presto
0.6.2
Immcantation Portal
Getting Started
Overview
Download
Installation
Example Workflows
Roche 454 BCR mRNA with Multiplexed Samples
Illumina MiSeq 2x250 BCR mRNA
UMI Barcoded Illumina MiSeq 2x250 BCR mRNA
UMI Barcoded Illumina MiSeq 325+275 paired-end 5’RACE BCR mRNA
Example Tasks
Importing Data
Manipulating Annotations
Filtering and Subsetting
Isotype and Primer Annotations
Fixing Assembly Problems
Fixing UMI Problems
Usage Documentation
Commandline Usage
API
About
Release Notes
Contact
Citation
License
presto
Docs
»
Index
Edit on Bitbucket
Index
Symbols
|
_
|
A
|
B
|
C
|
D
|
E
|
F
|
G
|
I
|
J
|
L
|
M
|
O
|
P
|
Q
|
R
|
S
|
T
|
U
|
V
|
W
Symbols
--1f <fields_1>
PairSeq command line option
--1f <head_fields>
AssemblePairs-align command line option
AssemblePairs-join command line option
AssemblePairs-reference command line option
AssemblePairs-sequential command line option
--2f <fields_2>
PairSeq command line option
--2f <tail_fields>
AssemblePairs-align command line option
AssemblePairs-join command line option
AssemblePairs-reference command line option
AssemblePairs-sequential command line option
--act {min,max,sum,first,last,set,cat}
ParseHeaders-collapse command line option
ParseHeaders-copy command line option
ParseHeaders-rename command line option
--act {min,max,sum,set,cat}
PairSeq command line option
ParseHeaders-merge command line option
--act {min,max,sum,set,majority}
BuildConsensus command line option
--act {min,max,sum,set}
CollapseSeq command line option
--aligner {blastn,usearch}
AssemblePairs-reference command line option
AssemblePairs-sequential command line option
--alpha <alpha>
AssemblePairs-align command line option
AssemblePairs-sequential command line option
--barcode
MaskPrimers-align command line option
MaskPrimers-extract command line option
MaskPrimers-score command line option
--bf <barcode_field>
AlignSets-muscle command line option
AlignSets-offset command line option
BuildConsensus command line option
MaskPrimers-align command line option
MaskPrimers-extract command line option
MaskPrimers-score command line option
--cf <copy_fields>
BuildConsensus command line option
CollapseSeq command line option
--cluster {usearch,vsearch,cd-hit-est}
ClusterSets-all command line option
ClusterSets-barcode command line option
ClusterSets-set command line option
--coord {illumina,solexa,sra,454,presto}
AssemblePairs-align command line option
AssemblePairs-join command line option
AssemblePairs-reference command line option
AssemblePairs-sequential command line option
PairSeq command line option
SplitSeq-samplepair command line option
--dbexec <db_exec>
AssemblePairs-reference command line option
AssemblePairs-sequential command line option
--delete
ParseHeaders-merge command line option
--delim <delimiter>
AlignSets-muscle command line option
AlignSets-offset command line option
AlignSets-table command line option
AssemblePairs-align command line option
AssemblePairs-join command line option
AssemblePairs-reference command line option
AssemblePairs-sequential command line option
BuildConsensus command line option
ClusterSets-all command line option
ClusterSets-barcode command line option
ClusterSets-set command line option
CollapseSeq command line option
ConvertHeaders-454 command line option
ConvertHeaders-genbank command line option
ConvertHeaders-generic command line option
ConvertHeaders-illumina command line option
ConvertHeaders-imgt command line option
ConvertHeaders-migec command line option
ConvertHeaders-sra command line option
EstimateError-barcode command line option
EstimateError-set command line option
MaskPrimers-align command line option
MaskPrimers-extract command line option
MaskPrimers-score command line option
PairSeq command line option
ParseHeaders-add command line option
ParseHeaders-collapse command line option
ParseHeaders-copy command line option
ParseHeaders-delete command line option
ParseHeaders-expand command line option
ParseHeaders-merge command line option
ParseHeaders-rename command line option
ParseHeaders-table command line option
ParseLog command line option
SplitSeq-group command line option
SplitSeq-sample command line option
SplitSeq-samplepair command line option
SplitSeq-select command line option
SplitSeq-sort command line option
UnifyHeaders-consensus command line option
UnifyHeaders-delete command line option
--dep
BuildConsensus command line option
--div
AlignSets-muscle command line option
AlignSets-offset command line option
--end <seq_end>
ClusterSets-all command line option
ClusterSets-set command line option
--evalue <evalue>
AssemblePairs-reference command line option
AssemblePairs-sequential command line option
--exec <aligner_exec>
AlignSets-muscle command line option
AlignSets-table command line option
AssemblePairs-reference command line option
AssemblePairs-sequential command line option
--exec <cluster_exec>
ClusterSets-all command line option
ClusterSets-barcode command line option
ClusterSets-set command line option
--failed
AlignSets-muscle command line option
AlignSets-offset command line option
AlignSets-table command line option
AssemblePairs-align command line option
AssemblePairs-join command line option
AssemblePairs-reference command line option
AssemblePairs-sequential command line option
BuildConsensus command line option
ClusterSets-set command line option
CollapseSeq command line option
ConvertHeaders-454 command line option
ConvertHeaders-genbank command line option
ConvertHeaders-generic command line option
ConvertHeaders-illumina command line option
ConvertHeaders-imgt command line option
ConvertHeaders-migec command line option
ConvertHeaders-sra command line option
FilterSeq-length command line option
FilterSeq-maskqual command line option
FilterSeq-missing command line option
FilterSeq-quality command line option
FilterSeq-repeats command line option
FilterSeq-trimqual command line option
MaskPrimers-align command line option
