Multi Loci Sequence Typing Analysis helpeR

This script matches and returns an ST type number for a given base reference sequence, MLST fragment files (all fasta
formatted), and ST type table file.

Usage: mlstar.pl -c <config file> [-quiet] [-debug] [-l <program log>] [-fast]

-c <config file = REQUIRED parameter with the name and path of the config file to use for this run. See below for details.
-quiet = Optional flag to reduce amount of output to standard out.  See the log file for full output.
-debug = Optional flag to generate additional debugging message (verbose).  Also stored in log file.
-l <program log> = Optional parameter to specify the log file to write to during the program run.
-fast = Tells mlstar to stop looking after finding the first matching allele of each gene fragment, and st type table.

By default, mlstar will look for matches in all alleles of all gene fragments and all entries in the st type table,
throwing an error if duplicates are found.  Use -fast if you are sure you have no such duplicates in your data.

The <config file> is a plain text file containing information in the following format (similar to a sectioned INI file):

------------------------------------------
# Comments and blank lines are ignored

[ST ALLELE TABLE FILES]
st_allele_table.txt

[ALLELE FILES]
arcc_alleles.fasta
aroe_alleles.fasta

[REF FILES]
NC007793_corrected.fsa

-------------------------------------------

In short, the config file has three sections, and the start of each section is indicated by a [SECTION] tag:
[ST ALLELE TABLE FILES]
[ALLELE FILES]
[REF FILES]

The non-blank, non-comment lines (beginning with #) after each section tag should be file names (and paths)
related to the given section.

Files in the [ST ALLEL TABLE FILES] section should contain the path and filenames to the ST allele table, with the
expected content format of:
<ST_type> <arcc_allele_#> <aroe_allele_#> <glpf_allele_#> <gmk_allele_#> <pta_allele_#> <tpi_allele_#> <yqil_allele_#>
(basically a table of numbers)

Files in the [ALLELE FILES] section should contain FASTA formatted files with the allele sequences for the housekeeping genes.

IMPORTANT NOTE: The top down order of the files in this section should match up against the left-to-right columnar order in the
ST allele table file.  So if you have files listed as:

arcc_alleles.fasta
aroe_alleles.fasta
gmk_allel.fasta

in the allele files section, then the table file columns should be in the order:

ST_Type   arc_allele_#   aroe_allele_#   gmk_allel_# ...

Files in the [REF FILES] section contains the base reference sequence files of the isolate that you want to determine
the ST type of.

Milstar will process each base reference file in the [REF FILES] section, matching against the files listed in the [ALLELE FILES]
section, and looking up the final ST type in the table files listed in the [ST ALLELE TABLE FILES] section.  If there is more
than one file in the [ST ALLELE TABLE FILES] section, mlstar will use them in top-down order, stopping when it finds the first
successful ST type lookup.

ST analysis output is logged to REF_FILE.mlstar.out (i.e. one for each reference file).  Program output is logged to
mlstar.log (or can be specified with the -l <logfile> parameter).