fastadigeststats

This script allows you to digest a fasta file with the specified enzymes, and ascertain what sort of proteome coverage can be expected with those enzymes.

Example usage

python fastadigeststats.py -f /home/chris/ref/RefSeq62.fa --enzyme trypsin

This will output:

522520 total peptides after digesting with trypsin
68740 proteins found out of 68835 total proteins in database.
24884 of these detectable proteins may be uniquely identified.
...tsv contents if no file is provided
average coverage is 0.6181 over entire proteome
average coverage is 0.6182 over detected proteins

Along with a tab delimited file (if specified, here we are just outputting to the screen) giving information on the proteins detectable, the coverage of the protein, if the protein can be uniquely identified, and more.

To digest with multiple enzymes, we just add them to the --enzyme parameter:

python fastadigeststats.py -f /home/chris/ref/RefSeq62.fa --enzyme trypsin,lysc

which outputs:

processing trypsin
522520 total peptides after digesting with trypsin
processing lysc
530439 total peptides after digesting with lysc
68759 proteins found out of 68835 total proteins in database.
25106 of these detectable proteins may be uniquely identified.
average coverage is 0.6308 over entire proteome
average coverage is 0.6300 over detected proteins

By default, it performs serial digestion in the order of enzymes specified (ie, here, it would digest with trypsin, then the products would be digested with lys-c -- similar to a FASP approach). We can add the --parallel flag to digest each independently.

The entire proteome means that we can detect via mass spec 63.08% of the all sequences within the proteome. The 63.00% of the detected proteome means that, over all detected proteins, we have 63% coverage.