Package Health Score

67 / 100

security
Security review needed
popularity
Limited
maintenance
Healthy
community
Active

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Popularity

Limited

GitHub Stars: 81
Forks: 25
Contributors: 20

Direct Usage Popularity

Based on project statistics from the GitHub repository for the PyPI package varcode, we found that it has been starred 81 times.

Security

Security review needed

Security and license risk for latest version

Release Date: Jul 3, 2024
Direct Vulnerabilities: 0
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0
H
0
M
0
L
Indirect Vulnerabilities: 0
C
0
H
0
M
0
L
License Risk: 1
H
2
M
0
L

All security vulnerabilities belong to production dependencies of direct and indirect packages.

License

Apache-2.0

Security Policy

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Maintenance

Healthy

Commit Frequency

Open Issues: 33
Open PR: 0
Last Release: 5 months ago
Last Commit: 5 months ago

Further analysis of the maintenance status of varcode based on released PyPI versions cadence, the repository activity, and other data points determined that its maintenance is Healthy.

We found that varcode demonstrates a positive version release cadence with at least one new version released in the past 12 months.

In the past month we didn't find any pull request activity or change in issues status has been detected for the GitHub repository.

Community

Active

Readme: Yes
Contributing.md: Yes
Code of Conduct: Yes
Contributors: 20
Funding: No

With more than 10 contributors for the varcode repository, this is possibly a sign for a growing and inviting community.

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Package

Python Versions Compatibility: Unspecified

Age: 10 years
Latest Release: 5 months ago
Dependencies: 0 Direct
Versions: 69
Maintainers: 5
Wheels: OS Independent

Readme

Varcode

Varcode is a library for working with genomic variant data in Python and predicting the impact of those variants on protein sequences.

Installation

You can install varcode using pip:

pip install varcode

You can install required reference genome data through PyEnsembl as follows:

# Downloads and installs the Ensembl releases (75 and 76)
pyensembl install --release 75 76

Example

import varcode

# Load TCGA MAF containing variants from their
variants = varcode.load_maf("tcga-ovarian-cancer-variants.maf")

print(variants)
### 
###  -- Variant(contig=1, start=69538, ref=G, alt=A, genome=GRCh37)
###  -- Variant(contig=1, start=881892, ref=T, alt=G, genome=GRCh37)
###  -- Variant(contig=1, start=3389714, ref=G, alt=A, genome=GRCh37)
###  -- Variant(contig=1, start=3624325, ref=G, alt=T, genome=GRCh37)
###  ...

# you can index into a VariantCollection and get back a Variant object
variant = variants[0]

# groupby_gene_name returns a dictionary whose keys are gene names
# and whose values are themselves VariantCollections
gene_groups = variants.groupby_gene_name()

# get variants which affect the TP53 gene
TP53_variants = gene_groups["TP53"]

# predict protein coding effect of every TP53 variant on
# each transcript of the TP53 gene
TP53_effects = TP53_variants.effects()

print(TP53_effects)
### 
### -- PrematureStop(variant=chr17 g.7574003G&gt;A, transcript_name=TP53-001, transcript_id=ENST00000269305, effect_description=p.R342*)
### -- ThreePrimeUTR(variant=chr17 g.7574003G&gt;A, transcript_name=TP53-005, transcript_id=ENST00000420246)
### -- PrematureStop(variant=chr17 g.7574003G&gt;A, transcript_name=TP53-002, transcript_id=ENST00000445888, effect_description=p.R342*)
### -- FrameShift(variant=chr17 g.7574030_7574030delG, transcript_name=TP53-001, transcript_id=ENST00000269305, effect_description=p.R333fs)
### ...

