changeo
stable
Immcantation Portal
Getting Started
Overview
Download
Installation
Data Standards
Release Notes
Usage Documentation
Commandline Usage
API
Examples
Using IgBLAST
Parsing IMGT output
Parsing 10X Genomics V(D)J data
Filtering records
Clustering sequences into clonal groups
Reconstructing germline sequences
IgPhyML lineage tree analysis
Generating MiAIRR compliant GenBank/TLS submissions
Methods
Clonal clustering methods
Reconstruction of germline sequences from alignment data
About
Contact
Citation
License
changeo
Index
Edit on Bitbucket
Index
Symbols
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O
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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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Y
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Z
Symbols
--10x <cellranger_files>
MakeDb.py-igblast command line option
MakeDb.py-igblast-aa command line option
MakeDb.py-ihmm command line option
MakeDb.py-imgt command line option
--act {first,set}
DefineClones.py command line option
--act {first}
AlignRecords.py-across command line option
AlignRecords.py-block command line option
--allele-delim <allele_delim>
ConvertDb.py-genbank command line option
--allow-stop
ConvertDb.py-genbank command line option
--append <append>
BuildTrees.py command line option
--asis-calls
ConvertDb.py-genbank command line option
MakeDb.py-igblast command line option
MakeDb.py-igblast-aa command line option
--asis-id
ConvertDb.py-genbank command line option
MakeDb.py-igblast command line option
MakeDb.py-igblast-aa command line option
MakeDb.py-ihmm command line option
MakeDb.py-imgt command line option
--asn
ConvertDb.py-genbank command line option
--asr <asr>
BuildTrees.py command line option
--calls {v,d,j}
AlignRecords.py-across command line option
AlignRecords.py-block command line option
--cdb <cdb>
AssignGenes.py-igblast command line option
--cell-type <cell_type>
ConvertDb.py-genbank command line option
--cf <c_field>
ConvertDb.py-genbank command line option
--cf <clone_field>
CreateGermlines.py command line option
--cf <cluster_field>
ConvertDb.py-baseline command line option
--clean {none,all}
BuildTrees.py command line option
--cloned
CreateGermlines.py command line option
--clones <target_clones>
BuildTrees.py command line option
--collapse
BuildTrees.py command line option
--db <db_xref>
ConvertDb.py-genbank command line option
--ddb <ddb>
AssignGenes.py-igblast command line option
--descend
ParseDb.py-sort command line option
--df <d_field>
CreateGermlines.py command line option
--dist <distance>
DefineClones.py command line option
--drop
ParseDb.py-merge command line option
--exec <igblast_exec>
AssignGenes.py-igblast command line option
AssignGenes.py-igblast-aa command line option
--exec <muscle_exec>
AlignRecords.py-across command line option
AlignRecords.py-block command line option
AlignRecords.py-within command line option
--exec <tbl2asn_exec>
ConvertDb.py-genbank command line option
--extended
MakeDb.py-igblast command line option
MakeDb.py-igblast-aa command line option
MakeDb.py-ihmm command line option
MakeDb.py-imgt command line option
--failed
AlignRecords.py-across command line option
AlignRecords.py-block command line option
AlignRecords.py-within command line option
BuildTrees.py command line option
CreateGermlines.py command line option
DefineClones.py command line option
MakeDb.py-igblast command line option
MakeDb.py-igblast-aa command line option
MakeDb.py-ihmm command line option
MakeDb.py-imgt command line option
--format {airr,changeo}
AlignRecords.py-across command line option
AlignRecords.py-block command line option
AlignRecords.py-within command line option
BuildTrees.py command line option
ConvertDb.py-genbank command line option
CreateGermlines.py command line option
DefineClones.py command line option
MakeDb.py-igblast command line option
MakeDb.py-igblast-aa command line option
MakeDb.py-ihmm command line option
MakeDb.py-imgt command line option
--format {blast,airr}
AssignGenes.py-igblast command line option
--gf <germ_field>
ConvertDb.py-baseline command line option
--gf <group_fields>
AlignRecords.py-across command line option
AlignRecords.py-block command line option
DefineClones.py command line option
--help
AlignRecords.py command line option
AlignRecords.py-across command line option
AlignRecords.py-block command line option
AlignRecords.py-within command line option
AssignGenes.py command line option
AssignGenes.py-igblast command line option
AssignGenes.py-igblast-aa command line option
BuildTrees.py command line option
ConvertDb.py command line option
ConvertDb.py-airr command line option
ConvertDb.py-baseline command line option
ConvertDb.py-changeo command line option
ConvertDb.py-fasta command line option
