vcfpy package¶
Submodules¶
vcfpy.bgzf module¶
Support code for writing BGZF files
Shamelessly taken from Biopython
-
class
vcfpy.bgzf.
BgzfWriter
(filename=None, mode='w', fileobj=None, compresslevel=6)[source]¶ Bases:
object
-
close
()[source]¶ Flush data, write 28 bytes BGZF EOF marker, and close BGZF file. samtools will look for a magic EOF marker, just a 28 byte empty BGZF block, and if it is missing warns the BAM file may be truncated. In addition to samtools writing this block, so too does bgzip - so this implementation does too.
-
-
vcfpy.bgzf.
make_virtual_offset
(block_start_offset, within_block_offset)[source]¶ Compute a BGZF virtual offset from block start and within block offsets. The BAM indexing scheme records read positions using a 64 bit ‘virtual offset’, comprising in C terms: block_start_offset << 16 | within_block_offset Here block_start_offset is the file offset of the BGZF block start (unsigned integer using up to 64-16 = 48 bits), and within_block_offset within the (decompressed) block (unsigned 16 bit integer). >>> make_virtual_offset(0, 0) 0 >>> make_virtual_offset(0, 1) 1 >>> make_virtual_offset(0, 2**16 - 1) 65535 >>> make_virtual_offset(0, 2**16) Traceback (most recent call last): ... ValueError: Require 0 <= within_block_offset < 2**16, got 65536 >>> 65536 == make_virtual_offset(1, 0) True >>> 65537 == make_virtual_offset(1, 1) True >>> 131071 == make_virtual_offset(1, 2**16 - 1) True >>> 6553600000 == make_virtual_offset(100000, 0) True >>> 6553600001 == make_virtual_offset(100000, 1) True >>> 6553600010 == make_virtual_offset(100000, 10) True >>> make_virtual_offset(2**48, 0) Traceback (most recent call last): ... ValueError: Require 0 <= block_start_offset < 2**48, got 281474976710656
vcfpy.exceptions module¶
Exceptions for the vcfpy module
-
exception
vcfpy.exceptions.
HeaderNotFound
[source]¶ Bases:
vcfpy.exceptions.VCFPyException
Raised when a VCF header could not be found
-
exception
vcfpy.exceptions.
IncorrectVCFFormat
[source]¶ Bases:
vcfpy.exceptions.VCFPyException
Raised on problems parsing VCF
-
exception
vcfpy.exceptions.
InvalidHeaderException
[source]¶ Bases:
vcfpy.exceptions.VCFPyException
Raised in the case of invalid header formatting
-
exception
vcfpy.exceptions.
InvalidRecordException
[source]¶ Bases:
vcfpy.exceptions.VCFPyException
Raised in the case of invalid record formatting
vcfpy.header module¶
Code for representing the VCF header part
The VCF header class structure is modeled after HTSJDK
-
class
vcfpy.header.
AltAlleleHeaderLine
(key, value, mapping, warning_helper=<vcfpy.warn_utils.WarningHelper object>)[source]¶ Bases:
vcfpy.header.SimpleHeaderLine
Alternative allele header line
Mostly used for defining symbolic alleles for structural variants and IUPAC ambiguity codes
-
classmethod
from_mapping
(klass, mapping)[source]¶ Construct from mapping, not requiring the string value
-
id
= None¶ name of the alternative allele
-
classmethod
-
class
vcfpy.header.
CompoundHeaderLine
(key, value, mapping, warning_helper=<vcfpy.warn_utils.WarningHelper object>)[source]¶ Bases:
vcfpy.header.HeaderLine
Base class for compound header lines, currently format and header lines
Compound header lines describe fields that can have more than one entry.
-
mapping
= None¶ OrderedDict with key/value mapping
-
value
¶
-
-
class
vcfpy.header.
ContigHeaderLine
(key, value, mapping, warning_helper=<vcfpy.warn_utils.WarningHelper object>)[source]¶ Bases:
vcfpy.header.SimpleHeaderLine
Contig header line
Most importantly, parses the
'length'
key into an integer-
classmethod
from_mapping
(klass, mapping)[source]¶ Construct from mapping, not requiring the string value
-
id
= None¶ name of the contig
-
length
= None¶ length of the contig,
None
if missing
-
classmethod
-
vcfpy.header.
