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EMBOSS: seqretall |
In early pre-release versions of EMBOSS, seqret read only one sequence so this program was needed to read more sequences. We have retained it for compatibility only.
% seqretall Reads and writes (returns) a set of sequences one at a time Input sequence(s): embl:eclac* Output sequence [eclac.fasta]:
Mandatory qualifiers: [-sequence] seqall Sequence database USA [-outseq] seqoutall Output sequence(s) 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 database USA | Readable sequence(s) | Required |
[-outseq] (Parameter 2) |
Output sequence(s) USA | Writeable sequence(s) | <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, for example if you try to read the output from the example run with seqretall and give no output format.
As seqretall reads only the first sequence before opening the output file it will overwrite the sequences before reading has completed, with unpredictable result. Note that this is not true of seqretset which reads all sequences into memory 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 |
seqretset | Reads and writes (returns) a set of sequences all at once |
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 |