changeo
0.4.6
Getting Started
Overview
Download
Installation
Data Standard
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
Usage Documentation
Commandline Usage
API
About
Release Notes
Contact
Citation
License
Related Projects
Immcantation Portal
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Index
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Index
Symbols
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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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I
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J
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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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Y
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Z
Symbols
--10x <cellranger_file>
MakeDb-igblast command line option
MakeDb-ihmm command line option
MakeDb-imgt command line option
--act {first,set}
DefineClones command line option
--act {first}
AlignRecords-across command line option
AlignRecords-block command line option
--allele-delim <allele_delim>
ConvertDb-genbank command line option
--allow-stop
ConvertDb-genbank command line option
--append <append>
BuildTrees command line option
--asis-calls
ConvertDb-genbank command line option
MakeDb-igblast command line option
--asis-id
ConvertDb-genbank command line option
MakeDb-igblast command line option
MakeDb-ihmm command line option
MakeDb-imgt command line option
--asn
ConvertDb-genbank command line option
--calls {v,d,j}
AlignRecords-across command line option
AlignRecords-block command line option
--cell-type <cell_type>
ConvertDb-genbank command line option
--cf <c_field>
ConvertDb-genbank command line option
--cf <cluster_field>
ConvertDb-baseline command line option
--clean {none,all}
BuildTrees command line option
--cloned
CreateGermlines command line option
--clones <target_clones>
BuildTrees command line option
--collapse
BuildTrees command line option
--db <db_xref>
ConvertDb-genbank command line option
--ddb <ddb>
AssignGenes-igblast command line option
--descend
ParseDb-sort command line option
--df <d_field>
CreateGermlines command line option
--dist <distance>
DefineClones command line option
--drop
ParseDb-merge command line option
--exec <igblast_exec>
AssignGenes-igblast command line option
--exec <muscle_exec>
AlignRecords-across command line option
AlignRecords-block command line option
AlignRecords-within command line option
--exec <tbl2asn_exec>
ConvertDb-genbank command line option
--extended
MakeDb-igblast command line option
MakeDb-ihmm command line option
MakeDb-imgt command line option
--failed
AlignRecords-across command line option
AlignRecords-block command line option
AlignRecords-within command line option
BuildTrees command line option
CreateGermlines command line option
DefineClones command line option
MakeDb-igblast command line option
MakeDb-ihmm command line option
MakeDb-imgt command line option
--format {blast,airr}
AssignGenes-igblast command line option
--format {changeo,airr}
AlignRecords-across command line option
AlignRecords-block command line option
AlignRecords-within command line option
BuildTrees command line option
ConvertDb-genbank command line option
CreateGermlines command line option
DefineClones command line option
MakeDb-igblast command line option
MakeDb-ihmm command line option
MakeDb-imgt command line option
--gf <germ_field>
ConvertDb-baseline command line option
--gf <group_fields>
AlignRecords-across command line option
AlignRecords-block command line option
DefineClones command line option
--hotness <hotness>
BuildTrees command line option
--if <id_field>
ConvertDb-baseline command line option
ConvertDb-fasta command line option
--if <index_field>
ConvertDb-genbank command line option
--igphyml
BuildTrees command line option
--inf <inference>
ConvertDb-genbank command line option
--isolate <isolate>
ConvertDb-genbank command line option
--jdb <jdb>
AssignGenes-igblast command line option
--jf <j_field>
CreateGermlines command line option
DefineClones command line option
--label <label>
ConvertDb-genbank command line option
--link {single,average,complete}
DefineClones command line option
--loci {ig,tr}
AssignGenes-igblast command line option
--log <log_file>
AlignRecords-across command line option
AlignRecords-block command line option
AlignRecords-within command line option
BuildTrees command line option
CreateGermlines command line option
DefineClones command line option
MakeDb-igblast command line option
MakeDb-ihmm command line option
MakeDb-imgt command line option
--logic {any,all}