premature_stop_effect = TP53_effects[0]

print(str(premature_stop_effect.mutant_protein_sequence))
### 'MEEPQSDPSVEPPLSQETFSDLWKLLPENNVLSPLPSQAMDDLMLSPDDIEQWFTEDPGPDEAPRMPEAAPPVAPAPAAPTPAAPAPAPSWPLSSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKMFCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRCPHHERCSDSDGLAPPQHLIRVEGNLRVEYLDDRNTFRHSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILTIITLEDSSGNLLGRNSFEVRVCACPGRDRRTEEENLRKKGEPHHELPPGSTKRALPNNTSSSPQPKKKPLDGEYFTLQIRGRERFEMF'

print(premature_stop_effect.aa_mutation_start_offset)
### 341

print(premature_stop_effect.transcript)
### Transcript(id=ENST00000269305, name=TP53-001, gene_name=TP53, biotype=protein_coding, location=17:7571720-7590856)

print(premature_stop_effect.gene.name)
### 'TP53'

If you are looking for a quick start guide, you can check out this iPython book that demonstrates simple use cases of Varcode

Effect Types

Effect type	Description
AlternateStartCodon	Replace annotated start codon with alternative start codon (e.g. "ATG>CAG").
ComplexSubstitution	Insertion and deletion of multiple amino acids.
Deletion	Coding mutation which causes deletion of amino acid(s).
ExonLoss	Deletion of entire exon, significantly disrupts protein.
ExonicSpliceSite	Mutation at the beginning or end of an exon, may affect splicing.
FivePrimeUTR	Variant affects 5' untranslated region before start codon.
FrameShiftTruncation	A frameshift which leads immediately to a stop codon (no novel amino acids created).
FrameShift	Out-of-frame insertion or deletion of nucleotides, causes novel protein sequence and often premature stop codon.
IncompleteTranscript	Can't determine effect since transcript annotation is incomplete (often missing either the start or stop codon).
Insertion	Coding mutation which causes insertion of amino acid(s).
Intergenic	Occurs outside of any annotated gene.
Intragenic	Within the annotated boundaries of a gene but not in a region that's transcribed into pre-mRNA.
IntronicSpliceSite	Mutation near the beginning or end of an intron but less likely to affect splicing than donor/acceptor mutations.
Intronic	Variant occurs between exons and is unlikely to affect splicing.
NoncodingTranscript	Transcript doesn't code for a protein.
PrematureStop	Insertion of stop codon, truncates protein.
Silent	Mutation in coding sequence which does not change the amino acid sequence of the translated protein.
SpliceAcceptor	Mutation in the last two nucleotides of an intron, likely to affect splicing.
SpliceDonor	Mutation in the first two nucleotides of an intron, likely to affect splicing.
StartLoss	Mutation causes loss of start codon, likely result is that an alternate start codon will be used down-stream (possibly in a different frame).
StopLoss	Loss of stop codon, causes extension of protein by translation of nucleotides from 3' UTR.
Substitution	Coding mutation which causes simple substitution of one amino acid for another.
ThreePrimeUTR	Variant affects 3' untranslated region after stop codon of mRNA.

Coordinate System

Varcode currently uses a "base counted, one start" genomic coordinate system, to match the Ensembl annotation database. We are planning to switch over to "space counted, zero start" (interbase) coordinates, since that system allows for more uniform logic (no special cases for insertions). To learn more about genomic coordinate systems, read this blog post.

FAQs

What is varcode?

Variant annotation in Python. Visit Snyk Advisor to see a full health score report for varcode, including popularity, security, maintenance & community analysis.

Is varcode popular?

The python package varcode receives a total of 706 weekly downloads. As such, varcode popularity was classified as limited. Visit the popularity section on Snyk Advisor to see the full health analysis.

Is varcode well maintained?

We found that varcode demonstrated a healthy version release cadence and project activity. It has a community of 20 open source contributors collaborating on the project. See the full package health analysis to learn more about the package maintenance status.

Is varcode safe to use?

While scanning the latest version of varcode, we found that a security review is needed. A total of 0 vulnerabilities or license issues were detected. See the full security scan results.

Last updated on 19 November-2024, at 01:58 (UTC).

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varcode

Variant annotation in Python For more information about how to use this package see README

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Readme

Varcode

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Readme

Varcode

Installation

Example

Effect Types

Coordinate System

FAQs

What is varcode?

Is varcode popular?

Is varcode well maintained?

Is varcode safe to use?

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Source Code

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