variantfile
Classes used to parse and store VCF data
VCFFile
Bases: object
- Class to instanciate a variant file (VCF)
- Used to apply a VCF file to a genome
- Instance variables:
filename
(str): path to the VCF filevcf_version
(tuple(int)): Tuple of ints to show the VCF version of the file. e.g 3.2 would be (3, 2).contig_lengths
(dict): Dictionary mapping contig_name->length for all defined contigs.format_fields_description
(dict): Dictionary mapping format_name->dict(description, id, type).records
(list(VCFRecord)): List of VCFRecord objects for each record within the file.calls
(dict): Dict of definite calls made in the VCF file, after any additional filtering has been appliedignore_filter
(bool): whether to ignore the FILTER in the VCF fileformat_fields_min_thresholds
(dict): dictionary specifying minimum thresholds to be applied to fields in the FORMAT field e.g. {'GTCONF':5}variants
(numpy.array): Numpy array of the detected variants in the VCF filenucleotide_index
(numpy.array): Array of genome indices which are affected by the VCFref_nucleotides
(numpy.array): Array of REF basesalt_nucleotides
(numpy.array): Array of ALT basesindel_length
(numpy.array): Array of lengths of insertions (+ve) or deletions (-ve) at each siteis_snp
(numpy.array): Array to act as a mask fornucleotide_index
to show which are SNPsis_het
(numpy.array): Array to act as a mask fornucleotide_index
to show which are heterozygous callsis_null
(numpy.array): Array to act as a mask fornucleotide_index
to show which are null callsis_indel
(numpy.array): Array to act as a mask fornucleotide_index
to show which are indel callssnp_distance
(int): SNP distance caused by the VCF
Source code in gumpy/variantfile.py
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__find_calls()
Private method to find changes within the genome based on the variant file.
Creates calls dict used elsewhere.
Source code in gumpy/variantfile.py
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__get_variants()
Private method to pull the variants out of the VCFFile object.
Builds arrays of the variant calls, and their respective genome indices, as well as masks to show whether there is a snp, het, null or indel call at the corresponding genome index: i.e is_snp[genome.nucleotide_number == indices[i]] gives a bool to determine if a genome has a SNP call at this position
Source code in gumpy/variantfile.py
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__init__(filename, ignore_filter=False, bypass_reference_calls=False, format_fields_min_thresholds=None, minor_population_indices=[], min_dp=None)
Constructor for the VCFFile object.
Parses the VCF file using pysam.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
filename |
str)
|
The name of the VCF file |
required |
ignore_filter |
bool
|
If True, ignore the FILTER column in the VCF file. Default is False. |
False
|
bypass_reference_calls |
bool
|
If True, skip any row in the VCF (and therefore do not record) which calls reference (i.e. 0/0). Default is False. |
False
|
format_fields_min_thresholds |
dict
|
Dict of field name in the FORMAT column and a minimum threshold to apply e.g. {'DP':5} |
None
|
minor_population_indices |
set
|
set of genome indices names within which to look for minor populations |
[]
|
min_dp |
int
|
Minimum depth to consider a call. Default is None |
None
|
Source code in gumpy/variantfile.py
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__repr__()
Overload the print function to write a summary of the VCF file
Returns:
Name | Type | Description |
---|---|---|
str |
str
|
String summarising the VCF file |
Source code in gumpy/variantfile.py
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to_df()
Convert the VCFFile to a pandas DataFrame.
Metadata is stored in the attrs
attribute of the DataFrame which may break
with some operations
(but pandas does not currently have a robust method for metadata storage...)
Returns:
Type | Description |
---|---|
DataFrame
|
pandas.DataFrame: DataFrame containing all of the information from the VCF file |
Source code in gumpy/variantfile.py
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VCFRecord
Bases: object
- Class for VCF records
- Instance variables:
chrom
(str): Name of the sample.pos
(int): Genome index for the change.ref
(str): Reference value for the nucleotide.alts
(tuple(str) | None): Alternative calls. Tuple can contain single values and indels.qual
(None): Values for quality (values other than None have yet to be found in testing files...).filter
(str): Whether this record has pass the filter.info
(dict): Dictionary of key->value for the info fields.values
(dict): Dictionary of key->value for the values. Usually this is the FORMAT field names with their corresponding values.is_filter_pass
(bool): does the filter column contain PASS?call1
(int): the index of the first callcall2
(int): the index of the second callis_reference
(bool): is the call for the reference?is_null
(bool): is the call a null call?is_heterozygous
(bool): is it a is_heterozygous call i.e. call1!=call2?is_alt
(bool): or, is the call for a single specified alt
Source code in gumpy/variantfile.py
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__init__(record, sample, min_dp)
Constructor for the VCFRecord object.
Parses the supplied pysam object and presents in a more Pythonic format
Parameters:
Name | Type | Description | Default |
---|---|---|---|
record |
VariantRecord
|
The record object |
required |
sample |
str | int)
|
Name of the sample to consider. Used for possible cases where there is more than 1 sample per record |
required |
min_dp |
int | None
|
Minimum depth to consider a call. |
required |
Source code in gumpy/variantfile.py
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__repr__()
Pretty print the record
Returns:
Name | Type | Description |
---|---|---|
str |
str
|
String representation of the record |
Source code in gumpy/variantfile.py
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