Table of Contents

  1. Translate and Reduce Alleles
  2. Inputs
  3. Running the Script
  4. Usage
  5. Outputs

Translate and Reduce Alleles

This script translates allele files from Enterobase in nucleotide format to amino acid, performs content and length checks, and removes duplicates.

In order for a translated allele to pass content and length checks, it must:

  1. Start with a Methionine residue
  2. Pass a minimum length threshold after trimming:
    • The length thresholds are:
      • ECs2973 (stx2B): 90 amino acid residues
      • ECs2974 (stx2A): 316 amino acid residues
      • ECs1205 (stx1A): 320 amino acid residues
      • ECs1206 (stx1B): 88 amino acid residues
  3. Not be a duplicate of an allele already in the reduced database

Inputs

  1. Nucleotide allele files from Enterobase in FASTA format. Download instructions.
  2. Reduced profile file prepared by profile_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_translate_reduce -a /path/to/allele_folder -p /path/to/profile_file -r /path/to/output/folder/aa_profile -t /path/to/output/folder/aa_alleles

An example with the nucleotide allele folder nt_alleles, the profile file profiles.txt in the nt_profile folder, the desired amino acid profile output folder aa_profile, and the desired amino acid allele output folder aa_alleles all in the current working directory: 

stec.py allele_translate_reduce -a nt_alleles -p nt_profile/profile.txt -r aa_profile -t aa_alleles

Usage 

usage: stec.py allele_translate_reduce [-h] [-version] [-v verbosity]
                                       [-a allele_path] [-p profile_file]
                                       [-r report_path] [-t translated_path]

Translate allele files in nucleotide format to amino acid. Remove duplicates. Keep notes

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.
  -a allele_path, --allele_path allele_path
                        Specify name and path of folder containing allele files. If not provided, the nt_alleles folder in the current working directory will be used by default
  -p profile_file, --profile_file profile_file
                        Optionally specify name and path of profile file. Parse the nucleic acid profile, and create the corresponding reduced amino acid profile
  -r report_path, --report_path report_path
                        Specify the name and path of the folder into which outputs are to be placed. If not provided, the aa_profile folder in the current working directory will be used
  -t translated_path, --translated_path translated_path
                        Specify the name and path of the folder into which alleles are to be placed. If not provided, the aa_alleles folder in the current working directory will be used

Outputs

These represent the folder structure of the directory containing the outputs

  • aa_alleles
    • notes
      • gene_name_notes.txt: text file containing the nucleotide allele, the corresponding amino acid allele, and any notes (whether it is a duplicate, trimmed, or filtered)
    • gene_name.fasta: FASTA-formatted text file containing sequences of all amino acid alleles that passed quality/content filters
    • gene_name_filtered.txt: FASTA-formatted text file containing sequences of all amino acid alleles that failed quality/content filters
  • aa_profile
    • profile
      • profile.txt: text file containing all unique amino acid profiles
      • reducing_notes.txt: text file containing all amino acid sequence types, the sequence type following duplicate reduction, and any notes
    • aa_full_profile.txt: text file containing all amino acid profiles before duplicate removal
    • aa_nt_profile_links.tsv: TSV file containing every amino acid sequence type and the corresponding nucleotide sequence type(s)
    • gene_names.txt: text file containing the extracted gene names from the analysis
    • profile.txt: copy of profile.txt from the profile folder. Allows for allele discovery without manually moving the file
  • nt_alleles
    • gene_name.fasta: FASTA-formatted text file containing sequences of all nucleotide alleles that passed quality/content filters
    • gene_name_filtered.txt: FASTA-formatted text file containing sequences of all nucleotide alleles that failed quality/content filters
  • nt_profile
    • profile.txt: text file containing all unique nucleotide profiles