ConvertDb.py-genbank command line option
CreateGermlines.py command line option
DefineClones.py command line option
MakeDb.py command line option
MakeDb.py-igblast command line option
MakeDb.py-igblast-aa command line option
MakeDb.py-ihmm command line option
MakeDb.py-imgt command line option
ParseDb.py command line option
ParseDb.py-add command line option
ParseDb.py-delete command line option
ParseDb.py-drop command line option
ParseDb.py-index command line option
ParseDb.py-merge command line option
ParseDb.py-rename command line option
ParseDb.py-select command line option
ParseDb.py-sort command line option
ParseDb.py-split command line option
ParseDb.py-update command line option
--hotness <hotness>
BuildTrees.py command line option
--if <id_field>
ConvertDb.py-baseline command line option
ConvertDb.py-fasta command line option
--if <index_field>
ConvertDb.py-genbank command line option
--igphyml
BuildTrees.py command line option
--imgt-id-len <imgt_id_len>
MakeDb.py-imgt command line option
--inf <inference>
ConvertDb.py-genbank command line option
--infer-junction
MakeDb.py-igblast command line option
--isolate <isolate>
ConvertDb.py-genbank command line option
--jdb <jdb>
AssignGenes.py-igblast command line option
--jf <j_field>
CreateGermlines.py command line option
DefineClones.py command line option
--label <label>
ConvertDb.py-genbank command line option
--link {single,average,complete}
DefineClones.py command line option
--loci {ig,tr}
AssignGenes.py-igblast command line option
AssignGenes.py-igblast-aa command line option
--log <log_file>
AlignRecords.py-across command line option
AlignRecords.py-block command line option
AlignRecords.py-within command line option
BuildTrees.py command line option
CreateGermlines.py command line option
DefineClones.py command line option
MakeDb.py-igblast command line option
MakeDb.py-igblast-aa command line option
MakeDb.py-ihmm command line option
MakeDb.py-imgt command line option
--logic {any,all}
ParseDb.py-delete command line option
ParseDb.py-select command line option
--maxmiss <max_missing>
DefineClones.py command line option
--md <meta_data>
BuildTrees.py command line option
--mf <meta_fields>
ConvertDb.py-baseline command line option
ConvertDb.py-fasta command line option
--minseq <min_seq>
BuildTrees.py command line option
--mode {allele,gene}
AlignRecords.py-across command line option
AlignRecords.py-block command line option
DefineClones.py command line option
--model {ham,aa,hh_s1f,hh_s5f,mk_rs1nf,mk_rs5nf,hs1f_compat,m1n_compat}
DefineClones.py command line option
--mol <molecule>
ConvertDb.py-genbank command line option
--motifs <motifs>
BuildTrees.py command line option
--ncdr3
BuildTrees.py command line option
--nf <count_field>
ConvertDb.py-genbank command line option
--nmask
BuildTrees.py command line option
--nohlp
BuildTrees.py command line option
--norm {len,mut,none}
DefineClones.py command line option
--nproc <nproc>
AlignRecords.py-across command line option
AlignRecords.py-block command line option
AlignRecords.py-within command line option
AssignGenes.py-igblast command line option
AssignGenes.py-igblast-aa command line option
BuildTrees.py command line option
DefineClones.py command line option
--num
ParseDb.py-sort command line option
--num <num_split>
ParseDb.py-split command line option
--oformat {tab,txt}
BuildTrees.py command line option
--omega <omega>
BuildTrees.py command line option
--optimize {n,r,l,lr,tl,tlr}
BuildTrees.py command line option
--organism <organism>
ConvertDb.py-genbank command line option
--organism {human,mouse,rabbit,rat,rhesus_monkey}
AssignGenes.py-igblast command line option
AssignGenes.py-igblast-aa command line option
--outdir <out_dir>
AlignRecords.py-across command line option
AlignRecords.py-block command line option
AlignRecords.py-within command line option
AssignGenes.py-igblast command line option
AssignGenes.py-igblast-aa command line option
BuildTrees.py command line option
ConvertDb.py-airr command line option
ConvertDb.py-baseline command line option
ConvertDb.py-changeo command line option
ConvertDb.py-fasta command line option
ConvertDb.py-genbank command line option
CreateGermlines.py command line option
DefineClones.py command line option
MakeDb.py-igblast command line option
MakeDb.py-igblast-aa command line option
MakeDb.py-ihmm command line option
MakeDb.py-imgt command line option
ParseDb.py-add command line option
ParseDb.py-delete command line option
ParseDb.py-drop command line option
ParseDb.py-index command line option
ParseDb.py-merge command line option
ParseDb.py-rename command line option
ParseDb.py-select command line option
ParseDb.py-sort command line option
ParseDb.py-split command line option
ParseDb.py-update command line option
--outname <out_name>
