The exports module

CIViCpy supports exporting of CIViC records to Variant Call Format (VCF) files. This enables downstream analyses such as integrating with IGV, VEP, and other common bioinformatics tools. VCF exports are maintained via the exports module:

>>>from civicpy import exports

Other file formats are planned for future releases. Suggestions are welcome on our GitHub issues page.

VCF

VCFs are written using the VCFWriter class, to which you add civic.Assertion, civic.Variant, civic.Gene, or civic.Evidence records using the addrecord or addrecords methods. The VCF output has one line per variant. Passing civic.Assertion, civic.Gene, or civic.Evidence objects will expand the record to all variants linked to those objects.

The addrecord function supports various variant types, depending on the curated coordinates available for a variant. All variants require the chromosome name and start position. For SNVs and complex variants the reference sequence and variant sequence information also need to be available. By contrast, insertions require only variant sequence information and deletions require only reference sequence information. Variants that do not meet these minimum requirements will not be added and a warning message is emitted instead. Fusions and other variants with a second set of coordinates are currently not supported.

In order to verify whether a variant can be added to a VCFWriter object, the convenience method is_valid_for_vcf can be called on a civic.Variant object before calling addrecord. Those variants that are unable to be exported into the VCF format are still retrievable as CIViCpy records. Once all desired variants are added to the VCFWriter object, writerecords needs to be called to write the VCF file.

The variants added to the VCFWriter object are written to the VCF file, one VCF record for each civic.Variant object. If two variants share the same chromosome, start position, and reference allele(s), they will not be combined into one VCF record but will instead be written as separate VCF records. Additional CIViC data are added to the VCF as annotations to the CSQ (consequence) INFO field. All CIViC molcular profiles that this variant is a part of are retrieved and all evidence items and assertions linked to these molecular profiles are added to the CSQ field with one CSQ entry for each evidence item and/or assertion. Whether a specific CSQ entry reflects an evidence item or an assertion is determined by the CIViC Entity Type CSQ field. To differentiate special characters in the field values from field delimiters, spaces are replaced with underscores and other special characters are hex-encoded. By utilizing the CSQ field for annotations, the resulting VCF is compatible for import into Google BigQuery (git.io/bigquery-variant-annotation).

