Package: varcode
VarcodeVarcode is a library for working with genomic variant data in Python and predicting the impact of those variants on protein sequences.InstallationYou can install varcode usingpip:pipinstallvarcodeYou can install required reference genome data throughPyEnsemblas follows:# Downloads and installs the Ensembl releases (75 and 76)pyensemblinstall--release7576Exampleimportvarcode# Load TCGA MAF containing variants from theirvariants=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 objectvariant=variants[0]# groupby_gene_name returns a dictionary whose keys are gene names# and whose values are themselves VariantCollectionsgene_groups=variants.groupby_gene_name()# get variants which affect the TP53 geneTP53_variants=gene_groups["TP53"]# predict protein coding effect of every TP53 variant on# each transcript of the TP53 geneTP53_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)### 341print(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 outthis iPython bookthat demonstrates simple use cases of VarcodeEffect TypesEffect typeDescriptionAlternateStartCodonReplace annotated start codon with alternative  start codon (e.g."ATG>CAG").ComplexSubstitutionInsertion and deletion of multiple amino acids.DeletionCoding mutation which causes deletion of amino acid(s).ExonLossDeletion of entire exon, significantly disrupts protein.ExonicSpliceSiteMutation at the beginning or end of an exon, may affect splicing.FivePrimeUTRVariant affects 5' untranslated region before start codon.FrameShiftTruncationA frameshift which leads immediately to a stop codon (no novel amino acids created).FrameShiftOut-of-frame insertion or deletion of nucleotides, causes novel protein sequence and often premature stop codon.IncompleteTranscriptCan't determine effect since transcript annotation is incomplete (often missing either the start or stop codon).InsertionCoding mutation which causes insertion of amino acid(s).IntergenicOccurs outside of any annotated gene.IntragenicWithin the annotated boundaries of a gene but not in a region that's transcribed into pre-mRNA.IntronicSpliceSiteMutation near the beginning or end of an intron but less likely to affect splicing than donor/acceptor mutations.IntronicVariant occurs between exons and is unlikely to affect splicing.NoncodingTranscriptTranscript doesn't code for a protein.PrematureStopInsertion of stop codon, truncates protein.SilentMutation in coding sequence which does not change the amino acid sequence of the translated protein.SpliceAcceptorMutation in the last two nucleotides of an intron, likely to affect splicing.SpliceDonorMutation in the first two nucleotides of an intron, likely to affect splicing.StartLossMutation causes loss of start codon, likely result is that an alternate start codon will be used down-stream (possibly in a different frame).StopLossLoss of stop codon, causes extension of protein by translation of nucleotides from 3' UTR.SubstitutionCoding mutation which causes simple substitution of one amino acid for another.ThreePrimeUTRVariant affects 3' untranslated region after stop codon of mRNA.Coordinate SystemVarcode 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 thisblog post.