SNPio
Contents:
Getting Started
Example script
snpio package
snpio
Changelog
SNPio
Index
Edit on GitHub
Index
_
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A
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C
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D
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E
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F
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G
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I
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L
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M
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N
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P
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Q
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R
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S
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T
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U
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V
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W
_
_has_popids (snpio.io.structure_reader.StructureReader attribute)
_onerow (snpio.io.structure_reader.StructureReader attribute)
A
alt (snpio.io.phylip_reader.PhylipReader property)
alt2 (snpio.io.phylip_reader.PhylipReader property)
C
chunk_size (snpio.io.vcf_reader.VCFReader attribute)
convert_012() (snpio.analysis.genotype_encoder.GenotypeEncoder method)
convert_int_iupac() (snpio.analysis.genotype_encoder.GenotypeEncoder method)
convert_onehot() (snpio.analysis.genotype_encoder.GenotypeEncoder method)
count_alleles() (in module snpio.utils.sequence_tools)
D
debug (snpio.analysis.tree_parser.TreeParser attribute)
(snpio.io.phylip_reader.PhylipReader attribute)
(snpio.io.structure_reader.StructureReader attribute)
(snpio.io.vcf_reader.VCFReader attribute)
decode_012() (snpio.analysis.genotype_encoder.GenotypeEncoder method)
E
exclude_pops (snpio.io.phylip_reader.PhylipReader attribute)
(snpio.io.vcf_reader.VCFReader attribute)
F
filename (snpio.io.phylip_reader.PhylipReader attribute)
(snpio.io.vcf_reader.VCFReader attribute)
filetype (snpio.analysis.genotype_encoder.GenotypeEncoder attribute)
(snpio.io.vcf_reader.VCFReader attribute)
force_popmap (snpio.io.phylip_reader.PhylipReader attribute)
(snpio.io.vcf_reader.VCFReader attribute)
G
genotype_data (snpio.analysis.tree_parser.TreeParser attribute)
GenotypeEncoder (class in snpio.analysis.genotype_encoder)
genotypes_012 (snpio.analysis.genotype_encoder.GenotypeEncoder property)
genotypes_int (snpio.analysis.genotype_encoder.GenotypeEncoder property)
genotypes_onehot (snpio.analysis.genotype_encoder.GenotypeEncoder property)
get_distance_matrix() (snpio.analysis.tree_parser.TreeParser method)
get_gt2iupac() (in module snpio.utils.misc)
get_int_iupac_dict() (in module snpio.utils.misc)
get_iupac2gt() (in module snpio.utils.misc)
get_iupac_caseless() (in module snpio.utils.sequence_tools)
get_major_allele() (in module snpio.utils.sequence_tools)
get_onehot_dict() (in module snpio.utils.misc)
get_revComp_caseless() (in module snpio.utils.sequence_tools)
get_subtree() (snpio.analysis.tree_parser.TreeParser method)
get_vcf_attributes() (snpio.io.vcf_reader.VCFReader method)
I
include_pops (snpio.io.phylip_reader.PhylipReader attribute)
(snpio.io.vcf_reader.VCFReader attribute)
info_fields (snpio.io.vcf_reader.VCFReader attribute)
inverse_int_iupac() (snpio.analysis.genotype_encoder.GenotypeEncoder method)
inverse_onehot() (snpio.analysis.genotype_encoder.GenotypeEncoder method)
L
load_aln() (snpio.io.phylip_reader.PhylipReader method)
(snpio.io.structure_reader.StructureReader method)
(snpio.io.vcf_reader.VCFReader method)
load_tree_from_string() (snpio.analysis.tree_parser.TreeParser method)
loci_indices (snpio.io.vcf_reader.VCFReader attribute)
logger (snpio.io.phylip_reader.PhylipReader attribute)
(snpio.io.structure_reader.StructureReader attribute)
