skipseq

 

Function

Reads and writes (returns) sequences, skipping the first few

Description

skipseq skips the first few sequences in a multiple set of sequences, and writes out the rest of them.

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.

Usage

Here is a sample session with skipseq:

% skipseq -skip 1
Reads and writes (returns) sequences, skipping the first few
Input sequence(s): tembl:eclac*
Output sequence [eclac.fasta]: 

Command line arguments

   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

Input file format

skipseq reads one or more sequences files.

See the documentation for seqret to see the full range of things that you can do when reading and writing sequences.

Output file format

skipseq writes one or more sequences files, having optionally skipped the first few sequences.

See the documentation for seqret to see the full range of things that you can do when reading and writing sequences.

Data files

None.

Notes

None.

References

None.

Warnings

You may skip all of the input files.
If the -skip value is greater than or equal to the number of input sequences, there is no warning: this is legal.

Diagnostic Error Messages

None.

Exit status

It always exits with status 0.

Known bugs

None.

See also

Program nameDescription
biosedReplace or delete sequence sections
cutseqRemoves a specified section from a sequence
degapseqRemoves gap characters from sequences
descseqAlter the name or description of a sequence
entretReads and writes (returns) flatfile entries
extractfeatExtract features from a sequence
extractseqExtract regions from a sequence
listorWrites a list file of the logical OR of two sets of sequences
maskfeatMask off features of a sequence
maskseqMask off regions of a sequence
newseqType in a short new sequence
noreturnRemoves carriage return from ASCII files
notseqExcludes a set of sequences and writes out the remaining ones
nthseqWrites one sequence from a multiple set of sequences
pasteseqInsert one sequence into another
revseqReverse and complement a sequence
seqretReads and writes (returns) sequences
seqretsplitReads and writes (returns) sequences in individual files
splitterSplit a sequence into (overlapping) smaller sequences
swissparseRetrieves sequences from swissprot using keyword search
trimestTrim poly-A tails off EST sequences
trimseqTrim ambiguous bits off the ends of sequences
unionReads sequence fragments and builds one sequence
vectorstripStrips out DNA between a pair of vector sequences
yankReads 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.

Author(s)

This application was written by Peter Rice (peter.rice@uk.lionbioscience.com)

History

Written (25 June 2002) - Peter Rice

Target users

This program is intended to be used by everyone and everything, from naive users to embedded scripts.

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