notseq

notseq

notseq splits the input sequences into those that you want to keep and those you want to exclude.

Here is a sample session with notseq. In this case the excluded sequences (clone186 and clone876) are simply thrown away and not saved to any file:

% notseq Excludes a set of sequences and writes out the remaining ones Input sequence(s): globins.fasta Sequence names to exclude: myg_phyca,lgb2_luplu Output sequence [hbb_human.fasta]: mydata.seq

Here is an example where the sequences to exclude are saved to another file:

% notseq -junkout excluded.seq Excludes a set of sequences and writes out the remaining ones Input sequence(s): globins.fasta Sequence names to exclude: hb* Output sequence [hbb_human.fasta]: mydata.seq

Mandatory qualifiers:

[-sequence] (seqall)

Sequence database USA.

[-exclude] (string)

Enter a list of sequence names or accession numbers to exclude from the sequences read. The excluded sequences are 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. A file containing a list of sequence names can be specified by giving the filename preceded by an at sign, e.g., @names.dat.

[-outseq] (seqoutall)

Output sequence(s) USA.

Optional qualifiers:

-junkout (seqoutall)

This file collects the sequences that were excluded from the main output file of sequences.



Sequence Analysis in a Nutshell
Sequence Analysis in a Nutshell: A Guide to Common Tools and Databases
ISBN: 059600494X
EAN: 2147483647
Year: 2005
Pages: 312

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