MaskPrimers-extract command line option
MaskPrimers-score command line option
PairSeq command line option
ParseHeaders-add command line option
ParseHeaders-collapse command line option
ParseHeaders-copy command line option
ParseHeaders-delete command line option
ParseHeaders-expand command line option
ParseHeaders-merge command line option
ParseHeaders-rename command line option
ParseHeaders-table command line option
UnifyHeaders-consensus command line option
UnifyHeaders-delete command line option
--fasta
AlignSets-muscle command line option
AlignSets-offset command line option
AssemblePairs-align command line option
AssemblePairs-join command line option
AssemblePairs-reference command line option
AssemblePairs-sequential command line option
BuildConsensus command line option
ClusterSets-all command line option
ClusterSets-barcode command line option
ClusterSets-set command line option
CollapseSeq command line option
ConvertHeaders-454 command line option
ConvertHeaders-genbank command line option
ConvertHeaders-generic command line option
ConvertHeaders-illumina command line option
ConvertHeaders-imgt command line option
ConvertHeaders-migec command line option
ConvertHeaders-sra command line option
FilterSeq-length command line option
FilterSeq-maskqual command line option
FilterSeq-missing command line option
FilterSeq-quality command line option
FilterSeq-repeats command line option
FilterSeq-trimqual command line option
MaskPrimers-align command line option
MaskPrimers-extract command line option
MaskPrimers-score command line option
PairSeq command line option
ParseHeaders-add command line option
ParseHeaders-collapse command line option
ParseHeaders-copy command line option
ParseHeaders-delete command line option
ParseHeaders-expand command line option
ParseHeaders-merge command line option
ParseHeaders-rename command line option
SplitSeq-count command line option
SplitSeq-group command line option
SplitSeq-sample command line option
SplitSeq-samplepair command line option
SplitSeq-select command line option
SplitSeq-sort command line option
UnifyHeaders-consensus command line option
UnifyHeaders-delete command line option
--fill
AssemblePairs-reference command line option
AssemblePairs-sequential command line option
--freq <min_freq>
BuildConsensus command line option
EstimateError-set command line option
--gap <gap>
AssemblePairs-join command line option
--gap <gap_penalty>
MaskPrimers-align command line option
--help
AlignSets command line option
AlignSets-muscle command line option
AlignSets-offset command line option
AlignSets-table command line option
AssemblePairs command line option
AssemblePairs-align command line option
AssemblePairs-join command line option
AssemblePairs-reference command line option
AssemblePairs-sequential command line option
BuildConsensus command line option
ClusterSets command line option
ClusterSets-all command line option
ClusterSets-barcode command line option
ClusterSets-set command line option
CollapseSeq command line option
ConvertHeaders command line option
ConvertHeaders-454 command line option
ConvertHeaders-genbank command line option
ConvertHeaders-generic command line option
ConvertHeaders-illumina command line option
ConvertHeaders-imgt command line option
ConvertHeaders-migec command line option
ConvertHeaders-sra command line option
EstimateError command line option
EstimateError-barcode command line option
EstimateError-set command line option
FilterSeq command line option
FilterSeq-length command line option
FilterSeq-maskqual command line option
FilterSeq-missing command line option
FilterSeq-quality command line option
FilterSeq-repeats command line option
FilterSeq-trimqual command line option
MaskPrimers command line option
MaskPrimers-align command line option
MaskPrimers-extract command line option
MaskPrimers-score command line option
PairSeq command line option
ParseHeaders command line option
ParseHeaders-add command line option
ParseHeaders-collapse command line option
ParseHeaders-copy command line option
ParseHeaders-delete command line option
ParseHeaders-expand command line option
ParseHeaders-merge command line option
ParseHeaders-rename command line option
ParseHeaders-table command line option
ParseLog command line option
SplitSeq command line option
SplitSeq-count command line option
SplitSeq-group command line option
SplitSeq-sample command line option
SplitSeq-samplepair command line option
SplitSeq-select command line option
SplitSeq-sort command line option
UnifyHeaders command line option
UnifyHeaders-consensus command line option
UnifyHeaders-delete command line option
--ident <ident>
ClusterSets-all command line option
ClusterSets-barcode command line option
ClusterSets-set command line option
--inner
CollapseSeq command line option
FilterSeq-length command line option
FilterSeq-missing command line option
FilterSeq-quality command line option
FilterSeq-repeats command line option
--keepmiss
CollapseSeq command line option
--len <length>
MaskPrimers-extract command line option
--length <length_ratio>
ClusterSets-all command line option
ClusterSets-barcode command line option
ClusterSets-set command line option
--log <log_file>
AlignSets-muscle command line option
AlignSets-offset command line option
AssemblePairs-align command line option
AssemblePairs-join command line option
AssemblePairs-reference command line option
AssemblePairs-sequential command line option
BuildConsensus command line option
ClusterSets-set command line option
CollapseSeq command line option
EstimateError-set command line option
FilterSeq-length command line option
FilterSeq-maskqual command line option
FilterSeq-missing command line option
FilterSeq-quality command line option
FilterSeq-repeats command line option
FilterSeq-trimqual command line option
MaskPrimers-align command line option
MaskPrimers-extract command line option
MaskPrimers-score command line option
