Sequence-fairies
0.9.1
General
Overview
Installation
Programs
concatenator
extractDomains
isoformCleaner
seqCheck
seqExtract
Appendix
Domain annotation
Sequence-fairies
»
Index
Index
Symbols
|
C
|
E
|
I
|
S
Symbols
--append
seqExtract command line option
--check-all
stopCleaner command line option
--check-alphabet
stopCleaner command line option
--check-duplications
stopCleaner command line option
--check-stops
stopCleaner command line option
--column <ARG>
seqExtract command line option
--comment
isoformCleaner command line option
--delim-extract <ARG>
seqExtract command line option
--delim-pos <ARG>
seqExtract command line option
--delimiter CHAR
concatenator command line option
--directory <DIRECTORY>
concatenator command line option
--domains <FILE>
extractDomains command line option
--ending <STRING>
concatenator command line option
--extract-order
seqExtract command line option
--fix-and-keep
stopCleaner command line option
--fix-and-remove
stopCleaner command line option
--fix-ending
stopCleaner command line option
--gffFILE <FILE>
isoformCleaner command line option
--help
concatenator command line option
extractDomains command line option
isoformCleaner command line option
seqExtract command line option
stopCleaner command line option
--id <ARG>
extractDomains command line option
--ignore-missing <ARG>
seqExtract command line option
--in
isoformCleaner command line option
stopCleaner command line option
--in <FILE>
seqExtract command line option
--in <FILES>
concatenator command line option
--index
seqExtract command line option
--indexFile <FILE>
seqExtract command line option
--inputList <FILE>
seqExtract command line option
--length <ARG>
seqExtract command line option
--lenient
concatenator command line option
--level1 <AEG>
isoformCleaner command line option
--level2 <AEG>
isoformCleaner command line option
--level3 <AEG>
isoformCleaner command line option
--min-length <ARG>
extractDomains command line option
--name
isoformCleaner command line option
--name <ARG>
extractDomains command line option
--namesFile <FILE>
seqExtract command line option
--numSeqs <ARG>
seqExtract command line option
--out <FILE>
concatenator command line option
extractDomains command line option
isoformCleaner command line option
seqExtract command line option
stopCleaner command line option
--pattern <STRINGS>
concatenator command line option
--preset <ARG>
isoformCleaner command line option
--regular <ARG>
isoformCleaner command line option
--remove
seqExtract command line option
--remove-alpha
stopCleaner command line option
--remove-comments
seqExtract command line option
--remove-duplicates
stopCleaner command line option
--remove-stop-genes
stopCleaner command line option
--rename-duplicates
stopCleaner command line option
--replace-char
stopCleaner command line option
--replace-stop
stopCleaner command line option
--report <FILE>
stopCleaner command line option
--revComp
seqExtract command line option
--seed <ARG>
seqExtract command line option
--sequences <FILE>
extractDomains command line option
--set-alphabet
stopCleaner command line option
--split-char <CHAR>
isoformCleaner command line option
--stop-char
stopCleaner command line option
--summary
isoformCleaner command line option
--table <ARG>
seqExtract command line option
--translate
seqExtract command line option
--use-evelope
extractDomains command line option
-A
stopCleaner command line option
-a
seqExtract command line option
-c
isoformCleaner command line option
seqExtract command line option
-C <ARG>
seqExtract command line option
-d
concatenator command line option
-D <ARG>
seqExtract command line option
-d <ARG>
seqExtract command line option
-d <FILE>
extractDomains command line option
-D CHAR
concatenator command line option
-e
extractDomains command line option
-e <ARG> --extract <ARG>
seqExtract command line option
-e <STRING>
concatenator command line option
-F <FILE>
seqExtract command line option
-g <FILE>
isoformCleaner command line option
-h
concatenator command line option
extractDomains command line option
isoformCleaner command line option
seqExtract command line option
stopCleaner command line option
-I
seqExtract command line option
-i
concatenator command line option
-i <FILE>
isoformCleaner command line option
seqExtract command line option
stopCleaner command line option
-l
concatenator command line option
-L <ARG>
seqExtract command line option
-l <FILE>
seqExtract command line option
-m <ARG>
seqExtract command line option
-n
isoformCleaner command line option
-n <ARG>
extractDomains command line option
seqExtract command line option
-N <FILE>
seqExtract command line option
-o
concatenator command line option
-o <FILE>
extractDomains command line option
isoformCleaner command line option
seqExtract command line option
stopCleaner command line option
-p <ARG>
isoformCleaner command line option
-p <STRINGS>
concatenator command line option
-R
seqExtract command line option
-r
seqExtract command line option
-r <ARG>
isoformCleaner command line option
-r <FILE>
stopCleaner command line option
-s <ARG>
seqExtract command line option
-s <CHAR>
isoformCleaner command line option
-s <FILE>
extractDomains command line option
-t
seqExtract command line option
-T <ARG>
seqExtract command line option
C
concatenator command line option
--delimiter CHAR
--directory <DIRECTORY>
--ending <STRING>
--help
--in <FILES>
--lenient
--out <FILE>
--pattern <STRINGS>
-d
-D CHAR
-e <STRING>
-h
-i
-l
-o
-p <STRINGS>
E
extractDomains command line option
--domains <FILE>
--help
--id <ARG>
--min-length <ARG>
--name <ARG>
--out <FILE>
--sequences <FILE>
--use-evelope
-d <FILE>
-e
-h
-n <ARG>
-o <FILE>
-s <FILE>
I
isoformCleaner command line option
--comment
--gffFILE <FILE>
--help
--in
--level1 <AEG>
--level2 <AEG>
--level3 <AEG>
--name
--out <FILE>
--preset <ARG>
--regular <ARG>
--split-char <CHAR>
--summary
-c
-g <FILE>
-h
-i <FILE>
-n
-o <FILE>
-p <ARG>
-r <ARG>
-s <CHAR>
S
seqExtract command line option
--append
--column <ARG>
--delim-extract <ARG>
--delim-pos <ARG>
--extract-order
--help
--ignore-missing <ARG>
--in <FILE>
--index
--indexFile <FILE>
--inputList <FILE>
--length <ARG>
--namesFile <FILE>
--numSeqs <ARG>
--out <FILE>
--remove
--remove-comments
--revComp
--seed <ARG>
--table <ARG>
--translate
-a
-c
-C <ARG>
-d <ARG>
-D <ARG>
-e <ARG> --extract <ARG>
-F <FILE>
-h
-I
-i <FILE>
-L <ARG>
-l <FILE>
-m <ARG>
-n <ARG>
-N <FILE>
-o <FILE>
-r
-R
-s <ARG>
-t
-T <ARG>
stopCleaner command line option
--check-all
--check-alphabet
--check-duplications
--check-stops
--fix-and-keep
--fix-and-remove
--fix-ending
--help
--in
--out <FILE>
--remove-alpha
--remove-duplicates
--remove-stop-genes
--rename-duplicates
--replace-char
--replace-stop
--report <FILE>
--set-alphabet
--stop-char
-A
-h
-i <FILE>
-o <FILE>
-r <FILE>