pydigree.io package

Submodules

pydigree.io.base module

class pydigree.io.base.PEDRecord(line, delimiter=' ')

Bases: object

create_individual(population=None)

Creates an Individual object from a Pedigree Record.

The individual will have the id tuple of (fam_id, ind_id)

Parameters:population (Population) – Population for the individual to belong to Return type:Individual

pydigree.io.base.connect_individuals(pop)

Makes the connections in the genealogy from parents to children and vice versa.

Parameters:population (IndividualContainer) – Set of individuals to connect Rtype void:

pydigree.io.base.genotypes_from_sequential_alleles(chromosomes, data, missing_code='0')

Takes a series of alleles and turns them into genotypes.

For example: The series ‘1 2 1 2 1 2’ becomes chrom1 = [1, 1, 1] chrom2 = [2, 2, 2]

These are returned in the a list in the form:

::

[(chroma, chromb), (chroma, chromb)...]

Parameters:

• chromosomes (list of ChromosomeTemplate) – genotype data
• data – The alleles to be turned into genotypes
• missing_code (string) – value representing a missing allele

Returns:

A list of 2-tuples of Alleles objects

pydigree.io.base.read_ped(filename, population=None, delimiter=None, affected_labels=None, population_handler=None, data_handler=None, connect_inds=True, onlyinds=None)

Reads a plink format pedigree file, ie:

::

familyid indid father mother sex whatever whatever whatever

into a pydigree pedigree object, with optional population to assign to pedigree members. If you don’t provide a population you can’t simulate genotypes!

Parameters:

• filename (string) – The file to be read
• population (Population) – The population to assign individuals to
• delimiter (string) – a string defining the field separator, default: any whitespace
• affected_labels (dict (str -> value)) – The labels that determine affection status.
• population_handler – a function to set up the population
• data_handler (callable) – a function to turn the data into useful individual information
• connect_inds (bool) – build references between individuals. Requires all individuals be present in the file
• onlyinds (iterable) – only include data for specified individuals

Returns:

individuals contained in the pedigree file

Return type:

PedigreeCollection

pydigree.io.base.read_phenotypes(pedigrees, csvfile, delimiter=', ', missingcode='X')

Reads a csv with header famid, ind, phen, phen, phen, phen etc etc

Arguments :param pedigrees: data to update :param csvfile: the filename of the file containing phenotypes. :param delimiter: the field delimiter for the file :param missingcode: the code for missing values :type pedigrees: PedigreeCollection :type csvfile: string :type missingcode: string

Return type:void

pydigree.io.base.sort_pedigrees(inds, population_handler)

Takes a set of individuals and sorts them into pedigrees.

Individuals must have labels that are (pedid, indid) tuples

Parameters:

• inds (iterable) – Individuals to be sorted
• population_handler (Callable) – a function to set up the population

Returns:

Collection of pedigrees from the individuals

Return type:

PedigreeCollections

pydigree.io.base.write_pedigree(pedigrees, filename, delim=' ')

Writes pedigree to a LINKAGE formatted pedigree file

Parameters:

• pedigrees – Data to write
• filename – filename to write to
• delim – output field separator

Return type:

void

pydigree.io.base.write_phenotypes(pedigrees, filename, predicate=None, missingcode='X', delim=', ')

Writes phenotypes to a CSV (or other field delimited) file

Parameters:

• pedigrees – Data to write
• filename – filename to write to
• missingcode (string) – code to use for missing values
• delim (string) – output field separator

pydigree.io.beagle module

Utilities for reading BEAGLE formatted genotype data

class pydigree.io.beagle.BeagleGenotypeRecord(line)

Bases: object

A class corresponding to a record in a BEAGLE genotype file

data

identifier

is_phenotype_record()

Returns true if record corresponds to a phenotype field

label

class pydigree.io.beagle.BeagleMarkerRecord(line)

Bases: object

A class corresponding to a marker in a BEAGLE marker file

alleles

alternates

The alternate alleles for the marker

Returns:Each alternate allele Return type:iterable

label

pos

reference

The reference allele for the marker

Returns:reference allele Return type:string

pydigree.io.beagle.read_beagle(genofile, markerfile)

Reads BEAGLE formatted genotype data

Parameters:

• genofile (string) – Filename containing genotype information for individuals
• markerfile (string) – Filename containing marker location and allele information corresponding to genofile

Return type:

Population

pydigree.io.beagle.read_beagle_genotypefile(filename, pop, missingcode='0')

Reads BEAGLE formatted genotype files

Arguments

Parameters:

• filename – Filename of BEAGLE genotype file
• pop – the population to add these individuals to
• missingcode (string) – The value that indicates a missing genotype

Return type:

void

pydigree.io.beagle.read_beagle_markerfile(filename, label=None)

Reads marker locations from a BEAGLE formatted file

Parameters:

• filename (string) – The file to be read
• label – An optional label to give the chromosome, since the BEAGLE format does not require it

Return type:

ChromosomeTemplate

pydigree.io.genomesimla module

Read GenomeSIMLA formatted chromosome templates

pydigree.io.genomesimla.read_gs_chromosome_template(templatef)

Reads a genomeSIMLA format chromosome template file

Parameters:templatef (string) – The filename of the template file Return type:A ChromosomeTemplate object corresponding to the file

pydigree.io.kinship module

Reads kinships from KinInbCoef

pydigree.io.kinship.read_kinship(filename)

Reads a KinInbCoef formatted file of kinship and inbreeding coefficients

Parameters:filename (string) – the filename to be read

Returns: a dictionary in the format {frozenset({(fam, ind_a), (fam, ind_b)}): kinship/inbreeding

pydigree.io.plink module

Functions for reading PLINK formatted genotype files

pydigree.io.plink.create_pop_handler_func(mapfile)

Creates a closure to provide as the population handler for pydigree.io.base.read_ped.