ParseDb-delete command line option
ParseDb-select command line option
--maxmiss <max_missing>
DefineClones command line option
--md <meta_data>
BuildTrees command line option
--mf <meta_fields>
ConvertDb-baseline command line option
ConvertDb-fasta command line option
--minseq <min_seq>
BuildTrees command line option
--mode {allele,gene}
AlignRecords-across command line option
AlignRecords-block command line option
DefineClones command line option
--model {ham,aa,hh_s1f,hh_s5f,mk_rs1nf,mk_rs5nf,hs1f_compat,m1n_compat}
DefineClones command line option
--mol <molecule>
ConvertDb-genbank command line option
--motifs <motifs>
BuildTrees command line option
--ncdr3
BuildTrees command line option
--nf <count_field>
ConvertDb-genbank command line option
--nohlp
BuildTrees command line option
--norm {len,mut,none}
DefineClones command line option
--nproc <nproc>
AlignRecords-across command line option
AlignRecords-block command line option
AlignRecords-within command line option
AssignGenes-igblast command line option
BuildTrees command line option
DefineClones command line option
--num
ParseDb-sort command line option
--num <num_split>
ParseDb-split command line option
--oformat {tab,txt}
BuildTrees command line option
--omega {e,ce,e,e,ce,e,e,ce,ce,ce}
BuildTrees command line option
--optimize {n,r,l,lr,tl,tlr}
BuildTrees command line option
--organism <organism>
ConvertDb-genbank command line option
--organism {human,mouse,rabbit,rat,rhesus_monkey}
AssignGenes-igblast command line option
--outdir <out_dir>
AlignRecords-across command line option
AlignRecords-block command line option
AlignRecords-within command line option
AssignGenes-igblast command line option
BuildTrees command line option
ConvertDb-airr command line option
ConvertDb-baseline command line option
ConvertDb-changeo command line option
ConvertDb-fasta command line option
ConvertDb-genbank command line option
CreateGermlines command line option
DefineClones command line option
MakeDb-igblast command line option
MakeDb-ihmm command line option
MakeDb-imgt command line option
ParseDb-add command line option
ParseDb-delete command line option
ParseDb-drop command line option
ParseDb-index command line option
ParseDb-merge command line option
ParseDb-rename command line option
ParseDb-select command line option
ParseDb-sort command line option
ParseDb-split command line option
ParseDb-update command line option
--outname <out_name>
AlignRecords-across command line option
AlignRecords-block command line option
AlignRecords-within command line option
AssignGenes-igblast command line option
BuildTrees command line option
ConvertDb-airr command line option
ConvertDb-baseline command line option
ConvertDb-changeo command line option
ConvertDb-fasta command line option
ConvertDb-genbank command line option
CreateGermlines command line option
DefineClones command line option
MakeDb-igblast command line option
MakeDb-ihmm command line option
MakeDb-imgt command line option
ParseDb-add command line option
ParseDb-delete command line option
ParseDb-drop command line option
ParseDb-index command line option
ParseDb-merge command line option
ParseDb-rename command line option
ParseDb-select command line option
ParseDb-sort command line option
ParseDb-split command line option
ParseDb-update command line option
--partial
MakeDb-igblast command line option
MakeDb-ihmm command line option
MakeDb-imgt command line option
--product <product>
ConvertDb-genbank command line option
--regex
ParseDb-delete command line option
ParseDb-select command line option
--sample <sample_depth>
BuildTrees command line option
--sbt <asn_template>
ConvertDb-genbank command line option
--sex <sex>
ConvertDb-genbank command line option
--sf <seq_field>
ConvertDb-baseline command line option
ConvertDb-fasta command line option
CreateGermlines command line option
DefineClones command line option
--sf <seq_fields>
AlignRecords-across command line option
AlignRecords-block command line option
AlignRecords-within command line option
--sym {avg,min}
DefineClones command line option
--tissue <tissue>
ConvertDb-genbank command line option
--vdb <vdb>
AssignGenes-igblast command line option
--version
AlignRecords command line option
AlignRecords-across command line option
AlignRecords-block command line option
AlignRecords-within command line option
AssignGenes command line option
AssignGenes-igblast command line option
BuildTrees command line option
ConvertDb command line option
ConvertDb-airr command line option
ConvertDb-baseline command line option
ConvertDb-changeo command line option
ConvertDb-fasta command line option
ConvertDb-genbank command line option