UnifyHeaders-consensus command line option
UnifyHeaders-delete command line option
--maxdiv <max_diversity>
BuildConsensus command line option
EstimateError-set command line option
--maxerror <max_error>
AssemblePairs-align command line option
AssemblePairs-sequential command line option
BuildConsensus command line option
MaskPrimers-align command line option
MaskPrimers-score command line option
--maxf <max_field>
CollapseSeq command line option
--maxgap <max_gap>
BuildConsensus command line option
--maxhits <max_hits>
AssemblePairs-reference command line option
AssemblePairs-sequential command line option
--maxlen <max_len>
AssemblePairs-align command line option
AssemblePairs-sequential command line option
MaskPrimers-align command line option
--minf <min_field>
CollapseSeq command line option
--minident <min_ident>
AssemblePairs-reference command line option
AssemblePairs-sequential command line option
--minlen <min_len>
AssemblePairs-align command line option
AssemblePairs-sequential command line option
--missing
FilterSeq-repeats command line option
--mode {cut,mask,trim,tag}
MaskPrimers-align command line option
MaskPrimers-extract command line option
MaskPrimers-score command line option
--mode {freq,qual}
EstimateError-set command line option
--mode {pad,cut}
AlignSets-offset command line option
--not
SplitSeq-select command line option
--nproc <nproc>
AlignSets-muscle command line option
AlignSets-offset command line option
AssemblePairs-align command line option
AssemblePairs-join command line option
AssemblePairs-reference command line option
AssemblePairs-sequential command line option
BuildConsensus command line option
ClusterSets-all command line option
ClusterSets-barcode command line option
ClusterSets-set command line option
EstimateError-set command line option
FilterSeq-length command line option
FilterSeq-maskqual command line option
FilterSeq-missing command line option
FilterSeq-quality command line option
FilterSeq-repeats command line option
FilterSeq-trimqual command line option
MaskPrimers-align command line option
MaskPrimers-extract command line option
MaskPrimers-score command line option
UnifyHeaders-consensus command line option
UnifyHeaders-delete command line option
--num
SplitSeq-sort command line option
--num <threshold>
SplitSeq-group command line option
--outdir <out_dir>
AlignSets-muscle command line option
AlignSets-offset command line option
AlignSets-table command line option
AssemblePairs-align command line option
AssemblePairs-join command line option
AssemblePairs-reference command line option
AssemblePairs-sequential command line option
BuildConsensus command line option
ClusterSets-all command line option
ClusterSets-barcode command line option
ClusterSets-set command line option
CollapseSeq command line option
ConvertHeaders-454 command line option
ConvertHeaders-genbank command line option
ConvertHeaders-generic command line option
ConvertHeaders-illumina command line option
ConvertHeaders-imgt command line option
ConvertHeaders-migec command line option
ConvertHeaders-sra command line option
EstimateError-barcode command line option
EstimateError-set command line option
FilterSeq-length command line option
FilterSeq-maskqual command line option
FilterSeq-missing command line option
FilterSeq-quality command line option
FilterSeq-repeats command line option
FilterSeq-trimqual command line option
MaskPrimers-align command line option
MaskPrimers-extract command line option
MaskPrimers-score command line option
PairSeq command line option
ParseHeaders-add command line option
ParseHeaders-collapse command line option
ParseHeaders-copy command line option
ParseHeaders-delete command line option
ParseHeaders-expand command line option
ParseHeaders-merge command line option
ParseHeaders-rename command line option
ParseHeaders-table command line option
ParseLog command line option
SplitSeq-count command line option
SplitSeq-group command line option
SplitSeq-sample command line option
SplitSeq-samplepair command line option
SplitSeq-select command line option
SplitSeq-sort command line option
UnifyHeaders-consensus command line option
UnifyHeaders-delete command line option
--outname <out_name>
AlignSets-muscle command line option
AlignSets-offset command line option
AlignSets-table command line option
AssemblePairs-align command line option
AssemblePairs-join command line option
AssemblePairs-reference command line option
AssemblePairs-sequential command line option
BuildConsensus command line option
ClusterSets-all command line option
ClusterSets-barcode command line option
ClusterSets-set command line option
CollapseSeq command line option
ConvertHeaders-454 command line option
ConvertHeaders-genbank command line option
ConvertHeaders-generic command line option
ConvertHeaders-illumina command line option
ConvertHeaders-imgt command line option
ConvertHeaders-migec command line option
ConvertHeaders-sra command line option
EstimateError-barcode command line option
EstimateError-set command line option
FilterSeq-length command line option
FilterSeq-maskqual command line option
FilterSeq-missing command line option
FilterSeq-quality command line option
FilterSeq-repeats command line option
FilterSeq-trimqual command line option
MaskPrimers-align command line option
MaskPrimers-extract command line option
MaskPrimers-score command line option
PairSeq command line option
ParseHeaders-add command line option
ParseHeaders-collapse command line option
ParseHeaders-copy command line option
ParseHeaders-delete command line option
ParseHeaders-expand command line option
ParseHeaders-merge command line option
ParseHeaders-rename command line option
ParseHeaders-table command line option
ParseLog command line option
SplitSeq-count command line option
SplitSeq-group command line option
SplitSeq-sample command line option
SplitSeq-samplepair command line option
SplitSeq-select command line option
