al(see References).It detects the presence or absence of 5 genes (lmo1118, lmo0737, ORF2110, ORF2819 and Prs).The patterns obtained reflect the four main serotypes (1/2a, 1/2b, 1/2c, and 4b)
obtained from food and human sources.The patterns are not based on genes involved in somatic (O) or flagellar (H) biosynthesis,
and are not specific to just one serotype, but rather to a group of serotypes.Serogrouplmo1118lmo0737ORF2110ORF2819Prs1/2a, 3a-+--+1/2b, 3b, 7---++1/2c, 3c++--+4b, 4d, 4e--+++4b, 4d, 4e*-++++Listeria spp.+If only Prs is detected, these isolates are often serotype 4a or 4c, though
LisSero reports these as "Nontypable".Usage$ lissero --help

Usage: lissero [OPTIONS] FASTA...

  In silico serogroup prediction for L. monocytogenes. Alleles: lmo1118,
  lmo0737, ORF2819, ORF2110, Prs

  References:

  * Doumith et al. Differentiation of the major Listeria monocytogenes
  serovars by multiplex PCR. J Clin Microbiol, 2004; 42:8; 3819-22

Options:
  -s, --serotype_db TEXT
  --min_id FLOAT          Minimum percent identity to accept a match. [0-100]
                          [default: 95.0]

  --min_cov FLOAT         Minimum coverage of the gene to accept a match.
                          [0-100]  [default: 95.0]
  --logfile TEXT          Save log to a file instead of printing to stderr
  --debug
  --helpExample usagelissero my_fasta.faExample outputIDSEROTYPEPRSLMO0737LMO1118ORF2110ORF2819COMMENT/path/to/my_fasta.fa4b, 4d, 4eFULLNONENONEFULLFULLOutput explainedThe output consist of 8 columns:ID: At the moment the full path to your fileSEROTYPE: A predicted serotype if possible, otherwiseNontypeableFive columns for each of the genes with either:FULL: for a complete match to the gene in the database (as defined by the--min_covand--min_idflags
which default to at least 95% coverage and percent id)NONE: when there is no match to the databasePARTIAL: where there are matches that fall below the--min_covand--min_idthresholdsCOMMENTS: Which will try to explain aNontypeableresults. Current cases are:No Prs found: when there is noFULLmatch to thePrsgene is not likely to be aListeria monocytogenesPresence of all 5 genes, not a known serotype: when all 5 genes are presentNo combination of fully matched genes resulted in a known serotype: An unknown combinationIn addition, it will sayUnusual 4b with lmo0737when reporting4b, 4d, 4e*serotypeChange LogVersion 0.4.1Implemented unit test for all possible 32 possible gene patternsImplemented more verbose output with presence/absence info for each geneImplemented test of FASTA file, and will exit with warning if a file does
not appear to be a FASTA fileImplement test of whether an input file exists or notImplemented logging using LoguruAdded option to log to a file (--logfile; stderr remains default)Logging now includes the BLAST command usedRemoved all references in the code to Binary TypingImplemented--versionflagAdded some better docsVersion 0.4.0Removed support for Binary TypingConsolidated repos in MDU-PHLChanged executable fromrun_lisserotolisseroBugsPlease submit via the GitHub issues page:https://github.com/MDU-PHL/LisSero/issuesSoftware LicenceGPLv2:https://github.com/MDU-PHL/LisSero/blob/master/LICENSEReferencesDoumith et al. Differentiation of the majorListeria monocytogenesserovars by multiplex PCR.J Clin Microbiol, 2004;42:8; 3819-22.