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stopfree

Rust Tests

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.

Metadata

Release files for stopfree 0.2.4

For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.

Source distribution (sdist)

Source distribution for stopfree 0.2.4
File Size Uploaded Provenance
stopfree-0.2.4.tar.gz 12.1 kB With provenance Details

Built distributions (wheels)

Table of built distributions (wheels) for stopfree 0.2.4
File
stopfree-0.2.4-pp311-pypy311_pp73-musllinux_1_2_x86_64.whl PyPy 3.11 PyPy 3.11 7.3 Linux musl 1.2+ x86-64 Details
stopfree-0.2.4-pp311-pypy311_pp73-musllinux_1_2_i686.whl PyPy 3.11 PyPy 3.11 7.3 Linux musl 1.2+ x86-32 Details
stopfree-0.2.4-pp311-pypy311_pp73-musllinux_1_2_armv7l.whl PyPy 3.11 PyPy 3.11 7.3 Linux musl 1.2+ ARMv7l Details
stopfree-0.2.4-pp311-pypy311_pp73-musllinux_1_2_aarch64.whl PyPy 3.11 PyPy 3.11 7.3 Linux musl 1.2+ ARM64 Details
stopfree-0.2.4-pp311-pypy311_pp73-manylinux_2_17_x86_64.manylinux2014_x86_64.whl PyPy 3.11 PyPy 3.11 7.3 Linux glibc 2.17+ x86-64 Details
stopfree-0.2.4-pp311-pypy311_pp73-manylinux_2_17_s390x.manylinux2014_s390x.whl PyPy 3.11 PyPy 3.11 7.3 Linux glibc 2.17+ IBM System/390x Details
stopfree-0.2.4-pp311-pypy311_pp73-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl PyPy 3.11 PyPy 3.11 7.3 Linux glibc 2.17+ PowerPC 64-le Details
stopfree-0.2.4-pp311-pypy311_pp73-manylinux_2_17_i686.manylinux2014_i686.whl PyPy 3.11 PyPy 3.11 7.3 Linux glibc 2.17+ x86-32 Details
stopfree-0.2.4-pp311-pypy311_pp73-manylinux_2_17_armv7l.manylinux2014_armv7l.whl PyPy 3.11 PyPy 3.11 7.3 Linux glibc 2.17+ ARMv7l Details
stopfree-0.2.4-pp311-pypy311_pp73-manylinux_2_17_aarch64.manylinux2014_aarch64.whl PyPy 3.11 PyPy 3.11 7.3 Linux glibc 2.17+ ARM64 Details
stopfree-0.2.4-cp314-cp314t-musllinux_1_2_x86_64.whl CPython 3.14 CPython 3.14 free-threading Linux musl 1.2+ x86-64 Details
stopfree-0.2.4-cp314-cp314t-musllinux_1_2_i686.whl CPython 3.14 CPython 3.14 free-threading Linux musl 1.2+ x86-32 Details
stopfree-0.2.4-cp314-cp314t-musllinux_1_2_armv7l.whl CPython 3.14 CPython 3.14 free-threading Linux musl 1.2+ ARMv7l Details
stopfree-0.2.4-cp314-cp314t-musllinux_1_2_aarch64.whl CPython 3.14 CPython 3.14 free-threading Linux musl 1.2+ ARM64 Details
stopfree-0.2.4-cp314-cp314t-manylinux_2_17_s390x.manylinux2014_s390x.whl CPython 3.14 CPython 3.14 free-threading Linux glibc 2.17+ IBM System/390x Details
stopfree-0.2.4-cp314-cp314t-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl CPython 3.14 CPython 3.14 free-threading Linux glibc 2.17+ PowerPC 64-le Details
stopfree-0.2.4-cp314-cp314t-manylinux_2_17_armv7l.manylinux2014_armv7l.whl CPython 3.14 CPython 3.14 free-threading Linux glibc 2.17+ ARMv7l Details
