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EMBOSS: notseq |
This program was written for the case where a file containing several sequences is being used as a small database, but some of the sequences are no longer required and must be deleted from the file.
notseq splits the input sequences into those that you wish to keep and those you wish to exclude.
notseq takes a set of sequences as input together with a list of sequence names or accession numbers. It also takes the name of a new file to write the files that you want to keep into, and optionally the name of a file that will contain the files that you want excluded from the set.
notseq then reads in the input sequences. It outputs the ones that match one of the sequence names or acession numbers to the file of excluded sequences, and those that don't match are output to the file of sequences to be kept.
% notseq Input sequence(s): mydata.seq Output sequence [clone001.fasta]: mydata2.seq Sequence names to exclude: clone186, clone876Here is an example where the sequences to be excluded are saved to another file:
% notseq -junkout excluded.seq Input sequence(s): mydata.seq Output sequence [clone001.fasta]: mydata2.seq Sequence names to exclude: clone99*
Mandatory qualifiers: [-sequence] seqall Sequence database USA [-exclude] string Enter a list of sequence names or accession numbers to exclude from the sequences read in. The excluded sequences will be written to the file specified in the 'junkout' parameter. The remainder will be written out to the file specified in the 'outseq' parameter. The list of sequence names can be separated by either spaces or commas. The sequence names can be wildcarded. The sequence names are case independent. An example of a list of sequences to be excluded is: myseq, hs*, one two three [-outseq] seqoutall Output sequence(s) USA Optional qualifiers: -junkout seqoutall This file collects the sequences which you have excluded from the main output file of sequences. 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 |
[-exclude] (Parameter 2) |
Enter a list of sequence names or accession numbers to exclude from the sequences read in. The excluded sequences will be written to the file specified in the 'junkout' parameter. The remainder will be written out to the file specified in the 'outseq' parameter. The list of sequence names can be separated by either spaces or commas. The sequence names can be wildcarded. The sequence names are case independent. An example of a list of sequences to be excluded is: myseq, hs*, one two three | Any string is accepted | An empty string is accepted |
[-outseq] (Parameter 3) |
Output sequence(s) USA | Writeable sequence(s) | <sequence>.format |
Optional qualifiers | Allowed values | Default | |
-junkout | This file collects the sequences which you have excluded from the main output file of sequences. | Writeable sequence(s) | /dev/null |
Advanced qualifiers | Allowed values | Default | |
(none) |
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 |
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 |