AlignRecords.py-across command line option
AlignRecords.py-block command line option
AlignRecords.py-within command line option
AssignGenes.py-igblast command line option
AssignGenes.py-igblast-aa command line option
BuildTrees.py command line option
ConvertDb.py-airr command line option
ConvertDb.py-baseline command line option
ConvertDb.py-changeo command line option
ConvertDb.py-fasta command line option
ConvertDb.py-genbank command line option
CreateGermlines.py command line option
DefineClones.py command line option
MakeDb.py-igblast command line option
MakeDb.py-igblast-aa command line option
MakeDb.py-ihmm command line option
MakeDb.py-imgt command line option
ParseDb.py-add command line option
ParseDb.py-delete command line option
ParseDb.py-drop command line option
ParseDb.py-index command line option
ParseDb.py-merge command line option
ParseDb.py-rename command line option
ParseDb.py-select command line option
ParseDb.py-sort command line option
ParseDb.py-split command line option
ParseDb.py-update command line option
--partial
MakeDb.py-igblast command line option
MakeDb.py-ihmm command line option
MakeDb.py-imgt command line option
--product <product>
ConvertDb.py-genbank command line option
--regex
ParseDb.py-delete command line option
ParseDb.py-select command line option
--regions {default,rhesus-igl}
MakeDb.py-igblast command line option
MakeDb.py-igblast-aa command line option
--sample <sample_depth>
BuildTrees.py command line option
--sbt <asn_template>
ConvertDb.py-genbank command line option
--sex <sex>
ConvertDb.py-genbank command line option
--sf <seq_field>
ConvertDb.py-baseline command line option
ConvertDb.py-fasta command line option
CreateGermlines.py command line option
DefineClones.py command line option
--sf <seq_fields>
AlignRecords.py-across command line option
AlignRecords.py-block command line option
AlignRecords.py-within command line option
--sym {avg,min}
DefineClones.py command line option
--tissue <tissue>
ConvertDb.py-genbank command line option
--vdb <vdb>
AssignGenes.py-igblast command line option
AssignGenes.py-igblast-aa command line option
--version
AlignRecords.py command line option
AlignRecords.py-across command line option
AlignRecords.py-block command line option
AlignRecords.py-within command line option
AssignGenes.py command line option
AssignGenes.py-igblast command line option
AssignGenes.py-igblast-aa command line option
BuildTrees.py command line option
ConvertDb.py command line option
ConvertDb.py-airr command line option
ConvertDb.py-baseline command line option
ConvertDb.py-changeo command line option
ConvertDb.py-fasta command line option
ConvertDb.py-genbank command line option
CreateGermlines.py command line option
DefineClones.py command line option
MakeDb.py command line option
MakeDb.py-igblast command line option
MakeDb.py-igblast-aa command line option
MakeDb.py-ihmm command line option
MakeDb.py-imgt command line option
ParseDb.py command line option
ParseDb.py-add command line option
ParseDb.py-delete command line option
ParseDb.py-drop command line option
ParseDb.py-index command line option
ParseDb.py-merge command line option
ParseDb.py-rename command line option
ParseDb.py-select command line option
ParseDb.py-sort command line option
ParseDb.py-split command line option
ParseDb.py-update command line option
--vf <v_field>
CreateGermlines.py command line option
DefineClones.py command line option
-b <igdata>
AssignGenes.py-igblast command line option
AssignGenes.py-igblast-aa command line option
-d <db_files>
AlignRecords.py-across command line option
AlignRecords.py-block command line option
AlignRecords.py-within command line option
BuildTrees.py command line option
ConvertDb.py-airr command line option
ConvertDb.py-baseline command line option
ConvertDb.py-changeo command line option
ConvertDb.py-fasta command line option
ConvertDb.py-genbank command line option
CreateGermlines.py command line option
DefineClones.py command line option
ParseDb.py-add command line option
ParseDb.py-delete command line option
ParseDb.py-drop command line option
ParseDb.py-index command line option
ParseDb.py-merge command line option
ParseDb.py-rename command line option
ParseDb.py-select command line option
ParseDb.py-sort command line option
ParseDb.py-split command line option
ParseDb.py-update command line option
-f <field>
ParseDb.py-index command line option
ParseDb.py-sort command line option
ParseDb.py-split command line option
ParseDb.py-update command line option
-f <fields>
ParseDb.py-add command line option
ParseDb.py-delete command line option
ParseDb.py-drop command line option
ParseDb.py-rename command line option
ParseDb.py-select command line option
-g {full,dmask,vonly,regions}
CreateGermlines.py command line option
-h
AlignRecords.py command line option
