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EMBOSS: seqretset |
% seqretset Reads and writes (returns) a set of sequences all at once Input sequence set: embl:eclac* Output sequence [outfile.fasta]:
Mandatory qualifiers: [-sequence] seqset Sequence set USA [-outseq] seqoutset Output sequence set USA Optional qualifiers: (none) Advanced qualifiers: (none) General qualifiers: -help bool 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 set USA | Readable sequences | Required |
[-outseq] (Parameter 2) |
Output sequence set USA | Writeable sequences | <sequence>.format |
Optional qualifiers | Allowed values | Default | |
(none) | |||
Advanced qualifiers | Allowed values | Default | |
(none) |
In some cases the output filename will be the same as the input filename, but as seqretset reads all the sequences before opening the output file it will safely overwrite. Note that this is not true of seqretall which only reads the first sequence before opening the ouput file, but is true of seqret which reads the first sequence at startup.
Program name | Description |
---|---|
biosed | Replace or delete sequence sections |
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 |
infoseq | Displays some simple information about sequences |
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 |
seqretall | Reads and writes (returns) a set of sequences one at a time |
seqretsplit | Reads and writes (returns) sequences in individual files |
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 |
vectorstrip | Strips out DNA between a pair of vector sequences |