FORMAT_TYPES
= ('Integer', 'Float', 'Character', 'String')¶ valid FORMAT value types
-
class
vcfpy.header.
FieldInfo
(type_, number, description=None)[source]¶ Bases:
object
Core information for describing field type and number
-
description
= None¶ Description for the header field, optional
-
number
= None¶ Number description, either an int or constant
-
type
= None¶ The type, one of INFO_TYPES or FORMAT_TYPES
-
-
class
vcfpy.header.
FilterHeaderLine
(key, value, mapping, warning_helper=<vcfpy.warn_utils.WarningHelper object>)[source]¶ Bases:
vcfpy.header.SimpleHeaderLine
FILTER header line
-
description
= None¶ description for the filter,
None
if missing
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classmethod
from_mapping
(klass, mapping)[source]¶ Construct from mapping, not requiring the string value
-
id
= None¶ token for the filter
-
-
class
vcfpy.header.
FormatHeaderLine
(key, value, mapping, warning_helper=<vcfpy.warn_utils.WarningHelper object>)[source]¶ Bases:
vcfpy.header.CompoundHeaderLine
Header line for FORMAT fields
-
description
= None¶ description, should be given,
None
if not given
-
classmethod
from_mapping
(klass, mapping)[source]¶ Construct from mapping, not requiring the string value
-
id
= None¶ key in the INFO field
-
source
= None¶ source of INFO field,
None
if not given
-
type
= None¶ value type
-
version
= None¶ version of INFO field,
None
if not given
-
-
vcfpy.header.
HEADER_NUMBER_ALLELES
= 'A'¶ number of alleles excluding reference
-
vcfpy.header.
HEADER_NUMBER_GENOTYPES
= 'G'¶ number of genotypes
-
vcfpy.header.
HEADER_NUMBER_REF
= 'R'¶ number of alleles including reference
-
vcfpy.header.
HEADER_NUMBER_UNBOUNDED
= '.'¶ unbounded number of values
-
class
vcfpy.header.
Header
(lines=[], samples=None, warning_helper=<vcfpy.warn_utils.WarningHelper object>)[source]¶ Bases:
object
Represent header of VCF file
While this class allows mutating records, it should not be changed once it has been assigned to
This class provides function for adding lines to a header and updating the supporting index data structures. There is no explicit API for removing header lines, the best way is to reconstruct a new
Header
instance with a filtered list of header lines.-
lines
= None¶ list
of :py:HeaderLine objects
-
samples
= None¶ SamplesInfo
object
-
-
class
vcfpy.header.
HeaderLine
(key, value, warning_helper=<vcfpy.warn_utils.WarningHelper object>)[source]¶ Bases:
object
Base class for VCF header lines
-
key
= None¶ str
with key of header line
-
value
¶
-
warning_helper
= None¶ Helper for printing warnings
-
-
vcfpy.header.
INFO_TYPES
= ('Integer', 'Float', 'Flag', 'Character', 'String')¶ valid INFO value types
-
class
vcfpy.header.
InfoHeaderLine
(key, value, mapping, warning_helper=<vcfpy.warn_utils.WarningHelper object>)[source]¶ Bases:
vcfpy.header.CompoundHeaderLine
Header line for INFO fields
Note that the
Number
field will be parsed into anint
if possible. Otherwise, the constantsHEADER_NUMBER_*
will be used.-
description
= None¶ description, should be given,
None
if not given
-
classmethod
from_mapping
(klass, mapping)[source]¶ Construct from mapping, not requiring the string value
-
id
= None¶ key in the INFO field
-
source
= None¶ source of INFO field,
None
if not given
-
type
= None¶ value type
-
version
= None¶ version of INFO field,
None
if not given
-
-
vcfpy.header.
LINES_WITH_ID
= ('ALT', 'contig', 'FILTER', 'FORMAT', 'INFO', 'META', 'PEDIGREE', 'SAMPLE')¶ header lines that contain an “ID” entry
-
class
vcfpy.header.