SplitSeq-sort command line option
UnifyHeaders-consensus command line option
UnifyHeaders-delete command line option
--pf <primer_field>
AlignSets-offset command line option
BuildConsensus command line option
MaskPrimers-align command line option
MaskPrimers-extract command line option
MaskPrimers-score command line option
--prcons <primer_freq>
BuildConsensus command line option
--prefix <cluster_prefix>
ClusterSets-all command line option
ClusterSets-barcode command line option
ClusterSets-set command line option
--rc {tail,head,both,none}
AssemblePairs-align command line option
AssemblePairs-join command line option
AssemblePairs-reference command line option
AssemblePairs-sequential command line option
--reverse
AlignSets-table command line option
FilterSeq-trimqual command line option
--revpr
MaskPrimers-align command line option
MaskPrimers-extract command line option
MaskPrimers-score command line option
--scanrev
AssemblePairs-align command line option
AssemblePairs-sequential command line option
--sep <separator>
ParseHeaders-expand command line option
--simple
ConvertHeaders-imgt command line option
--skiprc
MaskPrimers-align command line option
--start <seq_start>
ClusterSets-all command line option
ClusterSets-set command line option
--start <start>
MaskPrimers-extract command line option
MaskPrimers-score command line option
--uf <uniq_fields>
CollapseSeq command line option
--version
AlignSets command line option
AlignSets-muscle command line option
AlignSets-offset command line option
AlignSets-table command line option
AssemblePairs command line option
AssemblePairs-align command line option
AssemblePairs-join command line option
AssemblePairs-reference command line option
AssemblePairs-sequential command line option
BuildConsensus command line option
ClusterSets command line option
ClusterSets-all command line option
ClusterSets-barcode command line option
ClusterSets-set command line option
CollapseSeq command line option
ConvertHeaders command line option
ConvertHeaders-454 command line option
ConvertHeaders-genbank command line option
ConvertHeaders-generic command line option
ConvertHeaders-illumina command line option
ConvertHeaders-imgt command line option
ConvertHeaders-migec command line option
ConvertHeaders-sra command line option
EstimateError command line option
EstimateError-barcode command line option
EstimateError-set command line option
FilterSeq command line option
FilterSeq-length command line option
FilterSeq-maskqual command line option
FilterSeq-missing command line option
FilterSeq-quality command line option
FilterSeq-repeats command line option
FilterSeq-trimqual command line option
MaskPrimers command line option
MaskPrimers-align command line option
MaskPrimers-extract command line option
MaskPrimers-score command line option
PairSeq command line option
ParseHeaders command line option
ParseHeaders-add command line option
ParseHeaders-collapse command line option
ParseHeaders-copy command line option
ParseHeaders-delete command line option
ParseHeaders-expand command line option
ParseHeaders-merge command line option
ParseHeaders-rename command line option
ParseHeaders-table command line option
ParseLog command line option
SplitSeq command line option
SplitSeq-count command line option
SplitSeq-group command line option
SplitSeq-sample command line option
SplitSeq-samplepair command line option
SplitSeq-select command line option
SplitSeq-sort command line option
UnifyHeaders command line option
UnifyHeaders-consensus command line option
UnifyHeaders-delete command line option
--win <window>
FilterSeq-trimqual command line option
-1 <seq_files_1>
AssemblePairs-align command line option
AssemblePairs-join command line option
AssemblePairs-reference command line option
AssemblePairs-sequential command line option
PairSeq command line option
SplitSeq-samplepair command line option
-2 <seq_files_2>
AssemblePairs-align command line option
AssemblePairs-join command line option
AssemblePairs-reference command line option
AssemblePairs-sequential command line option
PairSeq command line option
SplitSeq-samplepair command line option
-d <offset_table>
AlignSets-offset command line option
-f <barcode_field>
ClusterSets-barcode command line option
EstimateError-barcode command line option
-f <field>
SplitSeq-group command line option
SplitSeq-sample command line option
SplitSeq-samplepair command line option
SplitSeq-select command line option
SplitSeq-sort command line option
-f <fields>
ParseHeaders-add command line option
ParseHeaders-collapse command line option
ParseHeaders-copy command line option
ParseHeaders-delete command line option
ParseHeaders-expand command line option
ParseHeaders-merge command line option
ParseHeaders-rename command line option
ParseHeaders-table command line option
ParseLog command line option
-f <set_field>
ClusterSets-set command line option
EstimateError-set command line option
UnifyHeaders-consensus command line option
UnifyHeaders-delete command line option
-h
AlignSets command line option
AlignSets-muscle command line option
AlignSets-offset command line option
AlignSets-table command line option
AssemblePairs command line option
AssemblePairs-align command line option
AssemblePairs-join command line option
AssemblePairs-reference command line option
AssemblePairs-sequential command line option
BuildConsensus command line option
ClusterSets command line option
ClusterSets-all command line option
ClusterSets-barcode command line option
ClusterSets-set command line option
CollapseSeq command line option
ConvertHeaders command line option
ConvertHeaders-454 command line option
ConvertHeaders-genbank command line option
ConvertHeaders-generic command line option
ConvertHeaders-illumina command line option
ConvertHeaders-imgt command line option
ConvertHeaders-migec command line option
ConvertHeaders-sra command line option
EstimateError command line option
