Overview

This is the repository created for COMP483 Project by group 2:
A Python wrapper to provide a convienacne way to generate K identifiers required for KEGG Mapper, by giving assembled genome sequences.

Perequisites

• Python3
  

  • Biopython
    

• SRA-Toolkit
  For downloading FASTA from NCBI
  

• Prokka
  For rapid prokaryotic genome annotation
  

Included within wrapper

This wrapper uses SilentGene - prokka2kegg_batch to automatically convert annotated gene from Prokka's (.gtk file) to K ids required.
The python script and database required for prokka2kegg are included in the wrapper, user does not need to download or install anything for this part.

Running wrapper

-i: (required) Specifiey the FASTA source and Taxonomy information for each sample in a json format
-e: (oprional) Email used for Biopython
-o: (optional) An optional flag for user to name the output folder for each run. Defalt will give output in a folder named 'formatkresults'.

GenBank assembly accession

The following code will run the wrapper by giving GenBank assembly accession

• Runing 1 sample: GCA_002861225.1

python3 formatk.py -i '{"GCA_002861225.1": "Escherichia coli"}' 

• Runing multiple samples: GCA_002861225.1 and GCA_002861815.1

python3 formatk.py \
-i '{"GCA_002861225.1": "Escherichia coli", "GCA_002861815.1": "Lactobacillus crispatus"}'

User specified FASTA

The following code will run the wrapper with user specified FASTA

• Runing 1 sample: Escherichia_coli.FASTA

python3 formatk.py -i '{"DIR/Escherichia_coli.FASTA": "Escherichia coli"}' 

• Runing multiple samples: Escherichia_coli.FASTA and Lactobacillus_crispatus.FASTA

python3 formatk.py \
-i '{"DIR/Escherichia_coli.FASTA": "Escherichia coli", "DIR/Lactobacillus_crispatus.FASTA": "Lactobacillus crispatus"}' 

Mixing both GenBank assembly accession and user specified FASTA

The following code will run the wrapper with mixed GenBank assembly accession and user specified FASTA

• Runing multiple samples: GCA_002861225.1 and Lactobacillus_crispatus.FASTA

python3 formatk.py \
-i '{"GCA_002861225.1": "Escherichia coli", "DIR/Lactobacillus_crispatus.FASTA": "Lactobacillus crispatus"}' 

With optional flags -o and -e

The following code will run the wrapper by giving GenBank assembly accession (GCA_002861225.1) and give the results in a folder named 'TESTRUN' under '$HOME/' directory with your own email

python3 formatk.py -i '{"GCA_002861225.1": "Escherichia coli"}' -e useremail -o TESTRUN 

Output

We rename each sample by the end of the process based on sample taxonomy information and it's input file name or GenBank assembly accession as 'genus_species_filename' or 'genus_species_GenBank_ID'.

The wrapper will generate a 'formatkresults' folder under '$HOME/' directory (or user specified folder if '-o' argument is supplied), and the folder contains the following:

• formatk_out.txt
  Final gene list required by KEGG MAPPER
• formatk_out_order.txt
  The order of each sample in formatk_out.txt and KEGG
• Others
  • Downloaded assemble genome data from NCBI (if applicable)
  • Prokka folder
    Prokka generated results for each entry
  • GBK folder
    Prokka generated gbk files output for each entry
  • 2kegg
    SlientGene generated results for each entry

Test data

• E. coli: GCA_002861225.1
• L. crispatus: GCA_002861815.1
• P. mirabilis: GCA_012030515.1

Color cods for KEGG MAPPER

• Pathway mapping of two organisms (global/overview maps)
  Organism 1 #00cc33
  Organism 2 #ff3366
  Organisms 1 and 2 #3366ff
  

• Pathway mapping of multiple organisms (regular maps)
  Organism 1 #bfffbf
  Organism 2 #ffbbcc
  Organism 3 #bbccff
  Organism 4 #cfffcf
  Organism 5 #ffcfef
  Organism 6 #cfefff
  Organism 7 #dfefcf
  Organism 8 #ffefcc
  Organism 9 #dfccff
  Organism 10 #dfdfcc