AlignRecords.py-across command line option
AlignRecords.py-block command line option
AlignRecords.py-within command line option
AssignGenes.py command line option
AssignGenes.py-igblast command line option
AssignGenes.py-igblast-aa command line option
BuildTrees.py command line option
ConvertDb.py command line option
ConvertDb.py-airr command line option
ConvertDb.py-baseline command line option
ConvertDb.py-changeo command line option
ConvertDb.py-fasta command line option
ConvertDb.py-genbank command line option
CreateGermlines.py command line option
DefineClones.py command line option
MakeDb.py command line option
MakeDb.py-igblast command line option
MakeDb.py-igblast-aa command line option
MakeDb.py-ihmm command line option
MakeDb.py-imgt command line option
ParseDb.py command line option
ParseDb.py-add command line option
ParseDb.py-delete command line option
ParseDb.py-drop command line option
ParseDb.py-index command line option
ParseDb.py-merge command line option
ParseDb.py-rename command line option
ParseDb.py-select command line option
ParseDb.py-sort command line option
ParseDb.py-split command line option
ParseDb.py-update command line option
-i <aligner_files>
MakeDb.py-igblast command line option
MakeDb.py-igblast-aa command line option
MakeDb.py-ihmm command line option
MakeDb.py-imgt command line option
-k <names>
ParseDb.py-rename command line option
-o <out_file>
ParseDb.py-merge command line option
-o <out_files>
AlignRecords.py-across command line option
AlignRecords.py-block command line option
AlignRecords.py-within command line option
AssignGenes.py-igblast command line option
AssignGenes.py-igblast-aa command line option
ConvertDb.py-airr command line option
ConvertDb.py-baseline command line option
ConvertDb.py-changeo command line option
ConvertDb.py-fasta command line option
ConvertDb.py-genbank command line option
CreateGermlines.py command line option
DefineClones.py command line option
MakeDb.py-igblast command line option
MakeDb.py-igblast-aa command line option
MakeDb.py-ihmm command line option
MakeDb.py-imgt command line option
ParseDb.py-add command line option
ParseDb.py-delete command line option
ParseDb.py-drop command line option
ParseDb.py-index command line option
ParseDb.py-rename command line option
ParseDb.py-select command line option
ParseDb.py-sort command line option
ParseDb.py-update command line option
-r <references>
CreateGermlines.py command line option
-r <repo>
MakeDb.py-igblast command line option
MakeDb.py-igblast-aa command line option
MakeDb.py-ihmm command line option
MakeDb.py-imgt command line option
-s <seq_files>
AssignGenes.py-igblast command line option
AssignGenes.py-igblast-aa command line option
MakeDb.py-igblast command line option
MakeDb.py-igblast-aa command line option
MakeDb.py-ihmm command line option
MakeDb.py-imgt command line option
-t <kappa>
BuildTrees.py command line option
-t <updates>
ParseDb.py-update command line option
-u <values>
ParseDb.py-add command line option
ParseDb.py-delete command line option
ParseDb.py-select command line option
ParseDb.py-update command line option
-y <yaml_config>
ConvertDb.py-genbank command line option
_
__iter__() (changeo.IO.IgBLASTReader method)
(changeo.IO.IHMMuneReader method)
(changeo.IO.IMGTReader method)
(changeo.IO.TSVReader method)
__next__() (changeo.IO.IgBLASTReader method)
(changeo.IO.IHMMuneReader method)
(changeo.IO.IMGTReader method)
(changeo.IO.TSVReader method)
A
AIRRReader (class in changeo.IO)
AIRRSchema (class in changeo.Receptor)
AIRRSchemaAA (class in changeo.Receptor)
AIRRWriter (class in changeo.IO)
alignmentPositions() (in module changeo.Alignment)
AlignRecords.py command line option
--help
--version
-h
AlignRecords.py-across command line option
--act {first}
--calls {v,d,j}
--exec <muscle_exec>
--failed
--format {airr,changeo}
--gf <group_fields>
--help
--log <log_file>
--mode {allele,gene}
--nproc <nproc>
--outdir <out_dir>
--outname <out_name>
--sf <seq_fields>
--version
-d <db_files>
-h
-o <out_files>
AlignRecords.py-block command line option
--act {first}
--calls {v,d,j}
--exec <muscle_exec>
--failed
--format {airr,changeo}
--gf <group_fields>
--help
--log <log_file>
--mode {allele,gene}
--nproc <nproc>
--outdir <out_dir>
--outname <out_name>
--sf <seq_fields>
--version
-d <db_files>
-h
-o <out_files>
AlignRecords.py-within command line option
--exec <muscle_exec>
--failed
--format {airr,changeo}
--help
--log <log_file>
--nproc <nproc>
--outdir <out_dir>
--outname <out_name>
--sf <seq_fields>
--version
-d <db_files>
-h
-o <out_files>
aminoacid() (changeo.Receptor.ReceptorData static method)
annotations (changeo.Receptor.ReceptorData attribute)
AssignGenes.py command line option
--help
--version
-h
AssignGenes.py-igblast command line option