stopfree-0.2.4-cp314-cp314t-manylinux_2_17_aarch64.manylinux2014_aarch64.whl CPython 3.14 CPython 3.14 free-threading Linux glibc 2.17+ ARM64 Details
stopfree-0.2.4-cp314-cp314-win_amd64.whl CPython 3.14 CPython 3.14 Windows x86-64 Details
stopfree-0.2.4-cp314-cp314-win32.whl CPython 3.14 CPython 3.14 Windows x86-32 Details
stopfree-0.2.4-cp314-cp314-musllinux_1_2_x86_64.whl CPython 3.14 CPython 3.14 Linux musl 1.2+ x86-64 Details
stopfree-0.2.4-cp314-cp314-musllinux_1_2_i686.whl CPython 3.14 CPython 3.14 Linux musl 1.2+ x86-32 Details
stopfree-0.2.4-cp314-cp314-musllinux_1_2_armv7l.whl CPython 3.14 CPython 3.14 Linux musl 1.2+ ARMv7l Details
stopfree-0.2.4-cp314-cp314-musllinux_1_2_aarch64.whl CPython 3.14 CPython 3.14 Linux musl 1.2+ ARM64 Details
stopfree-0.2.4-cp314-cp314-manylinux_2_17_x86_64.manylinux2014_x86_64.whl CPython 3.14 CPython 3.14 Linux glibc 2.17+ x86-64 Details
stopfree-0.2.4-cp314-cp314-manylinux_2_17_s390x.manylinux2014_s390x.whl CPython 3.14 CPython 3.14 Linux glibc 2.17+ IBM System/390x Details
stopfree-0.2.4-cp314-cp314-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl CPython 3.14 CPython 3.14 Linux glibc 2.17+ PowerPC 64-le Details
stopfree-0.2.4-cp314-cp314-manylinux_2_17_i686.manylinux2014_i686.whl CPython 3.14 CPython 3.14 Linux glibc 2.17+ x86-32 Details
stopfree-0.2.4-cp314-cp314-manylinux_2_17_armv7l.manylinux2014_armv7l.whl CPython 3.14 CPython 3.14 Linux glibc 2.17+ ARMv7l Details
stopfree-0.2.4-cp314-cp314-manylinux_2_17_aarch64.manylinux2014_aarch64.whl CPython 3.14 CPython 3.14 Linux glibc 2.17+ ARM64 Details
stopfree-0.2.4-cp314-cp314-macosx_11_0_arm64.whl CPython 3.14 CPython 3.14 macOS 11.0+ ARM64 Details
stopfree-0.2.4-cp313-cp313t-musllinux_1_2_x86_64.whl CPython 3.13 CPython 3.13 free-threading Linux musl 1.2+ x86-64 Details
stopfree-0.2.4-cp313-cp313t-musllinux_1_2_i686.whl CPython 3.13 CPython 3.13 free-threading Linux musl 1.2+ x86-32 Details
stopfree-0.2.4-cp313-cp313t-musllinux_1_2_armv7l.whl CPython 3.13 CPython 3.13 free-threading Linux musl 1.2+ ARMv7l Details
stopfree-0.2.4-cp313-cp313t-musllinux_1_2_aarch64.whl CPython 3.13 CPython 3.13 free-threading Linux musl 1.2+ ARM64 Details
stopfree-0.2.4-cp313-cp313t-manylinux_2_17_s390x.manylinux2014_s390x.whl CPython 3.13 CPython 3.13 free-threading Linux glibc 2.17+ IBM System/390x Details
stopfree-0.2.4-cp313-cp313t-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl CPython 3.13 CPython 3.13 free-threading Linux glibc 2.17+ PowerPC 64-le Details
stopfree-0.2.4-cp313-cp313t-manylinux_2_17_armv7l.manylinux2014_armv7l.whl CPython 3.13 CPython 3.13 free-threading Linux glibc 2.17+ ARMv7l Details
stopfree-0.2.4-cp313-cp313t-manylinux_2_17_aarch64.manylinux2014_aarch64.whl CPython 3.13 CPython 3.13 free-threading Linux glibc 2.17+ ARM64 Details
