Table of Contents

  1. Concatenate Allele Subunits
  2. Inputs
  3. Running the Script
  4. Usage
  5. Outputs

Concatenate Allele Subunits

This script concatenates allele subunits. The outputs from the STEC pipeline (by design) have separate STEC A and B subunits. This script concatenates the subunits in the correct order with the appropriate linker sequence (stx1: 9 nt / 3 aa, stx2: 12 nt / 4 aa). The linker is N for nucleotide and X for amino acid.

Inputs

  1. Nucleotide and amino acid allele files prepared by allele_translate_reduce
  2. Nucleotide and amino acid profile files prepared by allele_translate_reduce. Note that the allele files must contain sequence for the same genes that were used for the reduction of the profile, e.g.:
    • ECs2973
    • ECs2974

Running the Script 

stec.py allele_concatenate 
--nt_profile /path/to/nt_profile/profile.txt
--aa_profile /path/to/aa_profile/profile.txt
--nt_alleles /path/to/nt_alleles
--aa_alleles /path/to/aa_alleles
-c /path/to/outputs

Usage 

usage: stec.py allele_concatenate [-h] [-version] [-v verbosity]
                                  [--nt_profile nt_profile]
                                  [--aa_profile aa_profile]
                                  [--nt_alleles nt_alleles]
                                  [--aa_alleles aa_alleles]
                                  [-c concatenate_path]

Concatenate stx toxin subunit alleles with linkers

optional arguments:
  -h, --help            show this help message and exit
  -version, --version   show program's version number and exit
  -v verbosity, --verbosity verbosity
                        Set the logging level. Options are debug, info, warning, error, and critical. Default is info.
  --nt_profile nt_profile
                        Specify name and path of nucleotide profile file. If not provided, profile.txt in the nt_profile folder in the current working directory will be used by default
  --aa_profile aa_profile
                        Specify name and path of amino acid profile file. If not provided, profile.txt in the aa_profile folder in the current working directory will be used by default
  --nt_alleles nt_alleles
                        Specify name and path of folder containing nucleotide alleles. If not provided, the nt_allele folder in the current working directory will be used by default
  --aa_alleles aa_alleles
                        Specify name and path of folder containing amino acid alleles. If not provided, the aa_allele folder in the current working directory will be used by default
  -c concatenate_path, --concatenate_path concatenate_path
                        Specify name and path of folder into which concatenated subunit files are to be placed. If not provided, the concatenated_alleles folder in the current working directory will be used

Outputs

The concatenated alleles will be located in the provided concatenate_path. Nucleotide alleles will be in the nt subdirectory. Amino acid alleles will be in the aa subdirectory. Files are named based on the ordered alleles: stx1: stx1A_stx1B.fasta, stx2: stx2A_stx2B.fasta