mpm
0.14
Requirements
Installation
biofx
mpm
Docs
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Index
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A
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B
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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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H
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I
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L
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M
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N
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O
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P
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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
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Z
_
_id (biofx.parser.GSCDirectoryTreeParser.GSCDirectoryTree attribute)
A
add_comment() (biofx.variants.features.Variant method)
add_expression_analysis() (biofx.parser.GSCDirectoryTreeParser.GSCDirectoryTree method)
add_misc() (biofx.variants.features.Variant method)
add_paired_analysis() (biofx.parser.GSCDirectoryTreeParser.GSCDirectoryTree method)
add_wgs_bams() (biofx.parser.GSCDirectoryTreeParser.GSCDirectoryTree method)
alt (biofx.variants.features.Variant attribute)
alt_count (biofx.variants.features.Variant attribute)
annotate_with_snpeff() (biofx.annotator.VariantAnnotation.SnpEff method)
annotate_with_snpsift() (biofx.annotator.VariantAnnotation.SnpEff method)
B
bamfile (biofx.variants.features.Variant attribute)
biofx (module)
biofx.annotator (module)
biofx.annotator.GSCannotation (module)
biofx.annotator.VariantAnnotation (module)
biofx.parser (module)
biofx.parser.GSCDirectoryTreeParser (module)
biofx.parser.LRGparser (module)
biofx.parser.SnpEffparser (module)
biofx.utils (module)
biofx.utils.LogUtils (module)
biofx.variants (module)
biofx.variants.attributes (module)
biofx.variants.features (module)
biofx.variants.Genes (module)
biofx.variants.operations (module)
C
cgl_pathogenicity (biofx.variants.features.Variant attribute)
chromosome (biofx.variants.features.Variant attribute)
chunk_variants_by_chromosome() (in module biofx.variants.operations)
clnsig_values (biofx.variants.features.Variant attribute)
CNV (class in biofx.variants.features)
COMPLEX (biofx.variants.Genes.Inheritance attribute)
config (biofx.parser.GSCDirectoryTreeParser.GSCDirectoryTree attribute)
cosmic (biofx.variants.features.Variant attribute)
coverage (biofx.variants.features.Variant attribute)
D
dbsnp (biofx.variants.features.Variant attribute)
DEFAULT_CONFIG (biofx.parser.GSCDirectoryTreeParser.GSCDirectoryTree attribute)
DOMINANT (biofx.variants.Genes.Inheritance attribute)
E
eff_has_transcript() (in module biofx.parser.SnpEffparser)
effects (biofx.variants.features.Variant attribute)
end (biofx.variants.features.Variant attribute)
Ensembl (class in biofx.annotator.GSCannotation)
exit_program() (biofx.utils.LogUtils.OMICSLogger method)
F
filter() (biofx.utils.LogUtils.Masker method)
filter_snpeff_impact() (in module biofx.parser.SnpEffparser)
G
GAIN (biofx.variants.features.CNV attribute)
Gene (class in biofx.variants.Genes)
generate_mpileup() (in module biofx.variants.operations)
generate_status_file_names() (biofx.utils.LogUtils.OMICSLogger static method)
get_allele_frequencies() (biofx.variants.features.Indel method)
(biofx.variants.features.SNV method)
get_alt_count() (biofx.variants.features.SNV method)
get_chromosome_index() (biofx.variants.features.Variant method)
get_comments() (biofx.variants.features.Variant method)
get_coordinates() (biofx.variants.features.Variant method)
get_current_time() (biofx.utils.LogUtils.OMICSLogger method)
get_ensembl_gene_id() (biofx.annotator.GSCannotation.Ensembl method)
get_ensembl_transcript_id() (biofx.annotator.GSCannotation.Ensembl method)
get_ensg2symbol() (biofx.annotator.GSCannotation.WTSSGeneInfo method)
get_ensg_from_enst() (biofx.annotator.GSCannotation.WTSSGeneInfo method)
get_ensg_from_symbol() (biofx.annotator.GSCannotation.WTSSGeneInfo method)
get_enst2ensg() (biofx.annotator.GSCannotation.WTSSGeneInfo method)
get_file_with_id() (biofx.parser.GSCDirectoryTreeParser.GSCDirectoryTree method)
get_gene_name() (biofx.annotator.GSCannotation.Hugo method)
get_gene_symbol() (biofx.annotator.GSCannotation.WTSSGeneInfo method)
get_ids() (biofx.parser.GSCDirectoryTreeParser.GSCDirectoryTree method)
get_key() (biofx.variants.features.Variant method)
get_length() (biofx.variants.features.Indel method)
get_map() (biofx.annotator.GSCannotation.WTSSGeneExon method)
get_path_template() (biofx.parser.GSCDirectoryTreeParser.GSCDirectoryTemplate method)
get_pathogenicity() (biofx.variants.features.Variant method)
get_ref_count() (biofx.variants.features.SNV method)
get_rna_libraries() (biofx.parser.GSCDirectoryTreeParser.GSCDirectoryTree method)
get_sample_info() (biofx.parser.GSCDirectoryTreeParser.GSCDirectoryTree method)
get_strand_from_gene_symbol() (biofx.annotator.GSCannotation.WTSSGeneInfo method)
get_symbol2ensg() (biofx.annotator.GSCannotation.WTSSGeneInfo method)