MetaHeaderLine
(key, value, mapping, warning_helper=<vcfpy.warn_utils.WarningHelper object>)[source]¶ Bases:
vcfpy.header.SimpleHeaderLine
Alternative allele header line
Used for defining set of valid values for samples keys
-
classmethod
from_mapping
(klass, mapping)[source]¶ Construct from mapping, not requiring the string value
-
id
= None¶ name of the alternative allele
-
classmethod
-
class
vcfpy.header.
PedigreeHeaderLine
(key, value, mapping, warning_helper=<vcfpy.warn_utils.WarningHelper object>)[source]¶ Bases:
vcfpy.header.SimpleHeaderLine
Header line for defining a pedigree entry
-
classmethod
from_mapping
(klass, mapping)[source]¶ Construct from mapping, not requiring the string value
-
id
= None¶ name of the alternative allele
-
classmethod
-
vcfpy.header.
RESERVED_INFO
= {'CIEND': FieldInfo('Integer', 2, 'Confidence interval around END for imprecise variants'), 'DPADJ': FieldInfo('Integer', '.', 'Read Depth of adjacency'), 'ADR': FieldInfo('Integer', 'R', 'Reverse read depth for each allele'), 'CIPOS': FieldInfo('Integer', 2, 'Confidence interval around POS for imprecise variants'), 'CILEN': FieldInfo('Integer', 2, 'Confidence interval around the inserted material between breakends'), 'DB': FieldInfo('Flag', 0, 'dbSNP membership'), 'SVTYPE': FieldInfo('String', 1, 'Type of structural variant'), 'DBVARID': FieldInfo('String', 1, 'ID of this element in DBVAR'), 'IMPRECISE': FieldInfo('Flag', 0, 'Imprecise structural variation'), 'CIGAR': FieldInfo('String', 'A', 'CIGAR string describing how to align each ALT allele to the reference allele'), 'EVENT': FieldInfo('String', 1, 'ID of event associated to breakend'), 'H2': FieldInfo('Flag', 0, 'Membership in HapMap 2'), 'AF': FieldInfo('Float', 'A', 'Allele frequency for each ALT allele in the same order as listed: used for estimating from primary data not called genotypes'), 'AC': FieldInfo('Integer', 'A', 'Allele count in genotypes, for each ALT allele, in the same order as listed'), 'CNADJ': FieldInfo('Integer', '.', 'Copy number of adjacency'), 'PARID': FieldInfo('String', 1, 'ID of partner breakend'), 'NOVEL': FieldInfo('Flag', 0, 'Indicates a novel structural variation'), 'DBRIPID': FieldInfo('String', 1, 'ID of this element in DBRIP'), 'ADF': FieldInfo('Integer', 'R', 'Forward read depth for each allele'), 'AA': FieldInfo('String', 1, 'Ancestral Allele'), 'DP': FieldInfo('Integer', 1, 'Read Depth of segment containing breakend'), 'CICNADJ': FieldInfo('Integer', '.', 'Confidence interval around copy number for the adjacency'), 'HOMSEQ': FieldInfo('String', '.', 'Sequence of base pair identical micro-homology at event breakpoints'), 'NS': FieldInfo('Integer', 1, 'Number of samples with data'), 'MATEID': FieldInfo('String', '.', 'ID of mate breakends'), 'AN': FieldInfo('Integer', 1, 'Total number of alleles in called genotypes'), 'SB': FieldInfo('Integer', 4, 'Strand bias at this position'), 'HOMLEN': FieldInfo('Integer', '.', 'Length of base pair identical micro-homology at event breakpoints'), 'H3': FieldInfo('Flag', 0, 'Membership in HapMap 3'), 'CN': FieldInfo('Integer', 1, 'Copy number of segment containing breakend'), 'MQ': FieldInfo('Integer', 1, 'RMS mapping quality'), 'CICN': FieldInfo('Integer', 2, 'Confidence interval around copy number for the segment'), '1000G': FieldInfo('Flag', 0, 'Membership in 1000 Genomes'), 'AD': FieldInfo('Integer', 'R', 'Total read depth for each allele'), 'END': FieldInfo('Integer', 1, 'End position of the variant described in this record (for symbolic alleles)'), 'MEINFO': FieldInfo('String', 4, 'Mobile element info of the form NAME,START,END,POLARITY'), 'BKPTID': FieldInfo('String', '.', 'ID of the assembled alternate allele in the assembly file'), 'METRANS': FieldInfo('String', 4, 'Mobile element transduction info of the form CHR,START,END,POLARITY'), 'MQ0': FieldInfo('Integer', 1, 'Number of MAPQ == 0 reads covering this record'), 'SVLEN': FieldInfo('Integer', 1, 'Difference in length between REF and ALT alleles'), 'BQ': FieldInfo('Float', 1, 'RMS base quality at this position'), 'VALIDATED': FieldInfo('Flag', 0, 'Validated by follow-up experiment'), 'SOMATIC': FieldInfo('Flag', 0, 'Indicates that the record is a somatic mutation, for cancer genomics'), 'DGVID': FieldInfo('String', 1, 'ID of this element in Database of Genomic Variation')}¶ Reserved fields for INFO from VCF v4.3
-
class
vcfpy.header.
