simplevcf package¶
Module contents¶
Simple Pure Python VCF Parser
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class
simplevcf.Reader(stream: IO[Any])¶ Bases:
objectVCF Reader
- Parameters
stream – file-like object
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get_header() → simplevcf.header.Header¶ Get header
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get_samples() → List[str]¶ Get sample name list
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class
simplevcf.Record(CHROM: str, POS: int, ID: Optional[str], REF: str, ALT: List[str], QUAL: Optional[str], FILTER: Optional[str], INFO: Dict[str, Any], FORMAT: List[str], CALL: Dict[str, Dict[str, Any]])¶ Bases:
tupleVCF Record
Use parse method to parse VCF line
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ALT: List[str]¶ Alternative sequences
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CALL: Dict[str, Dict[str, Any]]¶ Called genotype
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CHROM: str¶ Chromosome name
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FILTER: Optional[str]¶ VCF entry Filter
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FORMAT: List[str]¶ Parsed VCF FORMAT record
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ID: Optional[str]¶ VCF entry ID
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INFO: Dict[str, Any]¶ Parsed VCF INFO record
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POS: int¶ VCF entry position
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QUAL: Optional[str]¶ Quality score
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REF: str¶ Reference sequence
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static
parse(line: str, samples: Iterable[str]) → simplevcf.Record¶ Parse VCF line and convert to Record object
- Parameters
line – A VCF line
samples – A list of sample names
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to_line(samples: List[str]) → str¶ Convert to VCF line
- Parameters
samples – Sample names
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class
simplevcf.Writer(stream: IO[Any], header: simplevcf.header.Header)¶ Bases:
objectVCF Writer
- Parameters
stream – file-like object
headers – A sequence of header lines
samples – A list of sample names
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write_record(record: simplevcf.Record)¶ Write VCF record
- Parameters
record – VCF record
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simplevcf.vcfopen(filename: str) → simplevcf.Reader¶ Open VCF file
- Parameters
filename – A VCF file name
Submodules¶
simplevcf.snpeff module¶
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class
simplevcf.snpeff.SnpEff(Allele: str, Annotation: str, Annotation_Impact: str, Gene_Name: str, Gene_ID: str, Feature_Type: str, Feature_ID: str, Transcript_BioType: str, Rank: str, HGVS_c: str, HGVS_p: str, cDNA_pos__cDNA_length: str, CDS_pos__CDS_length: str, AA_pos__AA_length: str, Distance: str, ERRORS: str)¶ Bases:
tupleSnpEff annotation representation
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AA_pos__AA_length: str¶ Alias for field number 13
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Allele: str¶ Alias for field number 0
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Annotation: str¶ Alias for field number 1
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Annotation_Impact: str¶ Alias for field number 2
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CDS_pos__CDS_length: str¶ Alias for field number 12
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Distance: str¶ Alias for field number 14
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ERRORS: str¶ Alias for field number 15
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Feature_ID: str¶ Alias for field number 6
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Feature_Type: str¶ Alias for field number 5
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Gene_ID: str¶ Alias for field number 4
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Gene_Name: str¶ Alias for field number 3
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HGVS_c: str¶ Alias for field number 9
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HGVS_p: str¶ Alias for field number 10
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Rank: str¶ Alias for field number 8
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Transcript_BioType: str¶ Alias for field number 7
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cDNA_pos__cDNA_length: str¶ Alias for field number 11
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static
parse(record: simplevcf.Record) → List[simplevcf.snpeff.SnpEff]¶ Parse VCF record
- Parameters
record – A VCF record
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simplevcf.header module¶
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class
simplevcf.header.Header(header_lines: List[HeaderLine], samples: List[str])¶ Bases:
objectVCF Header
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get_contig(info_id: str) → Optional[simplevcf.header.HeaderLine]¶
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get_format(info_id: str) → Optional[simplevcf.header.HeaderLine]¶
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get_header_lines() → List[simplevcf.header.HeaderLine]¶
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get_info(info_id: str) → Optional[simplevcf.header.HeaderLine]¶
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get_samples() → List[str]¶
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static
parse_header(lines: List[str]) → simplevcf.header.Header¶
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class
simplevcf.header.HeaderLine(line: str, header_tag: str, header_id: Optional[str], header_number: Optional[str], header_type: Optional[str], header_description: Optional[str], header_contents: Dict[str, str])¶ Bases:
tupleVCF Header line
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header_contents: Dict[str, str]¶ Dictionary of header contents
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header_description: Optional[str]¶ Description value in INFO/FORMAT
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header_id: Optional[str]¶ ID value in INFO/FORMAT
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header_number: Optional[str]¶ Nubmer value in INFO/FORMAT
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header_tag: str¶ Header tag type (INFO, FORMAT…)
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header_type: Optional[str]¶ Type value in INFO/FORMAT
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line: str¶ Raw header line
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static
parse(line: str) → simplevcf.header.HeaderLine¶ Parse single VCF Header
- Parameters
line – a header line
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