textsearch

textsearch

textsearch is a small utility search for words in the description text of a sequence and for each match list the sequence's name and/or description. It only searches the description line of the annotation, not the full annotation.

Search for matches to "lacZ":

% textsearch swissprot:\*  'lacz' stdout

Search for matches to "lacz" or "permease" in E.coli proteins:

% textsearch swissprot:\*_ecoli 'lacZ | permease' stdout

Output a search for "transport" formatted with HTML to a file:

% textsearch embl:\* 'transport' -html -outfile embl.transport stdout

Mandatory qualifiers:

[-sequence] (seqall)

Sequence database USA.

[-pattern] (string)

The search pattern is a regular expression. Use a | to indicate OR. For example: human|mouse will find text with either "human" OR "mouse" in the text

[-outfile] (outfile)

If you enter the name of a file here, this program will write the sequence details into that file.

Optional qualifiers:

-casesensitive (boolean)

Do a case-sensitive search.

-html (boolean)

Format output as an HTML table.

Advanced qualifiers:

-only (boolean)

This is a way of shortening the command line if you only want to display a few things. Instead of specifying: -nohead -noname -nousa -noacc -nodesc to get only the name output, you can specify -only -name.

-heading (boolean)

Display column headings.

-usa (boolean)

Display the USA of the sequence.

-accession (boolean)

Display "accession" column.

-name (boolean)

Display "name" column.

-description (boolean)

Display "description" column.



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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