SlimRSCollection.BitRSCollection Class Reference

Public Member Functions
def	__init__ (self)
def	__add__ (self, rsc)
def	__eq__ (self, rsc)
def	__getitem__ (self, key)
def	__iadd__ (self, rsc)
def	__len__ (self)
def	add_entry (self, rsidx, e)
def	add_entry_line (self, e)
def	add_entry_from_args (self, chrom, rsid, pos, silent=False)
def	get_by_chr_pos (self, chrom, pos)
def	get_by_rsid (self, rsid)
def	get_major (self, mut=True)
def	__init__ (self)
def	__add__ (self, rsc)
def	__eq__ (self, rsc)
def	__getitem__ (self, key)
def	__iadd__ (self, rsc)
def	__len__ (self)
def	add_entry (self, rsidx, e)
def	add_entry_line (self, e)
def	add_entry_from_args (self, chrom, rsid, pos, quiet=False)
def	dump_vcf (self, fn, cons=False, is_maj=False, append=False)
def	get_by_chr_pos (self, chrom, pos)
def	get_by_rsid (self, rsid)
def	get_major (self, mut=True)

Static Public Member Functions
def	decode_bit (bit_code)
def	encode_bit (var_list)
def	filter_vcf (rsc_dir, fn_in, fn_out, pop=None, log_fn=None, quiet=False)
def	get_chrom_from_filename (fn)
def	load_from_file_full (fn, quiet=False)
def	load_from_file_pop (fn, pop, quiet=False)
def	open (fn)
def	chrom_to_int (c)
def	decode_bit (bit_code)
def	encode_bit (var_list)
def	filter_vcf (rsc_dir, fn_in, fn_out, pop=None, log_fn=None, cons=False, keep_samps=False, quiet=False)
def	get_chrom_from_filename (fn)
def	load_from_file_full (fn, quiet=False)
def	load_from_file_pop (fn, pop, quiet=False)
def	open (fn)
def	sort_rsidx (rsidx)
def	var_list_to_vcf (rsidx, var_list, cons=False)

Public Attributes
	entries
	chr_pos_table
	rsid_table

Static Public Attributes
dictionary	BASE_ENC

Member Function Documentation

__add__() [1/2]

def SlimRSCollection.BitRSCollection.__add__	(		self,
			rsc
	)

Implement addition for two RSCollection objects.

__add__() [2/2]

def SlimRSCollection.BitRSCollection.__add__	(		self,
			rsc
	)

Implement addition for two RSCollection objects.

__eq__() [1/2]

def SlimRSCollection.BitRSCollection.__eq__	(		self,
			rsc
	)

Implement equality checking for two RSCollection objects.

__eq__() [2/2]

def SlimRSCollection.BitRSCollection.__eq__	(		self,
			rsc
	)

Implement equality checking for two RSCollection objects.

__getitem__() [1/2]

def SlimRSCollection.BitRSCollection.__getitem__	(		self,
			key
	)

Allow access to entries via the [] operator.

__getitem__() [2/2]

def SlimRSCollection.BitRSCollection.__getitem__	(		self,
			key
	)

Allow access to entries via the [] operator.

__iadd__() [1/2]

def SlimRSCollection.BitRSCollection.__iadd__	(		self,
			rsc
	)

Implement incremental addition.

__iadd__() [2/2]

def SlimRSCollection.BitRSCollection.__iadd__	(		self,
			rsc
	)

Implement incremental addition.

__len__() [1/2]

def SlimRSCollection.BitRSCollection.__len__

(

self

)

Implement len operator.

__len__() [2/2]

def SlimRSCollection.BitRSCollection.__len__

(

self

)

Implement len operator.

add_entry() [1/2]

def SlimRSCollection.BitRSCollection.add_entry	(		self,
			rsidx,
			e
	)

Add entry from a variant list.

Parameters:
rsidx: Tuple of (rsid, chrom, pos)
e: List of variants (output from decode_bit)

add_entry() [2/2]

def SlimRSCollection.BitRSCollection.add_entry	(		self,
			rsidx,
			e
	)

Add entry from a variant list.

Parameters:
rsidx: Tuple of (rsid, chrom, pos)
e: List of variants (output from decode_bit)

add_entry_from_args() [1/2]

def SlimRSCollection.BitRSCollection.add_entry_from_args	(		self,
			chrom,
			rsid,
			pos,
			quiet = False
	)

Add an entry based on the given arguments.

