scikit-allel (version 2)¶
This is an early work in progress. scikit-allel version 2 will eventually replace version 1, however it will take some time to reach feature parity. In the mean time, see the documentation for scikit-allel (version 1) if you need a more complete set of capabilities.
If you want to try scikit-allel version 2, install with:
$ pip install --pre skallel
You can install scikit-allel version 2 alongside version 1, they will
not interfere with each other. scikit-allel version 2 uses the new
skallel namespace, whereas scikit-allel version 1 uses the
allel namespace.
Contents¶
API docs¶
Data structures¶
Genotypes¶
-
skallel.genotypes_locate_hom(gt)¶ Locate homozygous genotype calls.
- Parameters
- gtarray_like, int
- Returns
- outarray_like, bool
-
skallel.genotypes_locate_het(gt)¶ Locate heterozygous genotype calls.
- Parameters
- gtarray_like, int
- Returns
- outarray_like, bool
-
skallel.genotypes_locate_call(gt, *, call)¶ Locate genotypes with the given call.
- Parameters
- gtarray_like, int
- callarray_like, int
- Returns
- outarray_like, bool
-
skallel.genotypes_count_alleles(gt, *, max_allele)¶ Count the number of calls for each allele.
- Parameters
- gtarray_like, int
- max_alleleint8
- Returns
- acarray_like, int
-
skallel.genotypes_to_called_allele_counts(gt)¶ Count non-missing alleles within genotype calls.
- Parameters
- gtarray_like, int
- Returns
- outarray_like, int
-
skallel.genotypes_to_missing_allele_counts(gt)¶ Count missing alleles within genotype calls.
- Parameters
- gtarray_like, int
- Returns
- outarray_like, bool
-
skallel.genotypes_to_allele_counts(gt, *, max_allele)¶ Convert genotypes to allele counts.
- Parameters
- gtarray_like, int
- max_alleleint
- Returns
- acarray_like, int
-
skallel.genotypes_to_allele_counts_melt(gt, *, max_allele)¶ Convert genotypes to allele counts, melting each allele into a separate row.
- Parameters
- gtarray_like, int
- max_alleleint
- Returns
- acarray_like, int
-
skallel.genotypes_to_major_allele_counts(gt, *, max_allele)¶ Convert genotypes to major allele counts.
- Parameters
- gtarray_like, int
- max_alleleint
- Returns
- acarray_like, int
-
skallel.genotypes_to_haplotypes(gt)¶ TODO
- Parameters
- gtarray_like, int
- Returns
- htarray_like, int
Haplotypes¶
Allele counts¶
-
skallel.allele_counts_to_frequencies(ac)¶ TODO
-
skallel.allele_counts_allelism(ac)¶ TODO
-
skallel.allele_counts_max_allele(ac)¶ TODO
Selections¶
-
skallel.select_slice(o, *, start=None, stop=None, step=None, axis=0)¶ TODO
-
skallel.select_indices(o, indices, *, axis=0)¶ TODO
-
skallel.select_mask(o, mask, *, axis=0)¶ TODO
-
skallel.select_range(o, index, *, begin=None, end=None, axis=0)¶
-
skallel.select_values(o, index, query, *, axis=0)¶
-
skallel.concatenate(seq, *, axis=0)¶ Concatenate two or more objects along the given axis.
- Parameters
- seqsequence of group or array_like
- axisint
- Returns
- outgroup or array_like