SampleHeaderLine
(key, value, mapping, warning_helper=<vcfpy.warn_utils.WarningHelper object>)[source]¶ Bases:
vcfpy.header.SimpleHeaderLine
Header line for defining a SAMPLE entry
-
classmethod
from_mapping
(klass, mapping)[source]¶ Construct from mapping, not requiring the string value
-
id
= None¶ name of the alternative allele
-
classmethod
-
class
vcfpy.header.
SamplesInfos
(sample_names)[source]¶ Bases:
object
Helper class for handling and mapping of sample names to numeric indices
-
name_to_idx
= None¶ mapping from sample name to index
-
names
= None¶ list of sample names
-
-
class
vcfpy.header.
SimpleHeaderLine
(key, value, mapping, warning_helper=<vcfpy.warn_utils.WarningHelper object>)[source]¶ Bases:
vcfpy.header.HeaderLine
Base class for simple header lines, currently contig and filter header lines
Raises: vcfpy.exceptions.InvalidHeaderException
in the case of missing key"ID"
-
mapping
= None¶ collections.OrderedDict
with key/value mapping of the attributes
-
value
¶
-
-
vcfpy.header.
VALID_NUMBERS
= ('A', 'R', 'G', '.')¶ valid values for “Number” entries, except for integers
vcfpy.parser module¶
Parsing of VCF files from str
-
class
vcfpy.parser.
FormatChecker
[source]¶ Bases:
object
Helper class for checking a FORMAT field
-
header
= None¶ VCFHeader to use for checking
-
run
(call, num_alts)[source]¶ Check
FORMAT
of a record.CallCurrently, only checks for consistent counts are implemented
-
warning_helper
= None¶ helper class for printing warnings
-
-
class
vcfpy.parser.
HeaderChecker
(warning_helper)[source]¶ Bases:
object
Helper class for checking a VCF header
-
run
(header)[source]¶ Check the header
Warnings will be printed using
self.warning_helper
while errors will raise an exception.Raises: vcfpy.exceptions.InvalidHeaderException
in the case of severe errors reading the header
-
warning_helper
= None¶ helper class for printing warnings
-
-
class
vcfpy.parser.
HeaderLineParserBase
(warning_helper)[source]¶ Bases:
object
Parse into appropriate HeaderLine
-
parse_key_value
(key, value)[source]¶ Parse the key/value pair
Parameters: - key (str) – the key to use in parsing
- value (str) – the value to parse
Returns: vcfpy.header.HeaderLine
object
-
warning_helper
= None¶ WarningHelper
to use for print warnings
-
-
class
vcfpy.parser.
HeaderParser
(warning_helper)[source]¶ Bases:
object
Helper class for parsing a VCF header
-
parse_line
(line)[source]¶ Parse VCF header
line
(trailing ‘ ‘ or ‘ ‘ is ignored)param str line: str
with line to parseparam dict sub_parsers: dict
mapping header line types to appropriate parser objectsreturns: appropriate HeaderLine
parsed fromline
raises: vcfpy.exceptions.InvalidHeaderException
if there was a problem parsing the file
-
sub_parsers
= None¶ Sub parsers to use for parsing the header lines
-
warning_helper
= None¶ WarningHelper to use for printing warnings
-
-
class
vcfpy.parser.