(snpio.io.vcf_reader.VCFReader attribute)
M
missing_vals (snpio.analysis.genotype_encoder.GenotypeEncoder attribute)
module
snpio
snpio.analysis
snpio.analysis.genotype_encoder
snpio.analysis.tree_parser
snpio.io
snpio.io.phylip_reader
snpio.io.structure_reader
snpio.io.vcf_reader
snpio.utils
snpio.utils.misc
snpio.utils.sequence_tools
N
num_inds (snpio.io.phylip_reader.PhylipReader attribute)
num_records (snpio.io.vcf_reader.VCFReader attribute)
num_snps (snpio.io.phylip_reader.PhylipReader attribute)
P
PhylipReader (class in snpio.io.phylip_reader)
plot_despine (snpio.io.vcf_reader.VCFReader attribute)
plot_dpi (snpio.io.vcf_reader.VCFReader attribute)
plot_fontsize (snpio.io.vcf_reader.VCFReader attribute)
plot_format (snpio.analysis.genotype_encoder.GenotypeEncoder attribute)
(snpio.io.phylip_reader.PhylipReader attribute)
(snpio.io.vcf_reader.VCFReader attribute)
popmapfile (snpio.io.phylip_reader.PhylipReader attribute)
(snpio.io.vcf_reader.VCFReader attribute)
prefix (snpio.analysis.genotype_encoder.GenotypeEncoder attribute)
(snpio.io.phylip_reader.PhylipReader attribute)
(snpio.io.vcf_reader.VCFReader attribute)
prune_tree() (snpio.analysis.tree_parser.TreeParser method)
Q
qmat (snpio.analysis.tree_parser.TreeParser property)
qmatrix (snpio.analysis.tree_parser.TreeParser attribute)
R
read_012() (snpio.analysis.genotype_encoder.GenotypeEncoder method)
read_tree() (snpio.analysis.tree_parser.TreeParser method)
ref (snpio.io.phylip_reader.PhylipReader property)
remove_items() (in module snpio.utils.sequence_tools)
replace_vals (snpio.analysis.genotype_encoder.GenotypeEncoder attribute)
reroot_tree() (snpio.analysis.tree_parser.TreeParser method)
resource_data (snpio.io.vcf_reader.VCFReader attribute)
S
sample_indices (snpio.io.vcf_reader.VCFReader attribute)
samples (snpio.analysis.genotype_encoder.GenotypeEncoder attribute)
(snpio.io.phylip_reader.PhylipReader attribute)
(snpio.io.vcf_reader.VCFReader attribute)
seqCounter() (in module snpio.utils.sequence_tools)
show_plots (snpio.io.vcf_reader.VCFReader attribute)
simplifySeq() (in module snpio.utils.sequence_tools)
site_rates (snpio.analysis.tree_parser.TreeParser property)
siterates (snpio.analysis.tree_parser.TreeParser attribute)
snp_data (snpio.analysis.genotype_encoder.GenotypeEncoder attribute)
(snpio.io.phylip_reader.PhylipReader attribute)
(snpio.io.vcf_reader.VCFReader attribute)
snpio
module
snpio.analysis
module
snpio.analysis.genotype_encoder
module
snpio.analysis.tree_parser
module
snpio.io
module
snpio.io.phylip_reader
module
snpio.io.structure_reader
module
snpio.io.vcf_reader
module
snpio.utils
module
snpio.utils.misc
module
snpio.utils.sequence_tools
module
StructureReader (class in snpio.io.structure_reader)
T
transform_gt() (snpio.io.vcf_reader.VCFReader method)
tree (snpio.analysis.tree_parser.TreeParser property)
tree_stats() (snpio.analysis.tree_parser.TreeParser method)
treefile (snpio.analysis.tree_parser.TreeParser attribute)
TreeParser (class in snpio.analysis.tree_parser)
U
update_vcf_attributes() (snpio.io.vcf_reader.VCFReader method)
V
validate_input_type() (in module snpio.utils.misc)
validate_input_vcf() (snpio.io.vcf_reader.VCFReader method)
validate_output_vcf() (snpio.io.vcf_reader.VCFReader method)
vcf_attributes_fn (snpio.io.vcf_reader.VCFReader property)
vcf_header (snpio.io.vcf_reader.VCFReader attribute)
VCFReader (class in snpio.io.vcf_reader)
verbose (snpio.analysis.genotype_encoder.GenotypeEncoder attribute)
(snpio.analysis.tree_parser.TreeParser attribute)
(snpio.io.phylip_reader.PhylipReader attribute)
(snpio.io.structure_reader.StructureReader attribute)
(snpio.io.vcf_reader.VCFReader attribute)
W
write_phylip() (snpio.io.phylip_reader.PhylipReader method)
write_structure() (snpio.io.structure_reader.StructureReader method)
write_tree() (snpio.analysis.tree_parser.TreeParser method)
write_vcf() (snpio.io.vcf_reader.VCFReader method)