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Variant annotation in Python

Project description

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 <https://pip.pypa.io/en/latest/quickstart.html>`__:

.. code:: bash

pip install varcode

Optionally, you can pre-populate metadata caches through
`PyEnsembl <https://github.com/hammerlab/pyensembl>`__ as follows:

.. code:: bash

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

This will eliminate a potential delay of several minutes required to
install the relevant data when using the Varcode for the first time.

Example
-------

.. code:: python

import varcode

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

print(variants)
### <VariantCollection from 'tcga-ovarian-cancer-variants.maf' with 6428 elements>
### -- 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)
### <EffectCollection with 789 elements>
### -- PrematureStop(variant=chr17 g.7574003G>A, transcript_name=TP53-001, transcript_id=ENST00000269305, effect_description=p.R342*)
### -- ThreePrimeUTR(variant=chr17 g.7574003G>A, transcript_name=TP53-005, transcript_id=ENST00000420246)
### -- PrematureStop(variant=chr17 g.7574003G>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 <./examples/varcode-quick_start.ipynb>`__ that demonstrates
simple use cases of Varcode

Effect Types
------------

+---------------+---------------+
| Effect type | Description |
+===============+===============+
| *AlternateSta | Replace |
| rtCodon* | annotated |
| | start codon |
| | with |
| | alternative |
| | start codon |
| | (*e.g.* |
| | "ATG>CAG"). |
+---------------+---------------+
| *ComplexSubst | Insertion and |
| itution* | deletion of |
| | multiple |
| | amino acids. |
+---------------+---------------+
| *Deletion* | Coding |
| | mutation |
| | which causes |
| | deletion of |
| | amino |
| | acid(s). |
+---------------+---------------+
| *ExonLoss* | Deletion of |
| | entire exon, |
| | significantly |
| | disrupts |
| | protein. |
+---------------+---------------+
| *ExonicSplice | Mutation at |
| Site* | the beginning |
| | or end of an |
| | exon, may |
| | affect |
| | splicing. |
+---------------+---------------+
| *FivePrimeUTR | Variant |
| * | affects 5' |
| | untranslated |
| | region before |
| | start codon. |
+---------------+---------------+
| *FrameShiftTr | A frameshift |
| uncation* | 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. |
+---------------+---------------+
| *IncompleteTr | Can't |
| anscript* | 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. |
+---------------+---------------+
| *IntronicSpli | Mutation near |
| ceSite* | the beginning |
| | or end of an |
| | intron but |
| | less likely |
| | to affect |
| | splicing than |
| | donor/accepto |
| | r |
| | mutations. |
+---------------+---------------+
| *Intronic* | Variant |
| | occurs |
| | between exons |
| | and is |
| | unlikely to |
| | affect |
| | splicing. |
+---------------+---------------+
| *NoncodingTra | Transcript |
| nscript* | doesn't code |
| | for a |
| | protein. |
+---------------+---------------+
| *PrematureSto | Insertion of |
| p* | stop codon, |
| | truncates |
| | protein. |
+---------------+---------------+
| *Silent* | Mutation in |
| | coding |
| | sequence |
| | which does |
| | not change |
| | the amino |
| | acid sequence |
| | of the |
| | translated |
| | protein. |
+---------------+---------------+
| *SpliceAccept | Mutation in |
| or* | 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. |
+---------------+---------------+
| *ThreePrimeUT | Variant |
| R* | 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 <http://alternateallele.blogspot.com/2012/03/genome-coordinate-conventions.html>`__.

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