InfoChecker
(header, warning_helper)[source]¶ Bases:
object
Helper class for checking an INFO field
-
header
= None¶ VCFHeader to use for checking
-
run
(key, value, num_alts)[source]¶ Check value in INFO[key] of record
Currently, only checks for consistent counts are implemented
Parameters: - key (str) – key of INFO entry to check
- value – value to check
- alts (int) – list of alternative alleles, for length
-
warning_helper
= None¶ helper class for printing warnings
-
-
class
vcfpy.parser.
MappingHeaderLineParser
(warning_helper, line_class)[source]¶ Bases:
vcfpy.parser.HeaderLineParserBase
Parse into HeaderLine (no particular structure)
-
line_class
= None¶ the class to use for the VCF header line
-
-
class
vcfpy.parser.
Parser
(stream, path=None, record_checks=[])[source]¶ Bases:
object
Class for line-wise parsing of VCF files
In most cases, you want to use
vcfpy.reader.Reader
instead.Parameters: - stream –
file
-like object to read from - path (str) – path the VCF is parsed from, for display purposes only, optional
-
header
= None¶ header, once it has been read
-
parse_header
()[source]¶ Read and parse
vcfpy.header.Header
from file, set intoself.header
and return itReturns: vcfpy.header.Header
Raises: vcfpy.exceptions.InvalidHeaderException
in the case of problems reading the header
-
parse_next_record
()[source]¶ Read, parse and return next
vcfpy.record.Record
Returns: next VCF record or None
if at endRaises: vcfpy.exceptions.InvalidRecordException
in the case of problems reading the record
-
record_checks
= None¶ checks to perform, can contain ‘INFO’ and ‘FORMAT’
-
samples
= None¶ vcfpy.header.SamplesInfos
with sample information; set on parsing the header
-
warning_helper
= None¶ helper for printing warnings
- stream –
-
class
vcfpy.parser.
QuotedStringSplitter
(delim=', ', quote='"', brackets='[]')[source]¶ Bases:
object
Helper class for splitting quoted strings
Has support for interpreting quoting strings but also brackets. Meant for splitting the VCF header line dicts
-
ARRAY
= 3¶ state constant for array
-
DELIM
= 4¶ state constant for delimiter
-
ESCAPED
= 2¶ state constant for delimiter
-
NORMAL
= 0¶ state constant for normal
-
QUOTED
= 1¶ state constant for quoted
-
delim
= None¶ string delimiter
-
quote
= None¶ quote character
-
run
(s)[source]¶ Split string
s
at delimiter, correctly interpreting quotesFurther, interprets arrays wrapped in one level of
[]
. No recursive brackets are interpreted (as this would make the grammar non-regular and currently this complexity is not needed). Currently, quoting inside of braces is not supported either. This is just to support the example from VCF v4.3.
-
-
class
vcfpy.parser.
RecordParser
(header, samples, warning_helper, record_checks=[])[source]¶ Bases:
object
Helper class for parsing VCF records
-
header
= None¶ Header with the meta information
-
parse_line
(line_str)[source]¶ Parse line from file (including trailing line break) and return resulting Record
-
record_checks
= None¶ The checks to perform, can contain ‘INFO’ and ‘FORMAT’
-
samples
= None¶ SamplesInfos with sample information
-
warning_helper
= None¶ Helper class for printing warnings
-
-
vcfpy.parser.
SUPPORTED_VCF_VERSIONS
= ('VCFv4.0', 'VCFv4.1', 'VCFv4.2', 'VCFv4.3')¶ Supported VCF versions, a warning will be issued otherwise
-
class
vcfpy.parser.
StupidHeaderLineParser
(warning_helper)[source]¶ Bases:
vcfpy.parser.HeaderLineParserBase
Parse into HeaderLine (no particular structure)
-
vcfpy.parser.
build_header_parsers
(warning_helper)[source]¶ Return mapping for parsers to use for each VCF header type
Inject the WarningHelper into the parsers.
