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EMBOSS: seqretsplit |
Its main use is therefore to split a file containing multiple sequences into many files, each containing one sequence.
The names of the files it creates are derived from the ID name of the sequence, followed by an extension denoting the format of the sequence. You have no control over the names of the files it writes out.
For example, if the files embl:hsfa11* are read in and the output is specified as wibble.seq, then the following files are expected to be created:
hsfa110.fasta hsfa111.fasta hsfa112.fasta hsfa113.fasta hsfa114.fasta
(No file wibble.seq is created.)
Why would you want to split a multiple sequence file into many individual files?
EMBOSS programs can read in many sequences from one file where this is sensible. Sometimes EMBOSS programs can only read in one sequence at a time because that is the sensible way to do things, but your sequence is one sequence of many in a file. You can specify that sequence using the USA filename:sequenceID, but you may still feel more comfortable splitting your sequences up into many files first.
Many non-EMBOSS programs will also have restrictions on whether they can read in multiple sequence files or not.
% seqretsplit Reads and writes (returns) sequences in individual files Input sequence(s): embl:hsfa11* Output sequence [hsfa110.fasta]:
The specification of the output file is not used in this case.
At some point this ought to change and you will not be prompted for the output file at all.
Mandatory qualifiers: [-sequence] seqall Sequence database USA [-outseq] seqoutall Output sequence(s) USA Optional qualifiers: (none) Advanced qualifiers: -firstonly bool Read one sequence and stop |
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 | |
-firstonly | Read one sequence and stop | Yes/No | No |
The names of the files it creates are derived from the ID name of the sequence, followed by an extension denoting the format of the sequence. You have no control over the names of the files it writes out.
For example, if the files embl:hsfa11* are read in and the output is specified as wibble.seq, then the following files are expected to be created:
hsfa110.fasta hsfa111.fasta hsfa112.fasta hsfa113.fasta hsfa114.fasta
(No file wibble.seq is created.)
Program name | Description |
---|---|
cirdna | Draws circular maps of DNA constructs |
lindna | Draws linear maps of DNA constructs |
remap | Display a sequence with restriction cut sites, translation etc |
seqret | Reads and writes (returns) sequences |
seqretall | Reads and writes (returns) a set of sequences one at a time |
seqretset | Reads and writes (returns) a set of sequences all at once |
showfeat | Show features of a sequence |
showseq | Display a sequence with features, translation etc |