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degapseqrunner |
Standard (Mandatory) qualifiers: [-gappedseqsdir] dirlist Input directory of files containing sequence pairs for degapping [-commandpath] directory Directory where degapping executable lives [-commandname] string Name of degapping executable [-degappedseqsoutdir] outdir Directory where degapped sequence pairs will be written [-outfilesuffix] string Appended to end of all output file names Additional (Optional) qualifiers: (none) Advanced (Unprompted) qualifiers: (none) Associated qualifiers: (none) General qualifiers: -auto boolean Turn off prompts -stdout boolean Write standard output -filter boolean Read standard input, write standard output -options boolean Prompt for standard and additional values -debug boolean Write debug output to program.dbg -verbose boolean Report some/full command line options -help boolean Report command line options. More information on associated and general qualifiers can be found with -help -verbose -warning boolean Report warnings -error boolean Report errors -fatal boolean Report fatal errors -die boolean Report deaths |
Standard (Mandatory) qualifiers | Allowed values | Default | |
---|---|---|---|
[-gappedseqsdir] (Parameter 1) |
Input directory of files containing sequence pairs for degapping | Directory with files | . |
[-commandpath] (Parameter 2) |
Directory where degapping executable lives | Directory | |
[-commandname] (Parameter 3) |
Name of degapping executable | Any string is accepted | degapseq |
[-degappedseqsoutdir] (Parameter 4) |
Directory where degapped sequence pairs will be written | Output directory | |
[-outfilesuffix] (Parameter 5) |
Appended to end of all output file names | Any string is accepted | .deg |
Additional (Optional) qualifiers | Allowed values | Default | |
(none) | |||
Advanced (Unprompted) qualifiers | Allowed values | Default | |
(none) |
Under development, no example input file(s) yet
Under development, no example output file(s) yet
Program name | Description |
---|---|
biosed | Replace or delete sequence sections |
codcopy | Reads and writes a codon usage table |
cutseq | Removes a specified section from a sequence |
degapseq | Removes gap characters from sequences |
descseq | Alter the name or description of a sequence |
entret | Reads and writes (returns) flatfile entries |
extractfeat | Extract features from a sequence |
extractseq | Extract regions from a sequence |
listor | Write a list file of the logical OR of two sets of sequences |
maskfeat | Mask off features of a sequence |
maskseq | Mask off regions of a sequence |
newseq | Type in a short new sequence |
noreturn | Removes carriage return from ASCII files |
notseq | Exclude a set of sequences and write out the remaining ones |
nthseq | Writes one sequence from a multiple set of sequences |
pasteseq | Insert one sequence into another |
revseq | Reverse and complement a sequence |
seqret | Reads and writes (returns) sequences |
seqretsplit | Reads and writes (returns) sequences in individual files |
skipseq | Reads and writes (returns) sequences, skipping first few |
splitter | Split a sequence into (overlapping) smaller sequences |
trimest | Trim poly-A tails off EST sequences |
trimseq | Trim ambiguous bits off the ends of sequences |
union | Reads sequence fragments and builds one sequence |
vectorstrip | Strips out DNA between a pair of vector sequences |
yank | Reads a sequence range, appends the full USA to a list file |