Salmonid_MHC_classifier

IPD-MHC classifier for Salmonids

Dependencies

Muscle, emboss (transep and water tools) which can installed with Conda as below

$ conda install muscle emboss

Uses os, sys, subprocess, Bio and ete3 packages in python. First three packages are available within python while the last two can be installed with Conda as below

$ conda install -c conda-forge biopython ete3 

Current version uses already downloaded data from IPD-MHC and the folder 'data' from github has to be downloaded and placed at the same place as the python file. This will change soon when the API access for IPD-MHC becomes publically available.

Initiation

$ python salmonid_mhc_classifier.py [input.fa] [output_folder] [report.txt] [Db_name]

input.fa: Sequences in fasta format
output_folder: Folder for output data report.txt: Name for the output report file
Db_name: SASA-DAA, SASA-DAB, SASA-UAB

Execution

Output files are saved to the [output_folder] as specified in the Each fasta record in the [input.fa] will be processed one at a time
Output: NAME.fa

Nucleotide record is translated into peptide
Output: NAME.aa

Nucleotide record is aligned with the relevant [Db_name] using muscle
Output: NAME_muscle_output.tree.txt and NAME_muscle_output.aln.txt

Muscle tree is converted to png using ete3
Output: NAME_muscle_output.tree.png

Sibligns in two neighbouring clades are extracted using ete3 Output: Detail in [report.txt]

Local alignment in performed between the query and each of the siblings at nucleotide and peptide level using Water
Output NAME_SIBLINGS_water_nt.txt and aa_txt

Sequence similarity and identity information from Water are included in the report
Output: Detail in [report.txt]

Output

Example output is provide in the folder output_example