![]() |
descseq |
Rather than using an editor to alter the name or the comments, descseq allows you to simply change them and write out a new file with the changes in and the sequence left unaltered.
The default action is to replace the existing name or description with your new one, but by using the qualifier '-append' what you enter is appended to the existing name or description.
Note that is you append to a description, no space is inserted by default bewteen the existing description and your appended text - you have to put in a space yourself if you require one.
% descseq -seq clone23 -out clone23.seq -name "myclone23"
Set the description of a sequence to "This is my clone number 244"
% descseq -seq xy24 -out xy24.seq -desc "This is my clone number 244"
Append some text to the description of a sequence
% descseq -seq est.seq -out est4.seq -desc " (submitted)" -append
Mandatory qualifiers: [-sequence] sequence Sequence USA [-outseq] seqout Output sequence USA Optional qualifiers: -name string Name of the sequence -description string Description of the sequence Advanced qualifiers: -append boolean This allows you to append the name or description you have given on to the end of the existing name or description of the sequence. General qualifiers: -help boolean Report command line options. More information on associated and general qualifiers can be found with -help -verbose |
Mandatory qualifiers | Allowed values | Default | |
---|---|---|---|
[-sequence] (Parameter 1) |
Sequence USA | Readable sequence | Required |
[-outseq] (Parameter 2) |
Output sequence USA | Writeable sequence | <sequence>.format |
Optional qualifiers | Allowed values | Default | |
-name | Name of the sequence | Any string is accepted | An empty string is accepted |
-description | Description of the sequence | Any string is accepted | An empty string is accepted |
Advanced qualifiers | Allowed values | Default | |
-append | This allows you to append the name or description you have given on to the end of the existing name or description of the sequence. | Yes/No | No |
Program name | Description |
---|---|
biosed | Replace or delete sequence sections |
cutseq | Removes a specified section from a sequence |
degapseq | Removes gap characters from sequences |
entret | Reads and writes (returns) flatfile entries |
extractfeat | Extract features from a sequence |
extractseq | Extract regions from a sequence |
listor | Writes 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 | Excludes a set of sequences and writes 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 the first few |
splitter | Split a sequence into (overlapping) smaller sequences |
swissparse | Retrieves sequences from swissprot using keyword search |
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 |