EstimateError-barcode command line option
EstimateError-set command line option
FilterSeq command line option
FilterSeq-length command line option
FilterSeq-maskqual command line option
FilterSeq-missing command line option
FilterSeq-quality command line option
FilterSeq-repeats command line option
FilterSeq-trimqual command line option
MaskPrimers command line option
MaskPrimers-align command line option
MaskPrimers-extract command line option
MaskPrimers-score command line option
PairSeq command line option
ParseHeaders command line option
ParseHeaders-add command line option
ParseHeaders-collapse command line option
ParseHeaders-copy command line option
ParseHeaders-delete command line option
ParseHeaders-expand command line option
ParseHeaders-merge command line option
ParseHeaders-rename command line option
ParseHeaders-table command line option
ParseLog command line option
SplitSeq command line option
SplitSeq-count command line option
SplitSeq-group command line option
SplitSeq-sample command line option
SplitSeq-samplepair command line option
SplitSeq-select command line option
SplitSeq-sort command line option
UnifyHeaders command line option
UnifyHeaders-consensus command line option
UnifyHeaders-delete command line option
-k <cluster_field>
ClusterSets-all command line option
ClusterSets-barcode command line option
ClusterSets-set command line option
-k <name>
ParseHeaders-merge command line option
-k <names>
ParseHeaders-copy command line option
ParseHeaders-rename command line option
-k <unify_field>
UnifyHeaders-consensus command line option
UnifyHeaders-delete command line option
-l <record_files>
ParseLog command line option
-n <max_count>
SplitSeq-count command line option
SplitSeq-sample command line option
SplitSeq-samplepair command line option
SplitSeq-sort command line option
-n <max_missing>
CollapseSeq command line option
FilterSeq-missing command line option
-n <max_repeat>
FilterSeq-repeats command line option
-n <min_count>
BuildConsensus command line option
EstimateError-set command line option
-n <min_length>
FilterSeq-length command line option
-o <out_file>
AlignSets-table command line option
-o <out_files>
AlignSets-muscle command line option
AlignSets-offset command line option
AssemblePairs-align command line option
AssemblePairs-join command line option
AssemblePairs-reference command line option
AssemblePairs-sequential command line option
BuildConsensus command line option
ClusterSets-all command line option
ClusterSets-barcode command line option
ClusterSets-set command line option
CollapseSeq command line option
ConvertHeaders-454 command line option
ConvertHeaders-genbank command line option
ConvertHeaders-generic command line option
ConvertHeaders-illumina command line option
ConvertHeaders-imgt command line option
ConvertHeaders-migec command line option
ConvertHeaders-sra command line option
FilterSeq-length command line option
FilterSeq-maskqual command line option
FilterSeq-missing command line option
FilterSeq-quality command line option
FilterSeq-repeats command line option
FilterSeq-trimqual command line option
MaskPrimers-align command line option
MaskPrimers-extract command line option
MaskPrimers-score command line option
ParseHeaders-add command line option
ParseHeaders-collapse command line option
ParseHeaders-copy command line option
ParseHeaders-delete command line option
ParseHeaders-expand command line option
ParseHeaders-merge command line option
ParseHeaders-rename command line option
ParseHeaders-table command line option
ParseLog command line option
SplitSeq-select command line option
UnifyHeaders-consensus command line option
UnifyHeaders-delete command line option
-p <primer_file>
AlignSets-table command line option
MaskPrimers-align command line option
MaskPrimers-score command line option
-q <min_qual>
BuildConsensus command line option
EstimateError-set command line option
FilterSeq-maskqual command line option
FilterSeq-quality command line option
FilterSeq-trimqual command line option
-r <ref_file>
AssemblePairs-reference command line option
AssemblePairs-sequential command line option
-s <seq_files>
AlignSets-muscle command line option
AlignSets-offset command line option
BuildConsensus command line option
ClusterSets-all command line option
ClusterSets-barcode command line option
ClusterSets-set command line option
CollapseSeq command line option
ConvertHeaders-454 command line option
ConvertHeaders-genbank command line option
ConvertHeaders-generic command line option
ConvertHeaders-illumina command line option
ConvertHeaders-imgt command line option
ConvertHeaders-migec command line option
ConvertHeaders-sra command line option
EstimateError-barcode command line option
EstimateError-set command line option
FilterSeq-length command line option
FilterSeq-maskqual command line option
FilterSeq-missing command line option
FilterSeq-quality command line option
FilterSeq-repeats command line option
FilterSeq-trimqual command line option
MaskPrimers-align command line option
MaskPrimers-extract command line option
MaskPrimers-score command line option
ParseHeaders-add command line option
ParseHeaders-collapse command line option
ParseHeaders-copy command line option
ParseHeaders-delete command line option
ParseHeaders-expand command line option
ParseHeaders-merge command line option
ParseHeaders-rename command line option
ParseHeaders-table command line option
SplitSeq-count command line option
SplitSeq-group command line option
SplitSeq-sample command line option
SplitSeq-select command line option
SplitSeq-sort command line option
UnifyHeaders-consensus command line option
UnifyHeaders-delete command line option
-t <value_file>
SplitSeq-select command line option
-u <value_list>
SplitSeq-select command line option
-u <values>
ParseHeaders-add command line option
SplitSeq-sample command line option
SplitSeq-samplepair command line option
_