CreateGermlines command line option
DefineClones command line option
MakeDb command line option
MakeDb-igblast command line option
MakeDb-ihmm command line option
MakeDb-imgt command line option
ParseDb command line option
ParseDb-add command line option
ParseDb-delete command line option
ParseDb-drop command line option
ParseDb-index command line option
ParseDb-merge command line option
ParseDb-rename command line option
ParseDb-select command line option
ParseDb-sort command line option
ParseDb-split command line option
ParseDb-update command line option
--vf <v_field>
CreateGermlines command line option
DefineClones command line option
-b <igdata>
AssignGenes-igblast command line option
-d <db_files>
AlignRecords-across command line option
AlignRecords-block command line option
AlignRecords-within command line option
BuildTrees command line option
ConvertDb-airr command line option
ConvertDb-baseline command line option
ConvertDb-changeo command line option
ConvertDb-fasta command line option
ConvertDb-genbank command line option
CreateGermlines command line option
DefineClones command line option
ParseDb-add command line option
ParseDb-delete command line option
ParseDb-drop command line option
ParseDb-index command line option
ParseDb-merge command line option
ParseDb-rename command line option
ParseDb-select command line option
ParseDb-sort command line option
ParseDb-split command line option
ParseDb-update command line option
-f <field>
ParseDb-index command line option
ParseDb-sort command line option
ParseDb-split command line option
ParseDb-update command line option
-f <fields>
ParseDb-add command line option
ParseDb-delete command line option
ParseDb-drop command line option
ParseDb-rename command line option
ParseDb-select command line option
-g {full,dmask,vonly,regions}
CreateGermlines command line option
-h, --help
AlignRecords command line option
AlignRecords-across command line option
AlignRecords-block command line option
AlignRecords-within command line option
AssignGenes command line option
AssignGenes-igblast command line option
BuildTrees command line option
ConvertDb command line option
ConvertDb-airr command line option
ConvertDb-baseline command line option
ConvertDb-changeo command line option
ConvertDb-fasta command line option
ConvertDb-genbank command line option
CreateGermlines command line option
DefineClones command line option
MakeDb command line option
MakeDb-igblast command line option
MakeDb-ihmm command line option
MakeDb-imgt command line option
ParseDb command line option
ParseDb-add command line option
ParseDb-delete command line option
ParseDb-drop command line option
ParseDb-index command line option
ParseDb-merge command line option
ParseDb-rename command line option
ParseDb-select command line option
ParseDb-sort command line option
ParseDb-split command line option
ParseDb-update command line option
-i <aligner_files>
MakeDb-igblast command line option
MakeDb-ihmm command line option
MakeDb-imgt command line option
-k <names>
ParseDb-rename command line option
-o <out_file>
ParseDb-merge command line option
-o <out_files>
AlignRecords-across command line option
AlignRecords-block command line option
AlignRecords-within command line option
AssignGenes-igblast command line option
ConvertDb-airr command line option
ConvertDb-baseline command line option
ConvertDb-changeo command line option
ConvertDb-fasta command line option
ConvertDb-genbank command line option
CreateGermlines command line option
DefineClones command line option
MakeDb-igblast command line option
MakeDb-ihmm command line option
MakeDb-imgt command line option
ParseDb-add command line option
ParseDb-delete command line option
ParseDb-drop command line option
ParseDb-index command line option
ParseDb-rename command line option
ParseDb-select command line option
ParseDb-sort command line option
ParseDb-update command line option
-r <references>
CreateGermlines command line option
-r <repo>
MakeDb-igblast command line option
MakeDb-ihmm command line option
MakeDb-imgt command line option
-s <seq_files>
AssignGenes-igblast command line option
MakeDb-igblast command line option
MakeDb-ihmm command line option
MakeDb-imgt command line option
-t <updates>
ParseDb-update command line option
-t {e,ce}
BuildTrees command line option
-u <values>
ParseDb-add command line option
ParseDb-delete command line option
ParseDb-select command line option
ParseDb-update command line option
-y <yaml_config>
ConvertDb-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)
AIRRWriter (class in changeo.IO)
alignmentPositions() (in module changeo.Alignment)
AlignRecords command line option