--cdb <cdb>
--ddb <ddb>
--exec <igblast_exec>
--format {blast,airr}
--help
--jdb <jdb>
--loci {ig,tr}
--nproc <nproc>
--organism {human,mouse,rabbit,rat,rhesus_monkey}
--outdir <out_dir>
--outname <out_name>
--vdb <vdb>
--version
-b <igdata>
-h
-o <out_files>
-s <seq_files>
AssignGenes.py-igblast-aa command line option
--exec <igblast_exec>
--help
--loci {ig,tr}
--nproc <nproc>
--organism {human,mouse,rabbit,rat,rhesus_monkey}
--outdir <out_dir>
--outname <out_name>
--vdb <vdb>
--version
-b <igdata>
-h
-o <out_files>
-s <seq_files>
B
buildClonalGermline() (in module changeo.Gene)
buildGermline() (in module changeo.Gene)
BuildTrees.py command line option
--append <append>
--asr <asr>
--clean {none,all}
--clones <target_clones>
--collapse
--failed
--format {airr,changeo}
--help
--hotness <hotness>
--igphyml
--log <log_file>
--md <meta_data>
--minseq <min_seq>
--motifs <motifs>
--ncdr3
--nmask
--nohlp
--nproc <nproc>
--oformat {tab,txt}
--omega <omega>
--optimize {n,r,l,lr,tl,tlr}
--outdir <out_dir>
--outname <out_name>
--sample <sample_depth>
--version
-d <db_files>
-h
-t <kappa>
C
c_call (changeo.Receptor.ReceptorData attribute)
calcDistances() (in module changeo.Distance)
cdr1_aa_imgt (changeo.Receptor.ReceptorData attribute)
cdr1_imgt (changeo.Receptor.ReceptorData attribute)
cdr2_aa_imgt (changeo.Receptor.ReceptorData attribute)
cdr2_imgt (changeo.Receptor.ReceptorData attribute)
cdr3_aa_imgt (changeo.Receptor.ReceptorData attribute)
cdr3_igblast (changeo.Receptor.ReceptorData attribute)
cdr3_igblast_aa (changeo.Receptor.ReceptorData attribute)
cdr3_imgt (changeo.Receptor.ReceptorData attribute)
cell (changeo.Receptor.ReceptorData attribute)
changeo.Alignment
module
changeo.Applications
module
changeo.Commandline
module
changeo.Distance
module
changeo.Gene
module
changeo.IO
module
changeo.Multiprocessing
module
changeo.Receptor
module
ChangeoReader (class in changeo.IO)
ChangeoSchema (class in changeo.Receptor)
ChangeoSchemaAA (class in changeo.Receptor)
ChangeoWriter (class in changeo.IO)
checkArgs() (in module changeo.Commandline)
checkFields() (in module changeo.IO)
clone (changeo.Receptor.ReceptorData attribute)
collectDbQueue() (in module changeo.Multiprocessing)
CommonHelpFormatter (class in changeo.Commandline)
conscount (changeo.Receptor.ReceptorData attribute)
ConvertDb.py command line option
--help
--version
-h
ConvertDb.py-airr command line option
--help
--outdir <out_dir>
--outname <out_name>
--version
-d <db_files>
-h
-o <out_files>
ConvertDb.py-baseline command line option
--cf <cluster_field>
--gf <germ_field>
--help
--if <id_field>
--mf <meta_fields>
--outdir <out_dir>
--outname <out_name>
--sf <seq_field>
--version
-d <db_files>
-h
-o <out_files>
ConvertDb.py-changeo command line option
--help
--outdir <out_dir>
--outname <out_name>
--version
-d <db_files>
-h
-o <out_files>
ConvertDb.py-fasta command line option
--help
--if <id_field>
--mf <meta_fields>
--outdir <out_dir>
--outname <out_name>
--sf <seq_field>
--version
-d <db_files>
-h
-o <out_files>
ConvertDb.py-genbank command line option
--allele-delim <allele_delim>
--allow-stop
--asis-calls
--asis-id
--asn
--cell-type <cell_type>
--cf <c_field>
--db <db_xref>
--exec <tbl2asn_exec>
--format {airr,changeo}
--help
--if <index_field>
--inf <inference>
--isolate <isolate>
--label <label>
--mol <molecule>
--nf <count_field>
--organism <organism>
--outdir <out_dir>
--outname <out_name>
--product <product>
--sbt <asn_template>
--sex <sex>
--tissue <tissue>
--version
-d <db_files>
-h
-o <out_files>
-y <yaml_config>
countDbFile() (in module changeo.IO)
CreateGermlines.py command line option
--cf <clone_field>
--cloned
--df <d_field>
--failed
--format {airr,changeo}
--help
--jf <j_field>
--log <log_file>
--outdir <out_dir>
--outname <out_name>
--sf <seq_field>
--version
--vf <v_field>
-d <db_files>
-g {full,dmask,vonly,regions}
-h
-o <out_files>
-r <references>
customFields() (changeo.IO.IgBLASTReader static method)
(changeo.IO.IgBLASTReaderAA static method)
(changeo.IO.IHMMuneReader static method)
(changeo.IO.IMGTReader static method)
D
d_btop (changeo.Receptor.ReceptorData attribute)
d_call (changeo.Receptor.ReceptorData attribute)
d_cigar (changeo.Receptor.ReceptorData attribute)
d_evalue (changeo.Receptor.ReceptorData attribute)
d_frame (changeo.Receptor.ReceptorData attribute)
d_germ_aa_end() (changeo.Receptor.Receptor property)
d_germ_aa_length (changeo.Receptor.ReceptorData attribute)
d_germ_aa_start (changeo.Receptor.ReceptorData attribute)
d_germ_end() (changeo.Receptor.Receptor property)
d_germ_length (changeo.Receptor.ReceptorData attribute)
d_germ_start (changeo.Receptor.ReceptorData attribute)
d_identity (changeo.Receptor.ReceptorData attribute)
d_score (changeo.Receptor.ReceptorData attribute)
d_seq_aa_end() (changeo.Receptor.Receptor property)