__bool__() (presto.Multiprocessing.SeqData method)
(presto.Multiprocessing.SeqResult method)
(presto.Sequence.PrimerAlignment method)
__len__() (presto.Multiprocessing.SeqData method)
(presto.Multiprocessing.SeqResult method)
(presto.Sequence.PrimerAlignment method)
A
addHeader() (in module presto.Annotation)
alignAssembly() (in module presto.Sequence)
AlignSets command line option
--help
--version
-h
AlignSets-muscle command line option
--bf <barcode_field>
--delim <delimiter>
--div
--exec <aligner_exec>
--failed
--fasta
--help
--log <log_file>
--nproc <nproc>
--outdir <out_dir>
--outname <out_name>
--version
-h
-o <out_files>
-s <seq_files>
AlignSets-offset command line option
--bf <barcode_field>
--delim <delimiter>
--div
--failed
--fasta
--help
--log <log_file>
--mode {pad,cut}
--nproc <nproc>
--outdir <out_dir>
--outname <out_name>
--pf <primer_field>
--version
-d <offset_table>
-h
-o <out_files>
-s <seq_files>
AlignSets-table command line option
--delim <delimiter>
--exec <aligner_exec>
--failed
--help
--outdir <out_dir>
--outname <out_name>
--reverse
--version
-h
-o <out_file>
-p <primer_file>
annotationConsensus() (in module presto.Annotation)
AssemblePairs command line option
--help
--version
-h
AssemblePairs-align command line option
--1f <head_fields>
--2f <tail_fields>
--alpha <alpha>
--coord {illumina,solexa,sra,454,presto}
--delim <delimiter>
--failed
--fasta
--help
--log <log_file>
--maxerror <max_error>
--maxlen <max_len>
--minlen <min_len>
--nproc <nproc>
--outdir <out_dir>
--outname <out_name>
--rc {tail,head,both,none}
--scanrev
--version
-1 <seq_files_1>
-2 <seq_files_2>
-h
-o <out_files>
AssemblePairs-join command line option
--1f <head_fields>
--2f <tail_fields>
--coord {illumina,solexa,sra,454,presto}
--delim <delimiter>
--failed
--fasta
--gap <gap>
--help
--log <log_file>
--nproc <nproc>
--outdir <out_dir>
--outname <out_name>
--rc {tail,head,both,none}
--version
-1 <seq_files_1>
-2 <seq_files_2>
-h
-o <out_files>
AssemblePairs-reference command line option
--1f <head_fields>
--2f <tail_fields>
--aligner {blastn,usearch}
--coord {illumina,solexa,sra,454,presto}
--dbexec <db_exec>
--delim <delimiter>
--evalue <evalue>
--exec <aligner_exec>
--failed
--fasta
--fill
--help
--log <log_file>
--maxhits <max_hits>
--minident <min_ident>
--nproc <nproc>
--outdir <out_dir>
--outname <out_name>
--rc {tail,head,both,none}
--version
-1 <seq_files_1>
-2 <seq_files_2>
-h
-o <out_files>
-r <ref_file>
AssemblePairs-sequential command line option
--1f <head_fields>
--2f <tail_fields>
--aligner {blastn,usearch}
--alpha <alpha>
--coord {illumina,solexa,sra,454,presto}
--dbexec <db_exec>
--delim <delimiter>
--evalue <evalue>
--exec <aligner_exec>
--failed
--fasta
--fill
--help
--log <log_file>
--maxerror <max_error>
--maxhits <max_hits>
--maxlen <max_len>
--minident <min_ident>
--minlen <min_len>
--nproc <nproc>
--outdir <out_dir>
--outname <out_name>
--rc {tail,head,both,none}
--scanrev
--version
-1 <seq_files_1>
-2 <seq_files_2>
-h
-o <out_files>
-r <ref_file>
AssemblyRecord (class in presto.Sequence)
AssemblyStats (class in presto.Sequence)
B
BuildConsensus command line option
--act {min,max,sum,set,majority}
--bf <barcode_field>
--cf <copy_fields>
--delim <delimiter>
--dep
--failed
--fasta
--freq <min_freq>
--help
--log <log_file>
--maxdiv <max_diversity>
--maxerror <max_error>
--maxgap <max_gap>
--nproc <nproc>
--outdir <out_dir>
--outname <out_name>
--pf <primer_field>
--prcons <primer_freq>
--version
-h
-n <min_count>
-o <out_files>
-q <min_qual>
-s <seq_files>
C
calculateDiversity() (in module presto.Sequence)
calculateSetError() (in module presto.Sequence)
checkArgs() (in module presto.Commandline)
checkSeqEqual() (in module presto.Sequence)
ClusterSets command line option
--help
--version
-h
ClusterSets-all command line option
--cluster {usearch,vsearch,cd-hit-est}
--delim <delimiter>
--end <seq_end>
--exec <cluster_exec>
--fasta
--help
--ident <ident>
--length <length_ratio>
--nproc <nproc>
--outdir <out_dir>
--outname <out_name>
--prefix <cluster_prefix>
--start <seq_start>
--version
-h
-k <cluster_field>
-o <out_files>
-s <seq_files>
ClusterSets-barcode command line option
--cluster {usearch,vsearch,cd-hit-est}
--delim <delimiter>
--exec <cluster_exec>
--fasta
--help
--ident <ident>
--length <length_ratio>
--nproc <nproc>
--outdir <out_dir>
--outname <out_name>
--prefix <cluster_prefix>
--version
-f <barcode_field>
-h
-k <cluster_field>
-o <out_files>
-s <seq_files>
ClusterSets-set command line option
--cluster {usearch,vsearch,cd-hit-est}
--delim <delimiter>
--end <seq_end>
--exec <cluster_exec>
--failed
--fasta
--help
--ident <ident>
--length <length_ratio>
--log <log_file>
--nproc <nproc>
--outdir <out_dir>
--outname <out_name>
--prefix <cluster_prefix>
--start <seq_start>
--version
-f <set_field>
-h
-k <cluster_field>
-o <out_files>
-s <seq_files>
collapseAnnotation() (in module presto.Annotation)
collapseHeader() (in module presto.Annotation)
CollapseSeq command line option
--act {min,max,sum,set}
--cf <copy_fields>
--delim <delimiter>
--failed
--fasta
--help
--inner
--keepmiss
--log <log_file>
--maxf <max_field>
--minf <min_field>
--outdir <out_dir>
--outname <out_name>
--uf <uniq_fields>
--version
-h
-n <max_missing>
-o <out_files>
-s <seq_files>
collectPairQueue() (in module presto.Multiprocessing)
collectSeqQueue() (in module presto.Multiprocessing)
CommonHelpFormatter (class in presto.Commandline)
compilePrimers() (in module presto.Sequence)
consensusUnify() (in module presto.Sequence)
convert454Header() (in module presto.Annotation)
convertGenbankHeader() (in module presto.Annotation)
convertGenericHeader() (in module presto.Annotation)
ConvertHeaders command line option
--help
--version
-h
ConvertHeaders-454 command line option
--delim <delimiter>
--failed
--fasta
--help
--outdir <out_dir>
--outname <out_name>
--version
-h
-o <out_files>
-s <seq_files>
ConvertHeaders-genbank command line option
--delim <delimiter>
