Data (data package)

Base class of DataHolder

class gadma.data.data.DataHolder(filename, projections, outgroup, population_labels, sequence_length)

Bases: object

Class for data holding.

: param filename: name of file with data : param outgroup: information if there is outgroup in data : type outgroup: bool : params pop_labels: labels of populations in data : param seq_len: length of sequence that was used to build data

get_total_sequence_length()

Returns total sequence length as it could be a dict for each chrom.

Input data types

class gadma.data.data.SFSDataHolder(sfs_file, projections=None, outgroup=None, population_labels=None, sequence_length=None, non_ascertained_pops=None)

Bases: DataHolder

Class for SFS and fastsimcoal2 data holding. if any parameter is None then it will be taken from the file (for SFS data)

Possible extensions for fastsimcoal2 data: _DAFpop0.obs - single sample, derived allele (unfolded spectrum) _MAFpop0.obs - single sample, minor allele (folded spectrum) _jointDAFpop1_0.obs - two samples unfolded _jointMAFpop1_0.obs - two samples folded _DSFS.obs - multidimensional SFS for derived allele _MSFS.obs - multidimensional SFS for minor allele

class gadma.data.data.VCFDataHolder(vcf_file, popmap_file, projections=None, outgroup=None, population_labels=None, sequence_length=None, recombination_maps=None, bed_files_dir=None, preprocessed_data=None)

Bases: DataHolder

Class for VCF data holding.