--version
-h, --help
AlignRecords-across command line option
--act {first}
--calls {v,d,j}
--exec <muscle_exec>
--failed
--format {changeo,airr}
--gf <group_fields>
--log <log_file>
--mode {allele,gene}
--nproc <nproc>
--outdir <out_dir>
--outname <out_name>
--sf <seq_fields>
--version
-d <db_files>
-h, --help
-o <out_files>
AlignRecords-block command line option
--act {first}
--calls {v,d,j}
--exec <muscle_exec>
--failed
--format {changeo,airr}
--gf <group_fields>
--log <log_file>
--mode {allele,gene}
--nproc <nproc>
--outdir <out_dir>
--outname <out_name>
--sf <seq_fields>
--version
-d <db_files>
-h, --help
-o <out_files>
AlignRecords-within command line option
--exec <muscle_exec>
--failed
--format {changeo,airr}
--log <log_file>
--nproc <nproc>
--outdir <out_dir>
--outname <out_name>
--sf <seq_fields>
--version
-d <db_files>
-h, --help
-o <out_files>
aminoacid() (changeo.Receptor.ReceptorData static method)
annotations (changeo.Receptor.ReceptorData attribute)
AssignGenes command line option
--version
-h, --help
AssignGenes-igblast command line option
--ddb <ddb>
--exec <igblast_exec>
--format {blast,airr}
--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, --help
-o <out_files>
-s <seq_files>
B
buildClonalGermline() (in module changeo.Gene)
buildGermline() (in module changeo.Gene)
BuildTrees command line option
--append <append>
--clean {none,all}
--clones <target_clones>
--collapse
--failed
--format {changeo,airr}
--hotness <hotness>
--igphyml
--log <log_file>
--md <meta_data>
--minseq <min_seq>
--motifs <motifs>
--ncdr3
--nohlp
--nproc <nproc>
--oformat {tab,txt}
--omega {e,ce,e,e,ce,e,e,ce,ce,ce}
--optimize {n,r,l,lr,tl,tlr}
--outdir <out_dir>
--outname <out_name>
--sample <sample_depth>
--version
-d <db_files>
-h, --help
-t {e,ce}
C
c_call (changeo.Receptor.ReceptorData attribute)
calcDistances() (in module changeo.Distance)
cdr1_imgt (changeo.Receptor.ReceptorData attribute)
cdr2_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)
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 command line option
--version
-h, --help
ConvertDb-airr command line option
--outdir <out_dir>
--outname <out_name>
--version
-d <db_files>
-h, --help
-o <out_files>
ConvertDb-baseline command line option
--cf <cluster_field>
--gf <germ_field>
--if <id_field>
--mf <meta_fields>
--outdir <out_dir>
--outname <out_name>
--sf <seq_field>
--version
-d <db_files>
-h, --help
-o <out_files>
ConvertDb-changeo command line option
--outdir <out_dir>
--outname <out_name>
--version
-d <db_files>
-h, --help
-o <out_files>
ConvertDb-fasta command line option
--if <id_field>
--mf <meta_fields>
--outdir <out_dir>
--outname <out_name>
--sf <seq_field>
--version
-d <db_files>
-h, --help
-o <out_files>
ConvertDb-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 {changeo,airr}
--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, --help
-o <out_files>
-y <yaml_config>
countDbFile() (in module changeo.IO)
CreateGermlines command line option
--cloned
--df <d_field>
--failed
--format {changeo,airr}
--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, --help
-o <out_files>
-r <references>
custom_fields (changeo.Receptor.AIRRSchema attribute)
(changeo.Receptor.ChangeoSchema attribute)
customFields() (changeo.IO.IgBLASTReader 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_end (changeo.Receptor.Receptor attribute)
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_end (changeo.Receptor.Receptor attribute)
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 attribute)
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 command line option
--act {first,set}
--dist <distance>
--failed
--format {changeo,airr}
--gf <group_fields>
--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, --help
-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_imgt (changeo.Receptor.ReceptorData attribute)
fwr2_imgt (changeo.Receptor.ReceptorData attribute)
fwr3_imgt (changeo.Receptor.ReceptorData attribute)
fwr4_imgt (changeo.Receptor.ReceptorData attribute)
G
gapV() (in module changeo.Alignment)
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)
getAlleleCalls() (changeo.Receptor.Receptor method)
getAlleleNumbers() (changeo.Receptor.Receptor method)
getChangeo() (changeo.Receptor.Receptor method)
getCommonArgParser() (in module changeo.Commandline)
getDAllele() (changeo.Receptor.Receptor method)
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)
getFamilyCalls() (changeo.Receptor.Receptor method)
getField() (changeo.Receptor.Receptor method)
getFormatOperators() (in module changeo.IO)
getGeneCalls() (changeo.Receptor.Receptor method)
getIgBLASTVersion() (in module changeo.Applications)