--failed
--fasta
--help
--outdir <out_dir>
--outname <out_name>
--version
-h
-o <out_files>
-s <seq_files>
ConvertHeaders-generic command line option
--delim <delimiter>
--failed
--fasta
--help
--outdir <out_dir>
--outname <out_name>
--version
-h
-o <out_files>
-s <seq_files>
ConvertHeaders-illumina command line option
--delim <delimiter>
--failed
--fasta
--help
--outdir <out_dir>
--outname <out_name>
--version
-h
-o <out_files>
-s <seq_files>
ConvertHeaders-imgt command line option
--delim <delimiter>
--failed
--fasta
--help
--outdir <out_dir>
--outname <out_name>
--simple
--version
-h
-o <out_files>
-s <seq_files>
ConvertHeaders-migec command line option
--delim <delimiter>
--failed
--fasta
--help
--outdir <out_dir>
--outname <out_name>
--version
-h
-o <out_files>
-s <seq_files>
ConvertHeaders-sra command line option
--delim <delimiter>
--failed
--fasta
--help
--outdir <out_dir>
--outname <out_name>
--version
-h
-o <out_files>
-s <seq_files>
convertIlluminaHeader() (in module presto.Annotation)
convertIMGTHeader() (in module presto.Annotation)
convertMIGECHeader() (in module presto.Annotation)
convertSRAHeader() (in module presto.Annotation)
copyHeader() (in module presto.Annotation)
countSeqFile() (in module presto.IO)
countSeqSets() (in module presto.IO)
D
data (presto.Multiprocessing.SeqData attribute)
(presto.Multiprocessing.SeqResult attribute)
data_count() (presto.Multiprocessing.SeqResult property)
deleteHeader() (in module presto.Annotation)
deleteSeqPositions() (in module presto.Sequence)
deletionUnify() (in module presto.Sequence)
E
EstimateError command line option
--help
--version
-h
EstimateError-barcode command line option
--delim <delimiter>
--help
--outdir <out_dir>
--outname <out_name>
--version
-f <barcode_field>
-h
-s <seq_files>
EstimateError-set command line option
--delim <delimiter>
--freq <min_freq>
--help
--log <log_file>
--maxdiv <max_diversity>
--mode {freq,qual}
--nproc <nproc>
--outdir <out_dir>
--outname <out_name>
--version
-f <set_field>
-h
-n <min_count>
-q <min_qual>
-s <seq_files>
expandHeader() (in module presto.Annotation)
extractAlignment() (in module presto.Sequence)
F
feedPairQueue() (in module presto.Multiprocessing)
feedSeqQueue() (in module presto.Multiprocessing)
filterLength() (in module presto.Sequence)
filterMissing() (in module presto.Sequence)
filterQuality() (in module presto.Sequence)
filterRepeats() (in module presto.Sequence)
FilterSeq command line option
--help
--version
-h
FilterSeq-length command line option
--failed
--fasta
--help
--inner
--log <log_file>
--nproc <nproc>
--outdir <out_dir>
--outname <out_name>
--version
-h
-n <min_length>
-o <out_files>
-s <seq_files>
FilterSeq-maskqual command line option
--failed
--fasta
--help
--log <log_file>
--nproc <nproc>
--outdir <out_dir>
--outname <out_name>
--version
-h
-o <out_files>
-q <min_qual>
-s <seq_files>
FilterSeq-missing command line option
--failed
--fasta
--help
--inner
--log <log_file>
--nproc <nproc>
--outdir <out_dir>
--outname <out_name>
--version
-h
-n <max_missing>
-o <out_files>
-s <seq_files>
FilterSeq-quality command line option
--failed
--fasta
--help
--inner
--log <log_file>
--nproc <nproc>
--outdir <out_dir>
--outname <out_name>
--version
-h
-o <out_files>
-q <min_qual>
-s <seq_files>
FilterSeq-repeats command line option
--failed
--fasta
--help
--inner
--log <log_file>
--missing
--nproc <nproc>
--outdir <out_dir>
--outname <out_name>
--version
-h
-n <max_repeat>
-o <out_files>
-s <seq_files>
FilterSeq-trimqual command line option
--failed
--fasta
--help
--log <log_file>
--nproc <nproc>
--outdir <out_dir>
--outname <out_name>
--reverse
--version
--win <window>
-h
-o <out_files>
-q <min_qual>
-s <seq_files>
findGapPositions() (in module presto.Sequence)
flattenAnnotation() (in module presto.Annotation)
frequencyConsensus() (in module presto.Sequence)
G
getAAScoreDict() (in module presto.Sequence)
getAnnotationValues() (in module presto.Annotation)
getCommonArgParser() (in module presto.Commandline)
getCoordKey() (in module presto.Annotation)
getDNAScoreDict() (in module presto.Sequence)
getFileType() (in module presto.IO)
getOutputHandle() (in module presto.IO)
I
id (presto.Multiprocessing.SeqData attribute)
(presto.Multiprocessing.SeqResult attribute)
indexSeqSets() (in module presto.Sequence)
J
joinAssembly() (in module presto.Sequence)
L
localAlignment() (in module presto.Sequence)
log (presto.Multiprocessing.SeqResult attribute)
M
makeBlastnDb() (in module presto.Applications)
makeUBlastDb() (in module presto.Applications)
manageProcesses() (in module presto.Multiprocessing)
MaskPrimers command line option
--help
--version
-h
MaskPrimers-align command line option
--barcode
--bf <barcode_field>
--delim <delimiter>
--failed
--fasta
--gap <gap_penalty>
--help
--log <log_file>
--maxerror <max_error>
--maxlen <max_len>
--mode {cut,mask,trim,tag}
--nproc <nproc>
--outdir <out_dir>
--outname <out_name>
--pf <primer_field>
--revpr
--skiprc
--version
-h
-o <out_files>
-p <primer_file>
-s <seq_files>
MaskPrimers-extract command line option
--barcode
--bf <barcode_field>
--delim <delimiter>
--failed
--fasta
--help
--len <length>
--log <log_file>
--mode {cut,mask,trim,tag}
--nproc <nproc>
--outdir <out_dir>
--outname <out_name>
--pf <primer_field>
--revpr
--start <start>
--version
-h
-o <out_files>
-s <seq_files>
MaskPrimers-score command line option
--barcode
--bf <barcode_field>
--delim <delimiter>
--failed
--fasta
--help
--log <log_file>
--maxerror <max_error>
--mode {cut,mask,trim,tag}
--nproc <nproc>
--outdir <out_dir>
--outname <out_name>
--pf <primer_field>
--revpr
--start <start>
--version
-h
-o <out_files>
-p <primer_file>
-s <seq_files>
maskQuality() (in module presto.Sequence)
maskSeq() (in module presto.Sequence)
mergeAnnotation() (in module presto.Annotation)
mergeHeader() (in module presto.Annotation)
module
presto.Annotation
presto.Applications
presto.Commandline
presto.IO
presto.Multiprocessing
