IgSNPer

a tool for transforming immunoglobulin V gene (IGHV) alleles into Single Nucleotide Polymorphisms (SNPs).

Requirements

• python 2 or 3
• Biopython
• Matplotlib
• NumPy
• pandas
• seaborn

Usage

python ig_snper.py -c config.txt -o output_dir

Example:

python ig_snper.py -c test_datasets/config_p1.txt -o ig_snper_p1_processed

Input files

Config format

TiggerOutputDir       ProjectID
Genotype_dir1         Project_id1
Genotype_dir2         Project_id2
Genotype_dir3         Project_id3

Genotype_dirN is a directory containing individual IGHV alleles inferred by TigGER tool (Gadala-Maria et al., 2019). Project identifier Project_idN is used in IgSNPer output files. An example of TiggerOutputDir can be found in data/vdjbase/tigger_results_p1/Genotypes, it corresponds to the project P1 (PRJEB26509; Gidoni et al., 2019) at the VDJbase (https://www.vdjbase.org/). The config file for the P1 project can be found in test_datasets/config_p1.txt and can take either of the following formats:

TiggerOutputDir	                          ProjectID
data/vdjbase/tigger_results_p1/Genotypes  p1

or

TiggerFilePath                           ProjectID     SubjectID
samples/P1/P1_I100_S1/P1_I100_S1.tsv     P1            P1_I100

TigGER genotype files

IgSNPer scans the directories described in the config and seeks for genotype files reported by TIgGER with names in the following format:

individualId_geno_H_binom.tab

E.g., for file P1_I1_S1_geno_H_binom.tab, individual ID is P1_I1_S1. Individual identifiers are extracted by IgSNPer and used in output files.

Output files

IgSNPer creates an output directory output_dir with the following structure:

output_dir
|_ html_reports
|_ plot_alleles
|_ plot_genotypes
|_ plot_haplotypes
|_ plot_snps
|_ txt_haplotypes_by_gene
|_ txt_snps_by_gene
|_ txt_snps_by_subject

• Directories starting with plot_ contain plots showing individual SNPs, SNPs combining alleles, haplotypes, and genotypes of IGHV genes.
• The directory html_reports contains HTML files, each of which corresponds to a single IGHV gene and combines plots corresponding to it.
• The directory txt_haplotypes_by_gene contains TXT files corresponding to IGHV genes and describing haplotypes across all individuals.
• The directory txt_snps_by_gene contains TXT files corresponding to IGHV genes and describing SNPs across all individuals.
• The directory txt_snps_by_subject contains TXT files corresponding to individuals and desribing their SNPs across all IGHV genes.

Individual SNP file

A fragment of the SNP file for individual P1_I1_S1 is shown below:

Dataset	Individual	Gene	    Haplotype   Pos	    State   AllelePos
p1	P1_I1_S1	IGHV1-18    1	        3	    G	    1
p1	P1_I1_S1	IGHV1-18    1	        5	    T	    1
p1	P1_I1_S1	IGHV1-18    1	        11	    G	    1
p1	P1_I1_S1	IGHV1-18    1	        23	    A	    1
p1	P1_I1_S1	IGHV1-18    1	        24	    G	    1
p1	P1_I1_S1	IGHV1-18    1	        95	    T	    1
p1	P1_I1_S1	IGHV1-18    1	        293	    A	    1
...
p1	P1_I1_S1	IGHV3-53    1-4	        15	    G	    1
p1	P1_I1_S1	IGHV3-53    1-4	        18	    T	    1
p1	P1_I1_S1	IGHV3-53    1-4	        33	    A/G	    1
p1	P1_I1_S1	IGHV3-53    1-4	        213	    C/G	    1
p1	P1_I1_S1	IGHV3-53    1-4	        260	    C/T	    1
...

Each line corresponds to a single V gene SNP described by a position (the column Pos) and a state (the column State). Positions are 0-based and given with respect to the IMGT allele with the minimum identifier. The identifier of an allele is the number coming after * in the allele name, e.g., identifier of allele IGHV1-69*10 is 10. The identifier of the allele determining the SNP position is provided in the column AllelePos. E.g., positions of SNPs of IGHV1-18 are provided with respect to allele IGHV1-18*01.