Updated pathotyping and toxin typing database by adding protein seque…

…nces to each record and adding subunit coordinates and intergenic region of shiga toxin records

README.md

@@ -246,8 +246,7 @@ The Shiga toxin subtyping module supports typing of the *`stx1`* and *`stx2`* ge
 
 Currently the database supports 4 *`stx1`* subtypes: *`stx1a`*, *`stx1c`*, *`stx1d`* and stx1e and 15 *`stx2`* subtypes: *`stx2a`*, *`stx2b`*, *`stx2c`*, *`stx2d`*, *`stx2e`*, *`stx2f`*, *`stx2g`* ,*`stx2h`*, *`stx2i`*, *`stx2j`*, *`stx2k`*,*`stx2l`*, *`stx2m`*, *`stx2n`*, *`stx2o`*.
 
-The input sequences are queried against the *`stx1`* and *`stx2`* markers via BLASTN and top hits are being reported separated by the `;` symbol. The module supports the multi-copy `stx` gene presence by taking into account the genomic `stx` location attributes for each `stx` subtype (i.e. gene coordinates, contig location, overlap with other `stx` hits). The multi-copy `stx` gene reporting is not exhaustive (not all hits are being reported). That is if multiple `stx` hits are found in the input, the highest quality longest hit per each `stx` subtype is being reported (i.e. the hit with the highest `bitscore`).  The `StxSubtypes` field lists all UNIQUE `stx` subtypes such as `stx2e;stx2k` even if their genomic locations overlap or are identical due to truncated incomplete `stx` alleles. The `StxContigNames` and `StxCoordinates` lists all contig names and corresponding genomic coordinates for each listed `stx` type in the  `StxSubtypes` field according to the alphabetical order.  
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+The input sequences are queried against the *`stx1`* and *`stx2`* markers via BLASTN and top hits are being reported separated by the `;` symbol. The module supports the multi-copy `stx` gene presence by taking into account the genomic `stx` location attributes for each `stx` subtype (i.e. gene coordinates, contig location, overlap with other `stx` hits). The multi-copy `stx` gene reporting is not exhaustive (not all hits are being reported). That is if multiple `stx` hits are found in the input, the highest quality hit(s) per each non-overlapping `stx` gene range is being reported (i.e. single or multiple top hits are possible with the highest identical `bitscore` value as some hits could not be resolved due to sequence truncation). For example, if several `stx` allele hits have identical `bitscore` in a given `stx` gene range, all such hits are being reported.  Note that the `StxSubtypes` field lists only UNIQUE `stx` subtypes for the entire input sample such as `stx2e;stx2k` even if their genomic locations overlap or are identical due to truncated incomplete `stx` allele signatures. The `StxContigNames` and `StxCoordinates` lists all contig names and corresponding genomic coordinates for each listed `stx` type in the  `StxSubtypes` field according to the alphabetical order. This allows to easily spot `stx` subtypes with the same genomic coordinates. Finally, these fields allow to better understand `stx` alleles context/function and spot truncated alleles while providing genomic location context.  
 
 ### Quality Control (QC) module
 To provide an easier interpretation of the results and typing metrics, following QC codes were developed.