VCF CSQ Field Attributes

CSQ Field	Description	Compound Field [*]
Allele	Alternate allele	No
Consequence	CIViC sequence ontology variant types for this variant	Yes
SYMBOL	HGNC gene symbol for the gene associated with this variant	No
Entrez Gene ID	Entrez gene identifier for the gene associated with this variant	No
Feature_type	“transcript”	No
Feature	The Ensembl identifier for the CIViC representative transcripts of this variant	No
HGVSc	Variant representation using HGVS notation (DNA level), corresponding to the Feature	No
HGVSp	Variant representation using HGVS notation (Protein level), corresponding to the Feature	No
CIViC Variant Name	The CIViC variant name of this variant	No
CIViC Variant ID	The CIViC internal identifier for this variant	No
CIViC Variant Aliases	CIViC aliases for this variant	Yes
CIViC Variant URL	CIViC URL for this variant	No
CIViC Molecular Profile Name	The CIViC molecular profile name for the molecular profile of the evidence item or assertion described in this CSQ record. The molecular profile may either be a simple molecular profile for just this variant or a complex molecular profile involving this variant in combination with other CIViC variants.	No
CIViC Molecular Profile ID	The CIViC internal identifier for the molecular profile	No
CIViC Molecular Profile Aliases	CIViC aliases for this molecular profile	Yes
CIViC Molecular Profile URL	CIViC URL for this molecular profile	No
CIViC HGVS	CIViC HGVS strings for this variant	Yes
Allele Registry ID	The allele registry identifier for this variant	No
ClinVar IDs	ClinVar IDs associated with this variant	Yes
CIViC Molecular Profile Score	The CIViC score reflecting the reelative abundance of total available curated evidence for this molecular profile	No
CIViC Entity Type	The type of entity being annotated, either “evidence” or “assertion”	No
CIViC Entity ID	The CIViC internal identifier for the entity being annotated	No
CIViC Entity URL	The CIViC direct URL to the entity being annotated	No
CIViC Entity Source	For evidence entities, the identifier of the publication used to create the evidence including the source type in the format “sourceId_(sourceType)”	No
CIViC Entity Variant Origin	The variant origin of the entity being annotated, either “Somatic”, “Rare Germline”, “Common Germline”, “Unknown”, “N/A”, or “Mixed”	No
CIViC Entity Status	The status of the CIViC entity being annotated, either “submitted”, “accepted”, or “rejected”	No
CIViC Entity Significance	The type of signifiance of the entity being annotated	No
CIViC Entity Direction	The direction of the significance of the entity being annotated, either “Supports”, or “Does Not Support”	No
CIViC Entity Disease	The cancer or cancer subtype context for the entity being annotated	No
CIViC Entity Therapies	A list of therapies applicable to the entity being annotated	Yes
CIViC Entity Therapy Interaction Type	A term describing now more than one therapy interact with each other in the context of the entity being annotated, either “Combination”, “Sequential”, or “Substitutes”	No
CIViC Evidence Phenotypes	A list of HPO phenotype terms linked to entity being annotated	Yes
CIViC Evidence Level	For evidence entities, a level describing the robustness of the of the study supporting the evidence	No
CIViC Evidence Rating	For evidence entities, a 1-5 rating indicating the curator’s confidence in the quality of the summarized evidence as a number of stars	No
CIViC Assertion ACMG Codes	For assertion entities, a list of ACMG codes used in the assessment of the variant under the ACMG/AMP classification guidelines	Yes
CIViC Assertion AMP Category	For assertion entities, a clinical classification by AMP/ASCO/CAP guidelines	No
CIViC Assertion NCCN Guideline	For assertoin entities, a string of the NCCN guideline and version	No
CIVIC Assertion Regulatory Approval	For assertion entities, a boolean indicating whether or not the therapies in this assertion have regulatory approval for the treatment of the assertion disease	No
CIVIC Assertion FDA Companion Test	For assertion entities, a boolean indication whether or not theassertion has an associated FDA companion test	No

[*]

Compound fields contain multiple values and use the ampersand (&) character to delineate values

VCFWriter

class exports.VCFWriter(f, version=4.2)

Parameters:

f (filehandle) – A filehandle for the VCF output file

addrecord(civic_record)

Takes either a civic.Evidence, civic.Assertion, civic.Variant, civic.Gene, or civic.MolecularProfile object and adds all civic.Variant objects associated with it to the VCFWriter object for processing and writing to the VCF.

Parameters:

civic_record (civic.CivicRecord) – Either a civic.Evidence, civic.Assertion, civic.Variant, civic.Gene, or civic.MolecularProfile object

addrecords(civic_records)

Takes multiple civic.Evidence, civic.Assertion, civic.Variant, and/or civic.Gene objects and adds all civic.Variant objects associated with them to the VCFWriter object for processing and writing to the VCF. civic_records can contain a mix of these object types.

Parameters:

civic_records (list) – A list of a civic.Evidence, civic.Assertion, civic.Variant, and/or civic.Gene objects

writeheader()

Writes the header lines to the VCF file.

writerecords(with_header=True)

Takes all variant objects saved to the VCFWriter object, processes them, and outputs them to the VCF file

Parameters:

with_header (bool) – Indicates weather or not the VCF header lines should be written as part of this function call.

Example

Here’s an example of how to export all variants from CIViC to VCF:

from civicpy import civic, exports

with open('civic_variants.vcf', 'w', newline='') as file:
        w = exports.VCFWriter(file)
        all_variants = civic.get_all_variants()
        w.addrecords(all_variants)
        w.writerecords()