-
vcfpy.parser.
convert_field_value
(key, type_, value)[source]¶ Convert atomic field value according to the type
-
vcfpy.parser.
parse_breakend
(alt_str)[source]¶ Parse breakend and return tuple with results, parameters for BreakEnd constructor
-
vcfpy.parser.
parse_mapping
(value, warning_helper)[source]¶ Parse the given VCF header line mapping
Such a mapping consists of “key=value” pairs, separated by commas and wrapped into angular brackets (“<...>”). Strings are usually quoted, for certain known keys, exceptions are made, depending on the tag key. this, however, only gets important when serializing.
Parameters: warning_helper (WarningHelper) – object to use for printing warning messages Raises: vcfpy.exceptions.InvalidHeaderException
if there was a problem parsing the file
-
vcfpy.parser.
process_alt
(header, ref, alt_str)[source]¶ Process alternative value using Header in
header
vcfpy.reader module¶
Parsing of VCF files from file
-like objects
-
class
vcfpy.reader.
Reader
(stream, path=None, tabix_path=None, record_checks=[])[source]¶ Bases:
object
Class for parsing of files from
file
-like objectsInstead of using the constructor, use the class methods
from_stream()
andfrom_path()
.On construction, the header will be read from the file which can cause problems. After construction,
Reader
can be used as an iterable ofRecord
.Raises: InvalidHeaderException
in the case of problems reading the header-
fetch
(chrom, begin, end)[source]¶ Jump to the start position of the given chromosomal position and limit iteration to the end position
Parameters: - chrom (str) – name of the chromosome to jump to
- begin (int) – 0-based begin position (inclusive)
- end (int) – 0-based end position (exclusive)
-
classmethod
from_path
(klass, path, tabix_path=None, record_checks=[])[source]¶ Create new
Reader
from pathParameters: - path – the path to load from (converted to
str
for compatibility withpath.py
) - tabix_path – optional string with path to TBI index,
automatic inferral from
path
will be tried on the fly if not given - record_checks (list) – record checks to perform, can contain ‘INFO’ and ‘FORMAT’
- path – the path to load from (converted to
-
classmethod
from_stream
(klass, stream, path=None, tabix_path=None, record_checks=[])[source]¶ Create new
Reader
from fileParameters: - stream –
file
-like object to read from - path – optional string with path to store (for display only)
- record_checks (list) – record checks to perform, can contain ‘INFO’ and ‘FORMAT’
- stream –
-
header
= None¶ the Header
-
parser
= None¶ the parser to use
-
path
= None¶ optional
str
with the path to the stream
-
record_checks
= None¶ checks to perform on records, can contain ‘FORMAT’ and ‘INFO’
-
samples
= None¶ the
vcfpy.header.SamplesInfos
object with the sample name information
-
stream
= None¶ stream (
file
-like object) to read from
-
tabix_file
= None¶ the
pysam.TabixFile
used for reading from index bgzip-ed VCF; constructed on the fly
-
tabix_path
= None¶ optional
str
with path to tabix file
-
vcfpy.record module¶
Code for representing a VCF record
The VCF record structure is modeled after the one of PyVCF
-
class
vcfpy.record.
AltRecord
(type_=None)[source]¶ Bases:
object
An alternative allele Record
Currently, can be a substitution, an SV placeholder, or breakend
-
type
= None¶ String describing the type of the variant, could be one of SNV, MNV, could be any of teh types described in the ALT header lines, such as DUP, DEL, INS, ...
-
-
vcfpy.record.
BND
= 'BND'¶ Code for break-end allele
-
class
vcfpy.record.
BreakEnd
(mate_chrom, mate_pos, orientation, mate_orientation, sequence, within_main_assembly)[source]¶ Bases:
vcfpy.record.AltRecord
A placeholder for a breakend
-
mate_chrom
= None¶ chromosome of the mate breakend
-
mate_orientation
= None¶ orientation breakend’s mate
-
mate_pos
= None¶ position of the mate breakend
-
orientation
= None¶ orientation of this breakend
-
sequence
= None¶ breakpoint’s connecting sequence
-
within_main_assembly
= None¶ bool
specifying if the breakend mate is within the assembly (True
) or in an ancillary assembly (False
)
-
-
class
vcfpy.record.