stopfree-0.2.4-cp313-cp313-win_amd64.whl CPython 3.13 CPython 3.13 Windows x86-64 Details
stopfree-0.2.4-cp313-cp313-musllinux_1_2_x86_64.whl CPython 3.13 CPython 3.13 Linux musl 1.2+ x86-64 Details
stopfree-0.2.4-cp313-cp313-musllinux_1_2_i686.whl CPython 3.13 CPython 3.13 Linux musl 1.2+ x86-32 Details
stopfree-0.2.4-cp313-cp313-musllinux_1_2_armv7l.whl CPython 3.13 CPython 3.13 Linux musl 1.2+ ARMv7l Details
stopfree-0.2.4-cp313-cp313-musllinux_1_2_aarch64.whl CPython 3.13 CPython 3.13 Linux musl 1.2+ ARM64 Details
stopfree-0.2.4-cp313-cp313-manylinux_2_17_x86_64.manylinux2014_x86_64.whl CPython 3.13 CPython 3.13 Linux glibc 2.17+ x86-64 Details
stopfree-0.2.4-cp313-cp313-manylinux_2_17_s390x.manylinux2014_s390x.whl CPython 3.13 CPython 3.13 Linux glibc 2.17+ IBM System/390x Details
stopfree-0.2.4-cp313-cp313-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl CPython 3.13 CPython 3.13 Linux glibc 2.17+ PowerPC 64-le Details
stopfree-0.2.4-cp313-cp313-manylinux_2_17_i686.manylinux2014_i686.whl CPython 3.13 CPython 3.13 Linux glibc 2.17+ x86-32 Details
stopfree-0.2.4-cp313-cp313-manylinux_2_17_armv7l.manylinux2014_armv7l.whl CPython 3.13 CPython 3.13 Linux glibc 2.17+ ARMv7l Details
stopfree-0.2.4-cp313-cp313-manylinux_2_17_aarch64.manylinux2014_aarch64.whl CPython 3.13 CPython 3.13 Linux glibc 2.17+ ARM64 Details
stopfree-0.2.4-cp313-cp313-macosx_11_0_arm64.whl CPython 3.13 CPython 3.13 macOS 11.0+ ARM64 Details
stopfree-0.2.4-cp312-cp312-win_amd64.whl CPython 3.12 CPython 3.12 Windows x86-64 Details
stopfree-0.2.4-cp312-cp312-musllinux_1_2_x86_64.whl CPython 3.12 CPython 3.12 Linux musl 1.2+ x86-64 Details
stopfree-0.2.4-cp312-cp312-musllinux_1_2_i686.whl CPython 3.12 CPython 3.12 Linux musl 1.2+ x86-32 Details
stopfree-0.2.4-cp312-cp312-musllinux_1_2_armv7l.whl CPython 3.12 CPython 3.12 Linux musl 1.2+ ARMv7l Details
stopfree-0.2.4-cp312-cp312-musllinux_1_2_aarch64.whl CPython 3.12 CPython 3.12 Linux musl 1.2+ ARM64 Details
stopfree-0.2.4-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl CPython 3.12 CPython 3.12 Linux glibc 2.17+ x86-64 Details
stopfree-0.2.4-cp312-cp312-manylinux_2_17_s390x.manylinux2014_s390x.whl CPython 3.12 CPython 3.12 Linux glibc 2.17+ IBM System/390x Details
stopfree-0.2.4-cp312-cp312-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl CPython 3.12 CPython 3.12 Linux glibc 2.17+ PowerPC 64-le Details
stopfree-0.2.4-cp312-cp312-manylinux_2_17_i686.manylinux2014_i686.whl CPython 3.12 CPython 3.12 Linux glibc 2.17+ x86-32 Details
stopfree-0.2.4-cp312-cp312-manylinux_2_17_armv7l.manylinux2014_armv7l.whl CPython 3.12 CPython 3.12 Linux glibc 2.17+ ARMv7l Details
stopfree-0.2.4-cp312-cp312-manylinux_2_17_aarch64.manylinux2014_aarch64.whl CPython 3.12 CPython 3.12 Linux glibc 2.17+ ARM64 Details