get_tumour_content() (biofx.parser.GSCDirectoryTreeParser.GSCDirectoryTree method)
get_type() (biofx.variants.features.CNV method)
get_variant_info() (biofx.variants.features.Variant method)
get_variant_mpileup() (biofx.variants.features.Variant method)
get_wgs_libraries() (biofx.parser.GSCDirectoryTreeParser.GSCDirectoryTree method)
GSCDirectoryTemplate (class in biofx.parser.GSCDirectoryTreeParser)
GSCDirectoryTree (class in biofx.parser.GSCDirectoryTreeParser)
H
has_chromosome_error() (in module biofx.parser.SnpEffparser)
has_pathogenicity_conflict() (biofx.variants.features.Variant static method)
HEMIZYGOUS (biofx.variants.attributes.Zygosity attribute)
(biofx.variants.Genes.Zygosity attribute)
HETEROZYGOUS (biofx.variants.attributes.Zygosity attribute)
(biofx.variants.Genes.Zygosity attribute)
homopolymer (biofx.variants.features.Variant attribute)
HOMOZYGOUS (biofx.variants.attributes.Zygosity attribute)
(biofx.variants.Genes.Zygosity attribute)
Hugo (class in biofx.annotator.GSCannotation)
I
identifier (biofx.variants.features.Variant attribute)
Indel (class in biofx.variants.features)
info (biofx.variants.features.Variant attribute)
Inheritance (class in biofx.variants.Genes)
init_logging() (biofx.utils.LogUtils.OMICSLogger method)
is_complex() (in module biofx.variants.Genes)
is_recessive() (in module biofx.variants.Genes)
is_snp() (biofx.variants.features.SNV method)
(biofx.variants.features.Variant method)
is_special (biofx.variants.features.Variant attribute)
is_str() (in module biofx.utils.LogUtils)
L
log_end_time() (biofx.utils.LogUtils.OMICSLogger method)
log_run_info() (biofx.utils.LogUtils.OMICSLogger method)
log_section() (biofx.utils.LogUtils.OMICSLogger static method)
log_start_time() (biofx.utils.LogUtils.OMICSLogger method)
LOSS (biofx.variants.features.CNV attribute)
M
Masker (class in biofx.utils.LogUtils)
merge_eff_maps() (in module biofx.parser.SnpEffparser)
misc (biofx.variants.features.Variant attribute)
N
NEUTRAL (biofx.variants.features.CNV attribute)
normalize_splice_site() (biofx.variants.features.Variant method)
NOT_FOUND (biofx.variants.attributes.Zygosity attribute)
(biofx.variants.Genes.Zygosity attribute)
O
OMICSLogger (class in biofx.utils.LogUtils)
P
parse_effect() (in module biofx.parser.SnpEffparser)
parse_libraries() (biofx.parser.GSCDirectoryTreeParser.GSCDirectoryTree method)
parse_LRG() (in module biofx.parser.LRGparser)
parse_snpeff() (in module biofx.parser.SnpEffparser)
project (biofx.parser.GSCDirectoryTreeParser.GSCDirectoryTree attribute)
PROJECT_CONFIG (biofx.parser.GSCDirectoryTreeParser.GSCDirectoryTree attribute)
provenance (biofx.variants.features.Variant attribute)
R
RECESSIVE (biofx.variants.Genes.Inheritance attribute)
ref (biofx.variants.features.Variant attribute)
ref_count (biofx.variants.features.Variant attribute)
root (biofx.parser.GSCDirectoryTreeParser.GSCDirectoryTree attribute)
run_fail() (biofx.utils.LogUtils.OMICSLogger method)
run_incomplete() (biofx.utils.LogUtils.OMICSLogger method)
run_success() (biofx.utils.LogUtils.OMICSLogger method)
S
select_eff_by_gene_symbol() (in module biofx.parser.SnpEffparser)
select_eff_by_transcript() (in module biofx.parser.SnpEffparser)
set_allele_model() (biofx.variants.features.Variant method)
set_alt() (biofx.variants.features.Indel method)
(biofx.variants.features.SNV method)
set_alternative() (biofx.variants.features.Variant method)
set_alternative_genes() (biofx.variants.features.Variant method)
set_alternative_transcripts() (biofx.variants.features.Variant method)
set_cosmic() (biofx.variants.features.Variant method)
set_dbsnp() (biofx.variants.features.Variant method)
set_eff() (biofx.variants.features.Variant method)
set_effects() (biofx.variants.features.Variant method)
set_end() (biofx.variants.features.Variant method)
set_id() (biofx.parser.GSCDirectoryTreeParser.GSCDirectoryTree method)
(biofx.variants.features.Variant method)
set_provenance() (biofx.variants.features.Variant method)
set_ref() (biofx.variants.features.Indel method)
(biofx.variants.features.SNV method)
set_start() (biofx.variants.features.Variant method)
set_state() (biofx.variants.features.Indel method)
set_zygosity() (biofx.variants.features.Variant method)
SnpEff (class in biofx.annotator.VariantAnnotation)
snpeff_effects (biofx.variants.features.Variant attribute)
SNV (class in biofx.variants.features)
source (biofx.variants.features.Variant attribute)
start (biofx.variants.features.Variant attribute)
state (biofx.variants.features.Variant attribute)
T
TEMPLATE_CONFIG (biofx.parser.GSCDirectoryTreeParser.GSCDirectoryTemplate attribute)
U
UNKNOWN (biofx.variants.attributes.Zygosity attribute)
(biofx.variants.Genes.Inheritance attribute)
(biofx.variants.Genes.Zygosity attribute)
V
Variant (class in biofx.variants.features)
verify_effects() (in module biofx.parser.SnpEffparser)
vt_normalize() (biofx.variants.features.Indel method)
W
WTSSGeneExon (class in biofx.annotator.GSCannotation)
WTSSGeneInfo (class in biofx.annotator.GSCannotation)
Z
Zygosity (class in biofx.variants.attributes)
(class in biofx.variants.Genes)