Call
(sample, data, site=None)[source]¶ Bases:
object
The information for a genotype callable
By VCF, this should always include the genotype information and can contain an arbitrary number of further annotation, e.g., the coverage at the variant position.
-
called
= None¶ whether or not the variant is fully called
-
data
= None¶ an OrderedDict with the key/value pair information from the call’s data
-
gt_alleles
= None¶ the allele numbers (0, 1, ...) in this calls or None for no-call
-
gt_bases
¶ Return the actual genotype bases, e.g. if VCF genotype is 0/1, could return (‘A’, ‘T’)
-
gt_phase_char
¶ Return character to use for phasing
-
gt_type
¶ The type of genotype, returns one of
HOM_REF
,HOM_ALT
, andHET
.
-
is_filtered
(require=None, ignore=['PASS'])[source]¶ Return
True
for filtered callsParameters: - ignore (iterable) – if set, the filters to ignore, make sure to include ‘PASS’, when setting
- require (iterable) – if set, the filters to require for returning
True
-
is_het
¶ Return
True
for heterozygous calls
-
is_phased
¶ Return boolean indicating whether this call is phased
-
is_variant
¶ Return
True
for non-hom-ref calls
-
plodity
= None¶ the number of alleles in this sample’s call
-
sample
= None¶ the name of the sample for which the call was made
-
-
vcfpy.record.
DEL
= 'DEL'¶ Code for “clean” deletion allele
-
vcfpy.record.
ESCAPE_MAPPING
= [('%', '%25'), (':', '%3A'), (';', '%3B'), ('=', '%3D'), (',', '%2C'), ('\r', '%0D'), ('\n', '%0A'), ('\t', '%09')]¶ Mapping for escaping reserved characters
-
vcfpy.record.
FORWARD
= '+'¶ code for forward orientation
-
vcfpy.record.
HET
= 1¶ Code for heterozygous
-
vcfpy.record.
HOM_ALT
= 2¶ Code for homozygous alternative
-
vcfpy.record.
HOM_REF
= 0¶ Code for homozygous reference
-
vcfpy.record.
INDEL
= 'INDEL'¶ Code for indel allele, includes substitutions of unequal length
-
vcfpy.record.
INS
= 'INS'¶ Code for “clean” insertion allele
-
vcfpy.record.
MIXED
= 'MIXED'¶ Code for mixed variant type
-
vcfpy.record.
MNV
= 'MNV'¶ Code for a multi nucleotide variant allele
-
vcfpy.record.
RESERVED_CHARS
= ':;=%,\r\n\t'¶ Characters reserved in VCF, have to be escaped
-
vcfpy.record.
REVERSE
= '-'¶ code for reverse orientation
-
class
vcfpy.record.
Record
(CHROM, POS, ID, REF, ALT, QUAL, FILTER, INFO, FORMAT, calls)[source]¶ Bases:
object
Represent one record from the VCF file
Record objects are iterators of their calls
-
CHROM
= None¶ A
str
with the chromosome name
-
FILTER
= None¶ A list of strings for the FILTER column
-
FORMAT
= None¶ A list of strings for the FORMAT column
-
ID
= None¶ A list of the semicolon-separated values of the ID column
-
INFO
= None¶ An OrderedDict giving the values of the INFO column, flags are mapped to
True
-
POS
= None¶ An
int
with a 1-based begin position
-
QUAL
= None¶ The quality value, can be
None
-
REF
= None¶ A
str
with the REF value
-
add_format
(key, value=None)[source]¶ Add an entry to format
The record’s calls
data[key]
will be set tovalue
if not yet set and value is notNone
. If key is already in FORMAT then nothing is done.
-
affected_end
¶ Return affected start position in 0-based coordinates
For SNVs, MNVs, and deletions, the behaviour is based on the start position and the length of the REF. In the case of insertions, the position behind the insert position is returned, yielding a 0-length interval together with
affected_start()
-
affected_start
¶ Return affected start position in 0-based coordinates
For SNVs, MNVs, and deletions, the behaviour is the start position. In the case of insertions, the position behind the insert position is returned, yielding a 0-length interval together with
affected_end()
-
begin
= None¶ An
int
with a 0-based begin position
-
call_for_sample
= None¶ A mapping from sample name to entry in self.calls
-
end
= None¶ An
int
with a 0-based end position
-
-
vcfpy.record.
