Index

Symbols

--10x 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 AlignRecords.py-across command line option AlignRecords.py-block command line option DefineClones.py command line option --allele-delim ConvertDb.py-genbank command line option --allow-stop ConvertDb.py-genbank command line option --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 BuildTrees.py command line option --calls AlignRecords.py-across command line option AlignRecords.py-block command line option --cdb AssignGenes.py-igblast command line option --cell-type ConvertDb.py-genbank command line option --cf ConvertDb.py-baseline command line option ConvertDb.py-genbank command line option CreateGermlines.py command line option --clean BuildTrees.py command line option --cloned CreateGermlines.py command line option --clones BuildTrees.py command line option --collapse BuildTrees.py command line option --db ConvertDb.py-genbank command line option --ddb AssignGenes.py-igblast command line option --descend ParseDb.py-sort command line option --df CreateGermlines.py command line option --dist DefineClones.py command line option --drop ParseDb.py-merge command line option --exec 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-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 AlignRecords.py-across command line option AlignRecords.py-block command line option AlignRecords.py-within command line option AssignGenes.py-igblast 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 --gf AlignRecords.py-across command line option AlignRecords.py-block command line option ConvertDb.py-baseline 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 BuildTrees.py command line option --if ConvertDb.py-baseline command line option ConvertDb.py-fasta command line option ConvertDb.py-genbank command line option --igphyml BuildTrees.py command line option --imgt-id-len MakeDb.py-imgt command line option --inf ConvertDb.py-genbank command line option --infer-junction MakeDb.py-igblast command line option --isolate ConvertDb.py-genbank command line option --jdb AssignGenes.py-igblast command line option --jf CreateGermlines.py command line option DefineClones.py command line option --label ConvertDb.py-genbank command line option --link DefineClones.py command line option --loci AssignGenes.py-igblast command line option AssignGenes.py-igblast-aa command line option --log 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 ParseDb.py-delete command line option ParseDb.py-select command line option --maxmiss DefineClones.py command line option --md BuildTrees.py command line option --mf ConvertDb.py-baseline command line option ConvertDb.py-fasta command line option --minseq BuildTrees.py command line option --mode AlignRecords.py-across command line option AlignRecords.py-block command line option DefineClones.py command line option --model DefineClones.py command line option --mol ConvertDb.py-genbank command line option --motifs BuildTrees.py command line option --ncdr3 BuildTrees.py command line option --nf ConvertDb.py-genbank command line option --nmask BuildTrees.py command line option --nohlp BuildTrees.py command line option --norm DefineClones.py command line option --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 ParseDb.py-split command line option --oformat BuildTrees.py command line option --omega BuildTrees.py command line option --optimize BuildTrees.py command line option --organism AssignGenes.py-igblast command line option AssignGenes.py-igblast-aa command line option ConvertDb.py-genbank command line option --outdir 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 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 ConvertDb.py-genbank command line option --regex ParseDb.py-delete command line option ParseDb.py-select command line option --regions MakeDb.py-igblast command line option MakeDb.py-igblast-aa command line option --sample BuildTrees.py command line option --sbt ConvertDb.py-genbank command line option --sex ConvertDb.py-genbank command line option --sf AlignRecords.py-across command line option AlignRecords.py-block command line option AlignRecords.py-within command line option ConvertDb.py-baseline command line option ConvertDb.py-fasta command line option CreateGermlines.py command line option DefineClones.py command line option --sym DefineClones.py command line option --tissue ConvertDb.py-genbank command line option --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 CreateGermlines.py command line option DefineClones.py command line option -b AssignGenes.py-igblast command line option AssignGenes.py-igblast-aa command line option -d 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 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-split command line option ParseDb.py-update command line option -g 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 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 ParseDb.py-rename command line option -o 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-merge 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 CreateGermlines.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 -s 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 BuildTrees.py command line option ParseDb.py-update command line option -u 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 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 --calls --exec --failed --format --gf --help --log --mode --nproc --outdir --outname --sf --version -d -h -o AlignRecords.py-block command line option --act --calls --exec --failed --format --gf --help --log --mode --nproc --outdir --outname --sf --version -d -h -o AlignRecords.py-within command line option --exec --failed --format --help --log --nproc --outdir --outname --sf --version -d -h -o

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 --ddb --exec --format --help --jdb --loci --nproc --organism --outdir --outname --vdb --version -b -h -o -s AssignGenes.py-igblast-aa command line option --exec --help --loci --nproc --organism --outdir --outname --vdb --version -b -h -o -s

B

buildClonalGermline() (in module changeo.Gene) buildGermline() (in module changeo.Gene) BuildTrees.py command line option --append --asr --clean --clones --collapse --failed --format --help --hotness --igphyml --log --md --minseq --motifs --ncdr3 --nmask --nohlp --nproc --oformat --omega --optimize --outdir --outname --sample --version -d -h -t

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 --outname --version -d -h -o ConvertDb.py-baseline command line option --cf --gf --help --if --mf --outdir --outname --sf --version -d -h -o ConvertDb.py-changeo command line option --help --outdir --outname --version -d -h -o

ConvertDb.py-fasta command line option --help --if --mf --outdir --outname --sf --version -d -h -o ConvertDb.py-genbank command line option --allele-delim --allow-stop --asis-calls --asis-id --asn --cell-type --cf --db --exec --format --help --if --inf --isolate --label --mol --nf --organism --outdir --outname --product --sbt --sex --tissue --version -d -h -o -y countDbFile() (in module changeo.IO) CreateGermlines.py command line option --cf --cloned --df --failed --format --help --jf --log --outdir --outname --sf --version --vf -d -g -h -o -r 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 --dist --failed --format --gf --help --jf --link --log --maxmiss --mode --model --norm --nproc --outdir --outname --sf --sym --version --vf -d -h -o 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 --asis-calls --asis-id --extended --failed --format --help --infer-junction --log --outdir --outname --partial --regions --version -h -i -o -r -s MakeDb.py-igblast-aa command line option --10x --asis-calls --asis-id --extended --failed --format --help --log --outdir --outname --regions --version -h -i -o -r -s MakeDb.py-ihmm command line option --10x --asis-id --extended --failed --format --help --log --outdir --outname --partial --version -h -i -o -r -s

MakeDb.py-imgt command line option --10x --asis-id --extended --failed --format --help --imgt-id-len --log --outdir --outname --partial --version -h -i -o -r -s 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 --outname --version -d -f -h -o -u ParseDb.py-delete command line option --help --logic --outdir --outname --regex --version -d -f -h -o -u ParseDb.py-drop command line option --help --outdir --outname --version -d -f -h -o ParseDb.py-index command line option --help --outdir --outname --version -d -f -h -o ParseDb.py-merge command line option --drop --help --outdir --outname --version -d -h -o

ParseDb.py-rename command line option --help --outdir --outname --version -d -f -h -k -o ParseDb.py-select command line option --help --logic --outdir --outname --regex --version -d -f -h -o -u ParseDb.py-sort command line option --descend --help --num --outdir --outname --version -d -f -h -o ParseDb.py-split command line option --help --num --outdir --outname --version -d -f -h ParseDb.py-update command line option --help --outdir --outname --version -d -f -h -o -t -u 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)