stopfree-0.2.4-cp312-cp312-macosx_11_0_arm64.whl CPython 3.12 CPython 3.12 macOS 11.0+ ARM64 Details
stopfree-0.2.4-cp311-cp311-win_amd64.whl CPython 3.11 CPython 3.11 Windows x86-64 Details
stopfree-0.2.4-cp311-cp311-musllinux_1_2_x86_64.whl CPython 3.11 CPython 3.11 Linux musl 1.2+ x86-64 Details
stopfree-0.2.4-cp311-cp311-musllinux_1_2_i686.whl CPython 3.11 CPython 3.11 Linux musl 1.2+ x86-32 Details
stopfree-0.2.4-cp311-cp311-musllinux_1_2_armv7l.whl CPython 3.11 CPython 3.11 Linux musl 1.2+ ARMv7l Details
stopfree-0.2.4-cp311-cp311-musllinux_1_2_aarch64.whl CPython 3.11 CPython 3.11 Linux musl 1.2+ ARM64 Details
stopfree-0.2.4-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl CPython 3.11 CPython 3.11 Linux glibc 2.17+ x86-64 Details
stopfree-0.2.4-cp311-cp311-manylinux_2_17_s390x.manylinux2014_s390x.whl CPython 3.11 CPython 3.11 Linux glibc 2.17+ IBM System/390x Details
stopfree-0.2.4-cp311-cp311-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl CPython 3.11 CPython 3.11 Linux glibc 2.17+ PowerPC 64-le Details
stopfree-0.2.4-cp311-cp311-manylinux_2_17_i686.manylinux2014_i686.whl CPython 3.11 CPython 3.11 Linux glibc 2.17+ x86-32 Details
stopfree-0.2.4-cp311-cp311-manylinux_2_17_armv7l.manylinux2014_armv7l.whl CPython 3.11 CPython 3.11 Linux glibc 2.17+ ARMv7l Details
stopfree-0.2.4-cp311-cp311-manylinux_2_17_aarch64.manylinux2014_aarch64.whl CPython 3.11 CPython 3.11 Linux glibc 2.17+ ARM64 Details
stopfree-0.2.4-cp311-cp311-macosx_11_0_arm64.whl CPython 3.11 CPython 3.11 macOS 11.0+ ARM64 Details
stopfree-0.2.4-cp310-cp310-win_amd64.whl CPython 3.10 CPython 3.10 Windows x86-64 Details
stopfree-0.2.4-cp310-cp310-musllinux_1_2_x86_64.whl CPython 3.10 CPython 3.10 Linux musl 1.2+ x86-64 Details
stopfree-0.2.4-cp310-cp310-musllinux_1_2_i686.whl CPython 3.10 CPython 3.10 Linux musl 1.2+ x86-32 Details
stopfree-0.2.4-cp310-cp310-musllinux_1_2_armv7l.whl CPython 3.10 CPython 3.10 Linux musl 1.2+ ARMv7l Details
stopfree-0.2.4-cp310-cp310-musllinux_1_2_aarch64.whl CPython 3.10 CPython 3.10 Linux musl 1.2+ ARM64 Details
stopfree-0.2.4-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl CPython 3.10 CPython 3.10 Linux glibc 2.17+ x86-64 Details
stopfree-0.2.4-cp310-cp310-manylinux_2_17_s390x.manylinux2014_s390x.whl CPython 3.10 CPython 3.10 Linux glibc 2.17+ IBM System/390x Details
stopfree-0.2.4-cp310-cp310-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl CPython 3.10 CPython 3.10 Linux glibc 2.17+ PowerPC 64-le Details
stopfree-0.2.4-cp310-cp310-manylinux_2_17_i686.manylinux2014_i686.whl CPython 3.10 CPython 3.10 Linux glibc 2.17+ x86-32 Details
stopfree-0.2.4-cp310-cp310-manylinux_2_17_armv7l.manylinux2014_armv7l.whl CPython 3.10 CPython 3.10 Linux glibc 2.17+ ARMv7l Details
