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Run PrecisonProDB for GENCODE

PATH_OF_PRECISONPRODB is the location of PrecisionProDB.

Check this page for explanation of output files
https://github.com/ATPs/PrecisionProDB/wiki/Outputs-of-PrecisionProDB

Run with example files

variants in tsv format

cd $PATH_OF_PRECISONPRODB
cd examples

python ../src/precisionprodb/PrecisionProDB.py -m gnomAD.variant.txt.gz -g ./GENCODE/GENCODE.genome.fa.gz -p ./GENCODE/GENCODE.protein.fa.gz -f ./GENCODE/GENCODE.gtf.gz -o ./GENCODE/GENCODE.tsv -a GENCODE_GTF --PEFF

# compress files to save disk space
gzip ./GENCODE/GENCODE.tsv*

Here --PEFF means the PEFF option is enabled, and a result protein in PEFF format with VariantSimple annotations will be generated.

The output files are

  • GENCODE.tsv.pergeno.aa_mutations.csv.gz
  • GENCODE.tsv.pergeno.protein_all.fa.gz
  • GENCODE.tsv.pergeno.protein_changed.fa.gz
  • GENCODE.tsv.pergeno.protein_PEFF.fa.gz: the PEFF file.

variants in vcf format

cd $PATH_OF_PRECISONPRODB
cd examples

python ../src/precisionprodb/PrecisionProDB.py -m celline.vcf.gz -g ./GENCODE/GENCODE.genome.fa.gz -p ./GENCODE/GENCODE.protein.fa.gz -f ./GENCODE/GENCODE.gtf.gz -o ./GENCODE/GENCODE.vcf -a GENCODE_GTF --PEFF

# compress files to save disk space
gzip ./GENCODE/GENCODE.vcf*

The output files are

  • GENCODE.vcf.pergeno.aa_mutations.csv.gz
  • GENCODE.vcf.pergeno.protein_all.fa.gz
  • GENCODE.vcf.pergeno.protein_changed.fa.gz
  • GENCODE.vcf.pergeno.protein_PEFF.fa.gz
  • GENCODE.vcf.vcf2mutation_1.tsv.gz
  • GENCODE.vcf.vcf2mutation_2.tsv.gz

Novel peptide output

--peptide reports altered-protein digestion products that are absent from the canonical GENCODE proteome under the same digestion profile. It requires a real annotation SQLite file; do not use --sqlite NONE.

Run the following commands from the PrecisionProDB repository root. The first command builds the annotation SQLite. The second command enables peptide mode and automatically creates a profile-specific canonical peptide SQLite index beside it when one is not already present.

python src/precisionprodb/buildSqlite.py \
  -S examples/GENCODE/GENCODE.peptide.sqlite \
  -g examples/GENCODE/GENCODE.genome.fa.gz \
  -p examples/GENCODE/GENCODE.protein.fa.gz \
  -f examples/GENCODE/GENCODE.gtf.gz \
  -a GENCODE_GTF \
  -o examples/GENCODE/GENCODE.peptide.build \
  -t 2

python src/precisionprodb/PrecisionProDB.py \
  -m examples/celline.vcf.gz \
  -S examples/GENCODE/GENCODE.peptide.sqlite \
  -o examples/GENCODE/GENCODE.peptide \
  -a GENCODE_GTF \
  --peptide \
  -t 2

sed -n '1,4p' examples/GENCODE/GENCODE.peptide.pergeno.peptide_novel.tsv
sed -n '1,8p' examples/GENCODE/GENCODE.peptide.pergeno.peptide_novel.fa

In addition to the ordinary VCF outputs, this creates the following uncompressed files:

  • GENCODE.peptide.pergeno.peptide_novel.tsv: peptide-to-altered-protein mappings with mutation and digestion-profile annotations.
  • GENCODE.peptide.pergeno.peptide_novel.fa: nonredundant peptide sequences with PPDBpep_######|n_mappings=N headers.

The default profile uses Trypsin, two missed cleavages, lengths 7–35, full specificity, both initiator-methionine forms, and exact I/L comparison. See the Novel peptide output Wiki page for custom profiles, reusable indexes, and complete output-column descriptions.