SNV
= 'SNV'¶ Code for single nucleotide variant allele
-
vcfpy.record.
SV
= 'SV'¶ Code for structural variant allele
-
vcfpy.record.
SYMBOLIC
= 'SYMBOLIC'¶ Code for symbolic allele that is neither SV nor BND
-
class
vcfpy.record.
SingleBreakEnd
(orientation, sequence)[source]¶ Bases:
vcfpy.record.BreakEnd
A placeholder for a single breakend
-
class
vcfpy.record.
Substitution
(type_, value)[source]¶ Bases:
vcfpy.record.AltRecord
A basic alternative allele record describing a REF->AltRecord substitution
Note that this subsumes MNVs, insertions, and deletions.
-
value
= None¶ The alternative base sequence to use in the substitution
-
-
class
vcfpy.record.
SymbolicAllele
(value)[source]¶ Bases:
vcfpy.record.AltRecord
A placeholder for a symbolic allele
The allele symbol must be defined in the header using an
ALT
header before being parsed. Usually, this is used for succinct descriptions of structural variants or IUPAC parameters.-
value
= None¶ The symbolic value, e.g. ‘DUP’
-
-
vcfpy.record.
UNESCAPE_MAPPING
= [('%25', '%'), ('%3A', ':'), ('%3B', ';'), ('%3D', '='), ('%2C', ','), ('%0D', '\r'), ('%0A', '\n'), ('%09', '\t')]¶ Mapping from escaped characters to reserved one
vcfpy.warn_utils module¶
Code for printing warnings
-
class
vcfpy.warn_utils.
WarningHelper
(prefix='[vcfpy] ', stream=<_io.TextIOWrapper name='<stderr>' mode='w' encoding='UTF-8'>)[source]¶ Bases:
object
Helper class for checkers
This class implements a “warn_once” function that allows to print warnings only once and a “print_summary” function that, in the end, allows to print a summary table with number of warnings.
-
prefix
= None¶ string to prepend before all warnings
-
print_summary
(title='WARNINGS', format='{: 6}\t{}')[source]¶ Print warning messages and count to
self.stream
-
stream
= None¶ the stream to write warnings to
-
warning_counter
= None¶ mapping from warning string to counter
-
vcfpy.writer module¶
Writing of VCF files to file
-like objects
Currently, only writing to plain-text files is supported
-
class
vcfpy.writer.
Writer
(stream, header, samples, path=None)[source]¶ Bases:
object
Class for writing VCF files to
file
-like objectsInstead of using the constructor, use the class methods
from_stream()
andfrom_path()
.The writer has to be constructed with a
Header
and aSamplesInfos
object and the full VCF header will be written immediately on construction. This, of course, implies that modifying the header after construction is illegal.-
classmethod
from_path
(klass, path, header, samples)[source]¶ Create new
Writer
from pathParameters: - path – the path to load from (converted to
str
for compatibility withpath.py
) - header – VCF header to use
- samples – SamplesInfos to use
- path – the path to load from (converted to
-
classmethod
from_stream
(klass, stream, header, samples, path=None, use_bgzf=None)[source]¶ Create new
Writer
from fileNote that for getting bgzf support, you have to pass in a stream opened in binary mode. Further, you either have to provide a
path
ending in".gz"
or setuse_bgzf=True
. Otherwise, you will get the notorious “TypeError: ‘str’ does not support the buffer interface”.Parameters: - stream –
file
-like object to write to - header – VCF header to use
- samples – SamplesInfos to use
- path – optional string with path to store (for display only)
- use_bgzf – indicator whether to write bgzf to
stream
ifTrue
, prevent ifFalse
, interpretpath
ifNone
- stream –
-
header
= None¶ the :py:class:~vcfpy.header.Header` written out
-
path
= None¶ optional
str
with the path to the stream
-
samples
= None¶ the :py:class:~vcfpy.header.SamplesInfos` written out
-
stream
= None¶ stream (
file
-like object) to read from
-
write_record
(record)[source]¶ Write out the given
vcfpy.record.Record
to this Writer
-
classmethod