presto.Sequence
O
overlap() (presto.Sequence.AssemblyRecord property)
overlapConsensus() (in module presto.Sequence)
P
PairSeq command line option
--1f <fields_1>
--2f <fields_2>
--act {min,max,sum,set,cat}
--coord {illumina,solexa,sra,454,presto}
--delim <delimiter>
--failed
--fasta
--help
--outdir <out_dir>
--outname <out_name>
--version
-1 <seq_files_1>
-2 <seq_files_2>
-h
parseAnnotation() (in module presto.Annotation)
parseCommonArgs() (in module presto.Commandline)
ParseHeaders command line option
--help
--version
-h
ParseHeaders-add command line option
--delim <delimiter>
--failed
--fasta
--help
--outdir <out_dir>
--outname <out_name>
--version
-f <fields>
-h
-o <out_files>
-s <seq_files>
-u <values>
ParseHeaders-collapse command line option
--act {min,max,sum,first,last,set,cat}
--delim <delimiter>
--failed
--fasta
--help
--outdir <out_dir>
--outname <out_name>
--version
-f <fields>
-h
-o <out_files>
-s <seq_files>
ParseHeaders-copy command line option
--act {min,max,sum,first,last,set,cat}
--delim <delimiter>
--failed
--fasta
--help
--outdir <out_dir>
--outname <out_name>
--version
-f <fields>
-h
-k <names>
-o <out_files>
-s <seq_files>
ParseHeaders-delete command line option
--delim <delimiter>
--failed
--fasta
--help
--outdir <out_dir>
--outname <out_name>
--version
-f <fields>
-h
-o <out_files>
-s <seq_files>
ParseHeaders-expand command line option
--delim <delimiter>
--failed
--fasta
--help
--outdir <out_dir>
--outname <out_name>
--sep <separator>
--version
-f <fields>
-h
-o <out_files>
-s <seq_files>
ParseHeaders-merge command line option
--act {min,max,sum,set,cat}
--delete
--delim <delimiter>
--failed
--fasta
--help
--outdir <out_dir>
--outname <out_name>
--version
-f <fields>
-h
-k <name>
-o <out_files>
-s <seq_files>
ParseHeaders-rename command line option
--act {min,max,sum,first,last,set,cat}
--delim <delimiter>
--failed
--fasta
--help
--outdir <out_dir>
--outname <out_name>
--version
-f <fields>
-h
-k <names>
-o <out_files>
-s <seq_files>
ParseHeaders-table command line option
--delim <delimiter>
--failed
--help
--outdir <out_dir>
--outname <out_name>
--version
-f <fields>
-h
-o <out_files>
-s <seq_files>
ParseLog command line option
--delim <delimiter>
--help
--outdir <out_dir>
--outname <out_name>
--version
-f <fields>
-h
-l <record_files>
-o <out_files>
parseLog() (in module presto.Annotation)
presto.Annotation
module
presto.Applications
module
presto.Commandline
module
presto.IO
module
presto.Multiprocessing
module
presto.Sequence
module
PrimerAlignment (class in presto.Sequence)
printCount() (in module presto.IO)
printDebug() (in module presto.IO)
printError() (in module presto.IO)
printLog() (in module presto.IO)
printMessage() (in module presto.IO)
printProgress() (in module presto.IO)
printWarning() (in module presto.IO)
processSeqQueue() (in module presto.Multiprocessing)
Q
qualityConsensus() (in module presto.Sequence)
R
readPrimerFile() (in module presto.IO)
readReferenceFile() (in module presto.IO)
readSeqFile() (in module presto.IO)
referenceAssembly() (in module presto.Sequence)
renameAnnotation() (in module presto.Annotation)
renameHeader() (in module presto.Annotation)
results (presto.Multiprocessing.SeqResult attribute)
reverseComplement() (in module presto.Sequence)
runBlastn() (in module presto.Applications)
runCDHit() (in module presto.Applications)
runMuscle() (in module presto.Applications)
runUBlast() (in module presto.Applications)
runUClust() (in module presto.Applications)
S
scoreAA() (in module presto.Sequence)
scoreAlignment() (in module presto.Sequence)
scoreDNA() (in module presto.Sequence)
scoreSeqPair() (in module presto.Sequence)
SeqData (class in presto.Multiprocessing)
SeqResult (class in presto.Multiprocessing)
sequentialAssembly() (in module presto.Sequence)
SplitSeq command line option
--help
--version
-h
SplitSeq-count command line option
--fasta
--help
--outdir <out_dir>
--outname <out_name>
--version
-h
-n <max_count>
-s <seq_files>
SplitSeq-group command line option
--delim <delimiter>
--fasta
--help
--num <threshold>
--outdir <out_dir>
--outname <out_name>
--version
-f <field>
-h
-s <seq_files>
SplitSeq-sample command line option
--delim <delimiter>
--fasta
--help
--outdir <out_dir>
--outname <out_name>
--version
-f <field>
-h
-n <max_count>
-s <seq_files>
-u <values>
SplitSeq-samplepair command line option
--coord {illumina,solexa,sra,454,presto}
--delim <delimiter>
--fasta
--help
--outdir <out_dir>
--outname <out_name>
--version
-1 <seq_files_1>
-2 <seq_files_2>
-f <field>
-h
-n <max_count>
-u <values>
SplitSeq-select command line option
--delim <delimiter>
--fasta
--help
--not
--outdir <out_dir>
--outname <out_name>
--version
-f <field>
-h
-o <out_files>
-s <seq_files>
-t <value_file>
-u <value_list>
SplitSeq-sort command line option
--delim <delimiter>
--fasta
--help
--num
--outdir <out_dir>
--outname <out_name>
--version
-f <field>
-h
-n <max_count>
-s <seq_files>
subsetSeqIndex() (in module presto.Sequence)
subsetSeqSet() (in module presto.Sequence)
T
translateAmbigDNA() (in module presto.Sequence)
trimQuality() (in module presto.Sequence)
U
UnifyHeaders command line option
--help
--version
-h
UnifyHeaders-consensus command line option
--delim <delimiter>
--failed
--fasta
--help
--log <log_file>
--nproc <nproc>
--outdir <out_dir>
--outname <out_name>
--version
-f <set_field>
-h
-k <unify_field>
-o <out_files>
-s <seq_files>
UnifyHeaders-delete command line option
--delim <delimiter>
--failed
--fasta
--help
--log <log_file>
--nproc <nproc>
--outdir <out_dir>
--outname <out_name>
--version
-f <set_field>
-h
-k <unify_field>
-o <out_files>
-s <seq_files>
V
valid (presto.Multiprocessing.SeqData attribute)
(presto.Multiprocessing.SeqResult attribute)
W
weightSeq() (in module presto.Sequence)
Read the Docs
v: 0.6.2
Versions
latest
stable
0.6.2
0.6.1
0.6.0
0.5.13
Downloads
On Read the Docs
Project Home
Builds
Free document hosting provided by
Read the Docs
.