Variant-Proteome-DB-Generator

A python command line based script for generating proteome databases for variants proteins from a list of variants.

How to use Variant-Proteome-DB-Generator

>python Variant_DB_generator.py proteome_database.fasta protein_variants_list.txt

usage: Variant_DB_generator.py [-h] -FA [-FA ...] -F [-F ...]

Custom generate proteome databases for protein variants such as SNPs from a list of SNPs corresponding to a protein.

positional arguments:
  -FA         Proteome database of interest
  -F          A .txt (text) file with a list of protein variants

optional arguments:
  -h, --help  show this help message and exit

How to extract the SnpEff annotated variants from vcf files

>python extract_annotated_variants.py test.vcf -f feature_table.txt

usage: extract_annotated_variants.py [-h]
                                     [-f FEATURE_TABLE [FEATURE_TABLE ...]]
                                     -i [-i ...]

Extract protein coding variants from snpEff annotated .vcf file and save it in .txt format

positional arguments:
  -i                    snpEff annotated .vcf files

optional arguments:
  -h, --help            show this help message and exit
  -f FEATURE_TABLE [FEATURE_TABLE ...], --feature_table FEATURE_TABLE [FEATURE_TABLE ...]
                        If snpEff provides only locus tag info, we need to
                        extract protein accession details from feature table
                        downloaded from RefSeq ftp path

How to check the uniqueness of variant peptides from variant DB search

>python Variant_peps_uniqueness.py -h
usage: Variant_peps_uniqueness.py [-h]
                                  -ip [-ip ...] -rf [-rf ...] -vf [-vf ...]

Uniqueness of variant peptides identified from the DDA database search can be
checked by matching it with reference and variant proteome databases

positional arguments:
  -ip         Exported PSMs of variant database search from Proteome
              Discoverer
  -rf         Reference proteome database of the same species in fasta format
  -vf         Variant proteome database in fasta format used for the search

optional arguments:
  -h, --help  show this help message and exit

Citation

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