getJAllele() (changeo.Receptor.Receptor method)
getJAlleleNumber() (changeo.Receptor.Receptor method)
getJFamily() (changeo.Receptor.Receptor method)
getJGene() (changeo.Receptor.Receptor method)
getJGermline() (in module changeo.Gene)
getNmers() (in module changeo.Distance)
getOutputHandle() (in module changeo.IO)
getOutputName() (in module changeo.IO)
getRegions() (in module changeo.Alignment)
getSeq() (changeo.Receptor.Receptor method)
getVAllele() (changeo.Receptor.Receptor method)
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)
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_end (changeo.Receptor.Receptor attribute)
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_end (changeo.Receptor.Receptor attribute)
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 attribute)
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 command line option
--version
-h, --help
MakeDb-igblast command line option
--10x <cellranger_file>
--asis-calls
--asis-id
--extended
--failed
--format {changeo,airr}
--log <log_file>
--outdir <out_dir>
--outname <out_name>
--partial
--version
-h, --help
-i <aligner_files>
-o <out_files>
-r <repo>
-s <seq_files>
MakeDb-ihmm command line option
--10x <cellranger_file>
--asis-id
--extended
--failed
--format {changeo,airr}
--log <log_file>
--outdir <out_dir>
--outname <out_name>
--partial
--version
-h, --help
-i <aligner_files>
-o <out_files>
-r <repo>
-s <seq_files>
MakeDb-imgt command line option
--10x <cellranger_file>
--asis-id
--extended
--failed
--format {changeo,airr}
--log <log_file>
--outdir <out_dir>
--outname <out_name>
--partial
--version
-h, --help
-i <aligner_files>
-o <out_files>
-r <repo>
-s <seq_files>
mutated_invariant (changeo.Receptor.ReceptorData attribute)
N
n1_length (changeo.Receptor.ReceptorData attribute)
n2_length (changeo.Receptor.ReceptorData attribute)
np1_length (changeo.Receptor.ReceptorData attribute)
np1_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)
parseAllele() (in module changeo.Gene)
parseBlock() (changeo.IO.IgBLASTReader method)
parseCommonArgs() (in module changeo.Commandline)
ParseDb command line option
--version
-h, --help
ParseDb-add command line option
--outdir <out_dir>
--outname <out_name>
--version
-d <db_files>
-f <fields>
-h, --help
-o <out_files>
-u <values>
ParseDb-delete command line option
--logic {any,all}
--outdir <out_dir>
--outname <out_name>
--regex
--version
-d <db_files>
-f <fields>
-h, --help
-o <out_files>
-u <values>
ParseDb-drop command line option
--outdir <out_dir>
--outname <out_name>
--version
-d <db_files>
-f <fields>
-h, --help
-o <out_files>
ParseDb-index command line option
--outdir <out_dir>
--outname <out_name>
--version
-d <db_files>
-f <field>
-h, --help
-o <out_files>
ParseDb-merge command line option
--drop
--outdir <out_dir>
--outname <out_name>
--version
-d <db_files>
-h, --help
-o <out_file>
ParseDb-rename command line option
--outdir <out_dir>
--outname <out_name>
--version
-d <db_files>
-f <fields>
-h, --help
-k <names>
-o <out_files>
ParseDb-select command line option
--logic {any,all}
--outdir <out_dir>
--outname <out_name>
--regex
--version
-d <db_files>
-f <fields>
-h, --help
-o <out_files>
-u <values>
ParseDb-sort command line option
--descend
--num
--outdir <out_dir>
--outname <out_name>
--version
-d <db_files>
-f <field>
-h, --help
-o <out_files>
ParseDb-split command line option
--num <num_split>
--outdir <out_dir>
--outname <out_name>
--version
-d <db_files>
-f <field>
-h, --help
ParseDb-update command line option
--outdir <out_dir>
--outname <out_name>
--version
-d <db_files>
-f <field>
-h, --help
-o <out_files>
-t <updates>
-u <values>
parseRecord() (changeo.IO.IHMMuneReader method)
(changeo.IO.IMGTReader method)
parsers (changeo.Receptor.ReceptorData attribute)
parseSections() (changeo.IO.IgBLASTReader 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)
results (changeo.Multiprocessing.DbResult attribute)
rev_comp (changeo.Receptor.ReceptorData attribute)
runASN() (in module changeo.Applications)
runIgBLAST() (in module changeo.Applications)
runIgPhyML() (in module changeo.Applications)
S
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)
standard_fields (changeo.Receptor.AIRRSchema attribute)
(changeo.Receptor.ChangeoSchema attribute)
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_germ_end_imgt (changeo.Receptor.Receptor attribute)
v_germ_end_vdj (changeo.Receptor.Receptor attribute)
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_end (changeo.Receptor.Receptor attribute)
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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