Parameters:
chrom: Chromosome of the entry being added
rsid: RefSNP ID of the entry being added
pos: Position of the entry being added
quiet: Suppress progress information being printed

add_entry_from_args() [2/2]

def SlimRSCollection.BitRSCollection.add_entry_from_args	(		self,
			chrom,
			rsid,
			pos,
			silent = False
	)

Add an entry based on the given arguments.

Parameters:
chrom: Chromosome of the entry being added
rsid: RefSNP ID of the entry being added
pos: Position of the entry being added
silent: Whether to suppress progress information being printed

add_entry_line() [1/2]

def SlimRSCollection.BitRSCollection.add_entry_line	(		self,
			e
	)

Add entry from a line in a ConsDB file.

Parameters:
e: Line from a ConsDB file containing the entry to add

add_entry_line() [2/2]

def SlimRSCollection.BitRSCollection.add_entry_line	(		self,
			e
	)

Add entry from a line in a ConsDB file.

Parameters:
e: Line from a ConsDB file containing the entry to add

chrom_to_int()

def SlimRSCollection.BitRSCollection.chrom_to_int (   c )

static

Function to use to sort chromosomes (numeric < X < Y < M)

Parameters:
c: Chromosome to convert

decode_bit() [1/2]

def SlimRSCollection.BitRSCollection.decode_bit (   bit_code )

static

Convert from bit-packed int to list of variants.

Parameters:
bit_code: int that can be unpacked into a list of variants

decode_bit() [2/2]

def SlimRSCollection.BitRSCollection.decode_bit (   bit_code )

static

Convert from bit-packed int to list of variants.

Parameters:
bit_code: int that can be unpacked into a list of variants

dump_vcf()

def SlimRSCollection.BitRSCollection.dump_vcf	(		self,
			fn,
			cons = False,
			is_maj = False,
			append = False
	)

Create a VCF file containing the variants in the BitRSCollection object.
If saving a consensus VCF file, makes sure that there is only one
alternate allele per line. The append argument allows support for
loading/saving in a piecewise fashion.

Parameters:
fn: File to save VCF to
cons: If this VCF file is a consensus VCF
is_maj: If this RSCollection object already contains only major alleles
append: If appending to an existing VCF file

encode_bit() [1/2]

def SlimRSCollection.BitRSCollection.encode_bit (   var_list )

static

Create a bit-packed int from a list of variants.

Parameters:
var_list: List of variants

encode_bit() [2/2]

def SlimRSCollection.BitRSCollection.encode_bit (   var_list )

static

Create a bit-packed int from a list of variants.

Parameters:
var_list: List of variants

filter_vcf() [1/2]

def SlimRSCollection.BitRSCollection.filter_vcf (   rsc_dir,   fn_in,   fn_out,   pop = None,   log_fn = None,   cons = False,   keep_samps = False,   quiet = False  )

static

Filter a given VCF file using ConsDB files stored in the given dir.

Remove all records that call a variant that is a major allele and write
all other records.

Parameters:
rsc_dir: Directory containing ConsDB files
fn_in: Input VCF file to filter
fn_out: Output filename
pop: Population to use
log_fn: Optional file to store progress/log output
cons: Making a consensus VCF (keep major alleles instead of minor)
keep_samps: Write sample information
quiet: Disable progress/log output to stdout

filter_vcf() [2/2]

def SlimRSCollection.BitRSCollection.filter_vcf (   rsc_dir,   fn_in,   fn_out,   pop = None,   log_fn = None,   quiet = False  )

static

Filter a given VCF file using ConsDB files stored in the given dir.

Remove all records that call a variant that is a major allele and write
all other records.

Parameters:
rsc_dir: Directory containing ConsDB files
fn_in: Input VCF file to filter
fn_out: Output filename
pop: Population to use
log_fn: Optional file to store progress/log output
quiet: Disable progress/log output to stdout

get_by_chr_pos() [1/2]

def SlimRSCollection.BitRSCollection.get_by_chr_pos	(		self,
			chrom,
			pos
	)

Return a list of all (rsid, chrom, pos) combinations that match the
given chrom and pos, and a list of corresponding entries.