d_seq_aa_length (changeo.Receptor.ReceptorData attribute)
d_seq_aa_start (changeo.Receptor.ReceptorData attribute)
d_seq_end() (changeo.Receptor.Receptor property)
d_seq_length (changeo.Receptor.ReceptorData attribute)
d_seq_start (changeo.Receptor.ReceptorData attribute)
data (changeo.Multiprocessing.DbData attribute)
(changeo.Multiprocessing.DbResult attribute)
data_count() (changeo.Multiprocessing.DbResult property)
data_fail (changeo.Multiprocessing.DbResult attribute)
data_pass (changeo.Multiprocessing.DbResult attribute)
DbData (class in changeo.Multiprocessing)
DbResult (class in changeo.Multiprocessing)
decodeBTOP() (in module changeo.Alignment)
decodeCIGAR() (in module changeo.Alignment)
DefineClones.py command line option
--act {first,set}
--dist <distance>
--failed
--format {airr,changeo}
--gf <group_fields>
--help
--jf <j_field>
--link {single,average,complete}
--log <log_file>
--maxmiss <max_missing>
--mode {allele,gene}
--model {ham,aa,hh_s1f,hh_s5f,mk_rs1nf,mk_rs5nf,hs1f_compat,m1n_compat}
--norm {len,mut,none}
--nproc <nproc>
--outdir <out_dir>
--outname <out_name>
--sf <seq_field>
--sym {avg,min}
--version
--vf <v_field>
-d <db_files>
-h
-o <out_files>
double() (changeo.Receptor.ReceptorData static method)
dupcount (changeo.Receptor.ReceptorData attribute)
E
encodeCIGAR() (in module changeo.Alignment)
end_fields (changeo.Receptor.ReceptorData attribute)
extractIMGT() (in module changeo.IO)
F
feedDbQueue() (in module changeo.Multiprocessing)
fields (changeo.IO.TSVReader attribute)
(changeo.Receptor.AIRRSchema attribute)
(changeo.Receptor.ChangeoSchema attribute)
formClusters() (in module changeo.Distance)
fromReceptor() (changeo.Receptor.AIRRSchema static method)
(changeo.Receptor.ChangeoSchema static method)
functional (changeo.Receptor.ReceptorData attribute)
fwr1_aa_imgt (changeo.Receptor.ReceptorData attribute)
fwr1_imgt (changeo.Receptor.ReceptorData attribute)
fwr2_aa_imgt (changeo.Receptor.ReceptorData attribute)
fwr2_imgt (changeo.Receptor.ReceptorData attribute)
fwr3_aa_imgt (changeo.Receptor.ReceptorData attribute)
fwr3_imgt (changeo.Receptor.ReceptorData attribute)
fwr4_aa_imgt (changeo.Receptor.ReceptorData attribute)
fwr4_imgt (changeo.Receptor.ReceptorData attribute)
G
gapV() (in module changeo.Alignment)
germline_aa_imgt (changeo.Receptor.ReceptorData attribute)
germline_aa_vdj (changeo.Receptor.ReceptorData attribute)
germline_imgt (changeo.Receptor.ReceptorData attribute)
germline_imgt_d_mask (changeo.Receptor.ReceptorData attribute)
germline_vdj (changeo.Receptor.ReceptorData attribute)
germline_vdj_d_mask (changeo.Receptor.ReceptorData attribute)
getAADistMatrix() (in module changeo.Distance)
getAIRR() (changeo.Receptor.Receptor method)
getAllele() (in module changeo.Gene)
getAlleleCalls() (changeo.Receptor.Receptor method)
getAlleleNumber() (in module changeo.Gene)
getAlleleNumbers() (changeo.Receptor.Receptor method)
getCAllele() (in module changeo.Gene)
getCGene() (in module changeo.Gene)
getChangeo() (changeo.Receptor.Receptor method)
getCommonArgParser() (in module changeo.Commandline)
getDAllele() (changeo.Receptor.Receptor method)
(in module changeo.Gene)
getDAlleleNumber() (changeo.Receptor.Receptor method)
getDbFields() (in module changeo.IO)
getDFamily() (changeo.Receptor.Receptor method)
getDGene() (changeo.Receptor.Receptor method)
getDGermline() (in module changeo.Gene)
getDNADistMatrix() (in module changeo.Distance)
getFamily() (in module changeo.Gene)
getFamilyCalls() (changeo.Receptor.Receptor method)
getField() (changeo.Receptor.Receptor method)
getFormatOperators() (in module changeo.IO)
getGene() (in module changeo.Gene)
getGeneCalls() (changeo.Receptor.Receptor method)
getIgBLASTVersion() (in module changeo.Applications)
getJAllele() (changeo.Receptor.Receptor method)
(in module changeo.Gene)
getJAlleleNumber() (changeo.Receptor.Receptor method)
getJFamily() (changeo.Receptor.Receptor method)
getJGene() (changeo.Receptor.Receptor method)
getJGermline() (in module changeo.Gene)
getLocus() (in module changeo.Gene)
getNmers() (in module changeo.Distance)
getOutputHandle() (in module changeo.IO)
getOutputName() (in module changeo.IO)
getRegions() (changeo.Alignment.RegionDefinition method)
(in module changeo.Alignment)
getSeq() (changeo.Receptor.Receptor method)
getVAllele() (changeo.Receptor.Receptor method)
(in module changeo.Gene)
getVAlleleNumber() (changeo.Receptor.Receptor method)
getVFamily() (changeo.Receptor.Receptor method)
getVGene() (changeo.Receptor.Receptor method)
getVGermline() (in module changeo.Gene)
I
id (changeo.Multiprocessing.DbData attribute)
(changeo.Multiprocessing.DbResult attribute)
identity() (changeo.Receptor.ReceptorData static method)
IgBLASTReader (class in changeo.IO)
IgBLASTReaderAA (class in changeo.IO)
