stopfree 0.2.4

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stopfree

This is a rust implementation of the stopFree coding potential tool defined in Evaluating computational tools for protein-coding sequence detection: Are they up to the task?

It measures the longest stop codon free length of sequence in each of the 6 possible reading frames.

Installation

You should be able to just

pip install stopfree

because there's a bunch of pre-built wheels available on pypi.

Usage

To calculate stop codon free lengths, you need to build a list of tuples of ID and sequence, like this:

all_fasta = []
for idx, item in enumerate(read_fasta("mgi.fasta")):
    seqid = item.defline
    seq = item.sequence
    all_fasta.append((seqid, seq))

(N.B. Here I used the fasta_reader package to read a FASTA file into an iterable)

Then call the stopfree functions like this:

stop_free_run_lengths = stopfree.calculate_stop_free_runs_with_ids(all_fasta) ## Gives the number of codons with no stop codon in
gc_contents = stopfree.calculate_gc_content(all_fasta) ## Calculates the per-sequence GC content for each sequence (not across all!)
run_probabilities = stopfree.calculate_run_probability(stop_free_run_lengths, gc_contents) ## Calculated the probability of a run of the observed length

Probability calculation

We use an iid assumption, with correction for GC content of the sequence. With this, the probability of a stop codon is given by

p_stop = ((1 - p_gc)**2 * (1 + p_gc))/8

where p_gc is the gc content fraction.

So the probability of observing no stop codon in a run of k codons is therefore:

p_nostop = (1 - p_stop)**k

You can set whatever threshold for 'protein coding' you like then, based on this probability.

Better probability

The iid assumption doesn't quite account for everything. To do a really stellar job, we would want to include dinucleotide biases, and the fact that the 6 reading frames are correlated. This is some future work though for now.