stopfree-0.2.4-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl CPython 3.10 CPython 3.10 Linux glibc 2.17+ ARM64 Details
stopfree-0.2.4-cp39-cp39-musllinux_1_2_x86_64.whl CPython 3.9 CPython 3.9 Linux musl 1.2+ x86-64 Details
stopfree-0.2.4-cp39-cp39-musllinux_1_2_i686.whl CPython 3.9 CPython 3.9 Linux musl 1.2+ x86-32 Details
stopfree-0.2.4-cp39-cp39-musllinux_1_2_armv7l.whl CPython 3.9 CPython 3.9 Linux musl 1.2+ ARMv7l Details
stopfree-0.2.4-cp39-cp39-musllinux_1_2_aarch64.whl CPython 3.9 CPython 3.9 Linux musl 1.2+ ARM64 Details
stopfree-0.2.4-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl CPython 3.9 CPython 3.9 Linux glibc 2.17+ x86-64 Details
stopfree-0.2.4-cp39-cp39-manylinux_2_17_s390x.manylinux2014_s390x.whl CPython 3.9 CPython 3.9 Linux glibc 2.17+ IBM System/390x Details
stopfree-0.2.4-cp39-cp39-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl CPython 3.9 CPython 3.9 Linux glibc 2.17+ PowerPC 64-le Details
stopfree-0.2.4-cp39-cp39-manylinux_2_17_i686.manylinux2014_i686.whl CPython 3.9 CPython 3.9 Linux glibc 2.17+ x86-32 Details
stopfree-0.2.4-cp39-cp39-manylinux_2_17_armv7l.manylinux2014_armv7l.whl CPython 3.9 CPython 3.9 Linux glibc 2.17+ ARMv7l Details
stopfree-0.2.4-cp39-cp39-manylinux_2_17_aarch64.manylinux2014_aarch64.whl CPython 3.9 CPython 3.9 Linux glibc 2.17+ ARM64 Details
stopfree-0.2.4-cp38-cp38-musllinux_1_2_x86_64.whl CPython 3.8 CPython 3.8 Linux musl 1.2+ x86-64 Details
stopfree-0.2.4-cp38-cp38-musllinux_1_2_i686.whl CPython 3.8 CPython 3.8 Linux musl 1.2+ x86-32 Details
stopfree-0.2.4-cp38-cp38-musllinux_1_2_armv7l.whl CPython 3.8 CPython 3.8 Linux musl 1.2+ ARMv7l Details
stopfree-0.2.4-cp38-cp38-musllinux_1_2_aarch64.whl CPython 3.8 CPython 3.8 Linux musl 1.2+ ARM64 Details
stopfree-0.2.4-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl CPython 3.8 CPython 3.8 Linux glibc 2.17+ x86-64 Details
stopfree-0.2.4-cp38-cp38-manylinux_2_17_s390x.manylinux2014_s390x.whl CPython 3.8 CPython 3.8 Linux glibc 2.17+ IBM System/390x Details
stopfree-0.2.4-cp38-cp38-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl CPython 3.8 CPython 3.8 Linux glibc 2.17+ PowerPC 64-le Details
stopfree-0.2.4-cp38-cp38-manylinux_2_17_i686.manylinux2014_i686.whl CPython 3.8 CPython 3.8 Linux glibc 2.17+ x86-32 Details
stopfree-0.2.4-cp38-cp38-manylinux_2_17_armv7l.manylinux2014_armv7l.whl CPython 3.8 CPython 3.8 Linux glibc 2.17+ ARMv7l Details
stopfree-0.2.4-cp38-cp38-manylinux_2_17_aarch64.manylinux2014_aarch64.whl CPython 3.8 CPython 3.8 Linux glibc 2.17+ ARM64 Details

Total release size: 46.0 MB

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Download URL stopfree-0.2.4-pp311-pypy311_pp73-musllinux_1_2_i686.whl
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