ihmmune_fields (changeo.IO.IHMMuneReader attribute)
IHMMuneReader (class in changeo.IO)
IMGTReader (class in changeo.IO)
in_frame (changeo.Receptor.ReceptorData attribute)
indels (changeo.Receptor.ReceptorData attribute)
inferJunction() (in module changeo.Alignment)
integer() (changeo.Receptor.ReceptorData static method)
J
j_btop (changeo.Receptor.ReceptorData attribute)
j_call (changeo.Receptor.ReceptorData attribute)
j_cigar (changeo.Receptor.ReceptorData attribute)
j_evalue (changeo.Receptor.ReceptorData attribute)
j_germ_aa_end() (changeo.Receptor.Receptor property)
j_germ_aa_length (changeo.Receptor.ReceptorData attribute)
j_germ_aa_start (changeo.Receptor.ReceptorData attribute)
j_germ_end() (changeo.Receptor.Receptor property)
j_germ_length (changeo.Receptor.ReceptorData attribute)
j_germ_start (changeo.Receptor.ReceptorData attribute)
j_identity (changeo.Receptor.ReceptorData attribute)
j_score (changeo.Receptor.ReceptorData attribute)
j_seq_aa_end() (changeo.Receptor.Receptor property)
j_seq_aa_length (changeo.Receptor.ReceptorData attribute)
j_seq_aa_start (changeo.Receptor.ReceptorData attribute)
j_seq_end() (changeo.Receptor.Receptor property)
j_seq_length (changeo.Receptor.ReceptorData attribute)
j_seq_start (changeo.Receptor.ReceptorData attribute)
junction (changeo.Receptor.ReceptorData attribute)
junction_aa (changeo.Receptor.ReceptorData attribute)
junction_end() (changeo.Receptor.Receptor property)
junction_length (changeo.Receptor.ReceptorData attribute)
junction_start (changeo.Receptor.ReceptorData attribute)
L
length_fields (changeo.Receptor.ReceptorData attribute)
log (changeo.Multiprocessing.DbResult attribute)
logical() (changeo.Receptor.ReceptorData static method)
M
MakeDb.py command line option
--help
--version
-h
MakeDb.py-igblast command line option
--10x <cellranger_files>
--asis-calls
--asis-id
--extended
--failed
--format {airr,changeo}
--help
--infer-junction
--log <log_file>
--outdir <out_dir>
--outname <out_name>
--partial
--regions {default,rhesus-igl}
--version
-h
-i <aligner_files>
-o <out_files>
-r <repo>
-s <seq_files>
MakeDb.py-igblast-aa command line option
--10x <cellranger_files>
--asis-calls
--asis-id
--extended
--failed
--format {airr,changeo}
--help
--log <log_file>
--outdir <out_dir>
--outname <out_name>
--regions {default,rhesus-igl}
--version
-h
-i <aligner_files>
-o <out_files>
-r <repo>
-s <seq_files>
MakeDb.py-ihmm command line option
--10x <cellranger_files>
--asis-id
--extended
--failed
--format {airr,changeo}
--help
--log <log_file>
--outdir <out_dir>
--outname <out_name>
--partial
--version
-h
-i <aligner_files>
-o <out_files>
-r <repo>
-s <seq_files>
MakeDb.py-imgt command line option
--10x <cellranger_files>
--asis-id
--extended
--failed
--format {airr,changeo}
--help
--imgt-id-len <imgt_id_len>
--log <log_file>
--outdir <out_dir>
--outname <out_name>
--partial
--version
-h
-i <aligner_files>
-o <out_files>
-r <repo>
-s <seq_files>
module
changeo.Alignment
changeo.Applications
changeo.Commandline
changeo.Distance
changeo.Gene
changeo.IO
changeo.Multiprocessing
changeo.Receptor
mutated_invariant (changeo.Receptor.ReceptorData attribute)
N
n1_length (changeo.Receptor.ReceptorData attribute)
n2_length (changeo.Receptor.ReceptorData attribute)
np1_aa_length (changeo.Receptor.ReceptorData attribute)
np1_aa_start (changeo.Receptor.ReceptorData attribute)
np1_length (changeo.Receptor.ReceptorData attribute)
np1_start (changeo.Receptor.ReceptorData attribute)
np2_aa_length (changeo.Receptor.ReceptorData attribute)
np2_aa_start (changeo.Receptor.ReceptorData attribute)
np2_length (changeo.Receptor.ReceptorData attribute)
np2_start (changeo.Receptor.ReceptorData attribute)
nucleotide() (changeo.Receptor.ReceptorData static method)
O
out_type (changeo.Receptor.AIRRSchema attribute)
(changeo.Receptor.ChangeoSchema attribute)
P
p3d_length (changeo.Receptor.ReceptorData attribute)
p3v_length (changeo.Receptor.ReceptorData attribute)
p5d_length (changeo.Receptor.ReceptorData attribute)
p5j_length (changeo.Receptor.ReceptorData attribute)
padAlignment() (in module changeo.Alignment)
parseBlock() (changeo.IO.IgBLASTReader method)
parseCommonArgs() (in module changeo.Commandline)
ParseDb.py command line option
--help
--version
-h
ParseDb.py-add command line option
--help
--outdir <out_dir>
--outname <out_name>
--version
-d <db_files>
-f <fields>
-h
-o <out_files>
-u <values>
ParseDb.py-delete command line option
--help
--logic {any,all}
--outdir <out_dir>
--outname <out_name>
--regex
--version
-d <db_files>
-f <fields>
-h
-o <out_files>
-u <values>
ParseDb.py-drop command line option
--help
--outdir <out_dir>
--outname <out_name>
--version
-d <db_files>
-f <fields>
-h
-o <out_files>
ParseDb.py-index command line option
--help
--outdir <out_dir>
--outname <out_name>
--version
-d <db_files>