Parameters:
chrom: Chromosome to get
pos: Position to get

get_by_chr_pos() [2/2]

def SlimRSCollection.BitRSCollection.get_by_chr_pos	(		self,
			chrom,
			pos
	)

Return a list of all (rsid, chrom, pos) combinations that match the
given chrom and position, and a list of corresponding entries.

Parameters:
chrom: Chromosome to get
pos: Position to get

get_by_rsid() [1/2]

def SlimRSCollection.BitRSCollection.get_by_rsid	(		self,
			rsid
	)

Return a list of all (rsid, chrom, pos) combinations that match the
given RefSNP ID, and a list of corresponding entries.

Parameters:
rsid: RefSNP ID number to get

get_by_rsid() [2/2]

def SlimRSCollection.BitRSCollection.get_by_rsid	(		self,
			rsid
	)

Return a list of all (rsid, chrom, pos) combinations that match the
given RefSNP ID, and a list of corresponding entries.

Parameters:
rsid: RefSNP ID number to get

get_chrom_from_filename() [1/2]

def SlimRSCollection.BitRSCollection.get_chrom_from_filename (   fn )

static

Helper method to parse a filename and find which chromosome it is.

Parameters:
fn: Filename to use

get_chrom_from_filename() [2/2]

def SlimRSCollection.BitRSCollection.get_chrom_from_filename (   fn )

static

Helper method to parse a filename and find which chromosome it is.

Parameters:
fn: Filename to use

get_major() [1/2]

def SlimRSCollection.BitRSCollection.get_major	(		self,
			mut = True
	)

Return a RSCollection object containing all major alleles.

Parameters:
mut: Whether to only include variants that are different between
    reference and alternate allele

get_major() [2/2]

def SlimRSCollection.BitRSCollection.get_major	(		self,
			mut = True
	)

Return a BitRSCollection object containing all major alleles.

Parameters:
mut: Whether to only include variants that are different between
    reference and alternate allele

load_from_file_full() [1/2]

def SlimRSCollection.BitRSCollection.load_from_file_full (   fn,   quiet = False  )

static

Load an entire ConsDB file.

Parameters:
fn: Filename to load
quiet: Disable progress/log output to stdout

load_from_file_full() [2/2]

def SlimRSCollection.BitRSCollection.load_from_file_full (   fn,   quiet = False  )

static

Load an entire ConsDB file.

Parameters:
fn: Filename to load
quiet: Disable progress/log output to stdout

load_from_file_pop() [1/2]

def SlimRSCollection.BitRSCollection.load_from_file_pop (   fn,   pop,   quiet = False  )

static

Load an entire ConsDB file, setting the allele frequency as the AF of
the given population.
Skip variants that are not present in the given population.

Parameters:
fn: Filename to use
pop: Population to load
quiet: Disable progress/log output to stdout

load_from_file_pop() [2/2]

def SlimRSCollection.BitRSCollection.load_from_file_pop (   fn,   pop,   quiet = False  )

static

Load an entire ConsDB file, setting the allele frequency as the AF of
the given population.
Skip variants that are not present in the given population.

Parameters:
fn: Filename to use
pop: Population to load
quiet: Disable progress/log output to stdout

open() [1/2]

def SlimRSCollection.BitRSCollection.open (   fn )

static

Helper method to appropriately open the given file.

open() [2/2]

def SlimRSCollection.BitRSCollection.open (   fn )

static

Helper method to appropriately open the given file.

Parameters:
fn: Filename to open

sort_rsidx()

def SlimRSCollection.BitRSCollection.sort_rsidx (   rsidx )

static

Helper method to sort a list of rsidx. Meant to be used as a
key for sorting. Returns the chromosome and position of the rsidx, both
in int form.

Parameters:
rsidx: List/tuple of (rsid, chrom, pos)

var_list_to_vcf()

def SlimRSCollection.BitRSCollection.var_list_to_vcf (   rsidx,   var_list,   cons = False  )

static

Helper method to convert a list of variants to vcf entry(ies).

Parameters:
rsidx: List/tuple of (rsid, chrom, pos)
var_list: List of variants (as returned from BitRSCollection.decode_bit)
cons: Making a consensus VCF file

Member Data Documentation

BASE_ENC

dictionary SlimRSCollection.BitRSCollection.BASE_ENC

static

Initial value:

=  {
        'A': 0,
        'C': 1,
        'G': 2,
        'T': 3
    }

---

The documentation for this class was generated from the following files:

• SlimRSCollection.old.py
• SlimRSCollection.py