Parameters:mapfile (string) – Filename of PLINK .map file Return type:callable

pydigree.io.plink.plink_data_handler(ind, data)

A function to handle the data payload from a plink line.

Parameters:

• ind (Individual) – Individual for the record
• data (string) – the data for the record

Return type:

void

pydigree.io.plink.read_map(mapfile)

Reads a PLINK map file into a list of ChromosomeTemplate objects

Parameters:mapfile (string) – Path of the file to be read Return type:a list of ChromosomeTemplate objects

pydigree.io.plink.read_plink(pedfile=None, mapfile=None, prefix=None, **kwargs)

Read a plink file by specifying pedfile and mapfile directly, or by using a prefix. Pass additional arguments to pydigree.io.base.read_ped with kwargs

Parameters:

• pedfile – a plink PED file to be read
• mapfile – a plink MAP file to be read
• prefix – sets mapfile to ‘prefix.map’ and pedfile to ‘prefix.ped’
• kwargs – additional arguments passed to read_ped

Returns: A PedigreeCollection object

pydigree.io.plink.write_map(pedigrees, mapfile, output_chromosomes=None)

Writes the genotype location data to a PLINK MAP file

Parameters:

• pedigrees – the population containing the data to be written
• mapfile – the name of the file to be output to
• output_chromosomes – which chromosomes to write

Returns: Nothing

pydigree.io.plink.write_ped(pedigrees, pedfile, delim=' ', predicate=None, output_chromosomes=None)

write_ped writes data in a plink-format PED file, and optionally a plink-format map file.

Parameters:

• pedigrees – An object of class PedigreeCollection containing what you want to output
• pedfile – a string giving the name out the file to output to.
• mapfile – the name of a mapfile to output, if you want to output one. an object that evaluates as False or None will skip the mapfile
• genotypes – Should genotypes be output True/False
• delim – Field seperator
• predicate – Which inputs to include in the output file. If not specified all are output. If the string is ‘affected’, only affected individuals are output. If the string is ‘phenotyped’, all individuals with phenotype information are output. Any other value of predicate must be a function to perform on the individual that evaluates to True/False for whether the individual should be output.

Returns: Nothing

pydigree.io.plink.write_plink(pedigrees, filename_prefix, predicate=None, mapfile=False, compression=None, output_chromosomes=None)

Write individual genotypes to a file in plink PED data format. Optionally outputs the genotype locations to the mapfile.

Parameters:

• pedigrees (IndividualContainer) – the pedigrees to be written
• filename_prefix (string) – The output ped file (‘.ped’ will be appended)
• predicate (callable) – a callable that evaluates True when the individual should be outputted to the file
• mapfile (string) – True if the plink MAP file should be written
• compression ('gzip' or 'bz2') – Compress the data? Options are bz2 and gzip, otherwise data will be written uncompressed

Return type:

void

pydigree.io.sgs module

Utilities for file I/O with SGS data

class pydigree.io.sgs.GermlineRecord(line)

Bases: object

A class for working with records in GERMLINE formatted files

bp_locations

Are the segments provided in physical or genetic positions?

Returns:True if physical, False if centimorgans Return type:bool

location

Returns the location of the segment

pair

Returns the individuals for the segment

pydigree.io.sgs.read_germline(filename)

Reads a GERMLINE formatted SGS filename into an SGSAnalysis object

GERMLINE files are text files with the format:

0. Family ID 1
1. Individual ID 1
2. Family ID 2
3. Individual ID 2
4. Chromosome
5. Segment start (bp/cM)
6. Segment end (bp/cM)
7. Segment start (SNP)
8. Segment end (SNP)
9. Total SNPs in segment
10. Length of segment
11. Units for genetic length (cM or MB)
12. Mismatching SNPs in segment
13. 1 if Individual 1 is homozygous in match; 0 otherwise
14. 1 if Individual 2 is homozygous in match; 0 otherwise

This function only uses 0-6.

pydigree.io.sgs.write_sgs(data, filename)

GERMLINE files are text files with the format:

0. Family ID 1
1. Individual ID 1
2. Family ID 2
3. Individual ID 2
4. Chromosome
5. Segment start (bp/cM)
6. Segment end (bp/cM)
7. Segment start (SNP)
8. Segment end (SNP)
9. Total SNPs in segment
10. Genetic length of segment
11. Units for genetic length (cM or MB)
12. Mismatching SNPs in segment
13. 1 if Individual 1 is homozygous in match; 0 otherwise
14. 1 if Individual 2 is homozygous in match; 0 otherwise

pydigree.io.smartopen module

pydigree.io.smartopen.smartopen(filename, mode='r')

Seamlessly open compressed files. Use in place of regular open.

Note

Python’s compression modules iterate over compressed files as bytes, not strings. Unless ‘b’ (binary) is specified in the mode, we add ‘t’ (text) to the mode to force iteration as strings, operating consistently

pydigree.io.vcf module

class pydigree.io.vcf.VCFRecord(line)

Bases: object

A class for parsing lines in VCF files

genotypes()

Extracts the genotypes from a VCF record

getitems(item)

Gets the value in each data field for the key specified in the format field.

Parameters:item – key to find Returns:values for each individual Return type:list

info

A dictionary representing the INFO field in a VCF record

Rtype dict:

pydigree.io.vcf.read_vcf(filename, require_pass=False, freq_info=None)

Reads a VCF file and returns a Population object with the individuals represented in the file

Genotypes generated by this function will be sparse

Parameters:

• require_pass (bool) – only allow variants with PASS under FILTER
• freq_info – INFO field to get allele frequency from
• freq_info – string

Returns:

Individuals in the VCF

Return type:

Population

Module contents