-f <field>
-h
-o <out_files>
ParseDb.py-merge command line option
--drop
--help
--outdir <out_dir>
--outname <out_name>
--version
-d <db_files>
-h
-o <out_file>
ParseDb.py-rename command line option
--help
--outdir <out_dir>
--outname <out_name>
--version
-d <db_files>
-f <fields>
-h
-k <names>
-o <out_files>
ParseDb.py-select command line option
--help
--logic {any,all}
--outdir <out_dir>
--outname <out_name>
--regex
--version
-d <db_files>
-f <fields>
-h
-o <out_files>
-u <values>
ParseDb.py-sort command line option
--descend
--help
--num
--outdir <out_dir>
--outname <out_name>
--version
-d <db_files>
-f <field>
-h
-o <out_files>
ParseDb.py-split command line option
--help
--num <num_split>
--outdir <out_dir>
--outname <out_name>
--version
-d <db_files>
-f <field>
-h
ParseDb.py-update command line option
--help
--outdir <out_dir>
--outname <out_name>
--version
-d <db_files>
-f <field>
-h
-o <out_files>
-t <updates>
-u <values>
parseGeneCall() (in module changeo.Gene)
parseRecord() (changeo.IO.IHMMuneReader method)
(changeo.IO.IMGTReader method)
parsers (changeo.Receptor.ReceptorData attribute)
parseSections() (changeo.IO.IgBLASTReader method)
(changeo.IO.IgBLASTReaderAA method)
processDbQueue() (in module changeo.Multiprocessing)
R
reader (changeo.IO.TSVReader attribute)
readGermlines() (in module changeo.IO)
Receptor (class in changeo.Receptor)
ReceptorData (class in changeo.Receptor)
RegionDefinition (class in changeo.Alignment)
required (changeo.Receptor.AIRRSchema attribute)
(changeo.Receptor.AIRRSchemaAA attribute)
(changeo.Receptor.ChangeoSchema attribute)
(changeo.Receptor.ChangeoSchemaAA attribute)
results (changeo.Multiprocessing.DbResult attribute)
rev_comp (changeo.Receptor.ReceptorData attribute)
runASN() (in module changeo.Applications)
runIgBLASTN() (in module changeo.Applications)
runIgBLASTP() (in module changeo.Applications)
runIgPhyML() (in module changeo.Applications)
S
sequence_aa_imgt (changeo.Receptor.ReceptorData attribute)
sequence_aa_input (changeo.Receptor.ReceptorData attribute)
sequence_aa_vdj (changeo.Receptor.ReceptorData attribute)
sequence_id (changeo.Receptor.ReceptorData attribute)
sequence_imgt (changeo.Receptor.ReceptorData attribute)
sequence_input (changeo.Receptor.ReceptorData attribute)
sequence_vdj (changeo.Receptor.ReceptorData attribute)
setDefaultFields() (in module changeo.Commandline)
setDict() (changeo.Receptor.Receptor method)
setField() (changeo.Receptor.Receptor method)
splitName() (in module changeo.IO)
start_fields (changeo.Receptor.ReceptorData attribute)
stitchRegions() (in module changeo.Gene)
stitchVDJ() (in module changeo.Gene)
stop (changeo.Receptor.ReceptorData attribute)
T
toDict() (changeo.Receptor.Receptor method)
toReceptor() (changeo.Receptor.AIRRSchema static method)
(changeo.Receptor.ChangeoSchema static method)
TSVReader (class in changeo.IO)
TSVWriter (class in changeo.IO)
U
umicount (changeo.Receptor.ReceptorData attribute)
V
v_btop (changeo.Receptor.ReceptorData attribute)
v_call (changeo.Receptor.ReceptorData attribute)
v_cigar (changeo.Receptor.ReceptorData attribute)
v_evalue (changeo.Receptor.ReceptorData attribute)
v_frameshift (changeo.Receptor.ReceptorData attribute)
v_germ_aa_end_imgt() (changeo.Receptor.Receptor property)
v_germ_aa_end_vdj() (changeo.Receptor.Receptor property)
v_germ_aa_length_imgt (changeo.Receptor.ReceptorData attribute)
v_germ_aa_length_vdj (changeo.Receptor.ReceptorData attribute)
v_germ_aa_start_imgt (changeo.Receptor.ReceptorData attribute)
v_germ_aa_start_vdj (changeo.Receptor.ReceptorData attribute)
v_germ_end_imgt() (changeo.Receptor.Receptor property)
v_germ_end_vdj() (changeo.Receptor.Receptor property)
v_germ_length_imgt (changeo.Receptor.ReceptorData attribute)
v_germ_length_vdj (changeo.Receptor.ReceptorData attribute)
v_germ_start_imgt (changeo.Receptor.ReceptorData attribute)
v_germ_start_vdj (changeo.Receptor.ReceptorData attribute)
v_identity (changeo.Receptor.ReceptorData attribute)
v_score (changeo.Receptor.ReceptorData attribute)
v_seq_aa_end() (changeo.Receptor.Receptor property)
v_seq_aa_length (changeo.Receptor.ReceptorData attribute)
v_seq_aa_start (changeo.Receptor.ReceptorData attribute)
v_seq_end() (changeo.Receptor.Receptor property)
v_seq_length (changeo.Receptor.ReceptorData attribute)
v_seq_start (changeo.Receptor.ReceptorData attribute)
valid (changeo.Multiprocessing.DbData attribute)
(changeo.Multiprocessing.DbResult attribute)
vdj_score (changeo.Receptor.ReceptorData attribute)
W
writeDict() (changeo.IO.TSVWriter method)
writeHeader() (changeo.IO.TSVWriter method)
writeReceptor() (changeo.IO.AIRRWriter method)
(changeo.IO.ChangeoWriter method)
Y
yamlDict() (in module changeo.IO)
Z
zip_equal() (in module changeo.Distance)
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