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skipseq |
skipseq is a variant of the standard program for reading and writing sequences, seqret.
seqret has an option to allow it to only read the first sequence from a multiple set of sequences (-firstonly). seqret cannot, however, skip the first few sequences from a multiple set of sequence, writing out the rest; this is what skipseq is for.
In all other respects, skipseq is the same as seqret.
% skipseq -skip 1 Reads and writes (returns) sequences, skipping the first few Input sequence(s): tembl:eclac* Output sequence [eclac.fasta]:
Mandatory qualifiers: [-sequence] seqall Sequence database USA -skip integer Number of sequences to skip at start [-outseq] seqoutall Output sequence(s) USA Optional qualifiers: (none) Advanced qualifiers: -feature boolean Use feature information 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 database USA | Readable sequence(s) | Required |
-skip | Number of sequences to skip at start | Any integer value | 0 |
[-outseq] (Parameter 2) |
Output sequence(s) USA | Writeable sequence(s) | <sequence>.format |
Optional qualifiers | Allowed values | Default | |
(none) | |||
Advanced qualifiers | Allowed values | Default | |
-feature | Use feature information | Yes/No | No |
See the documentation for seqret to see the full range of things that you can do when reading and writing sequences.
See the documentation for seqret to see the full range of things that you can do when reading and writing sequences.
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 |
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 |
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 |
skipseq is a variant of the standard program for reading and writing sequences, seqret.