EMBOSS: textsearch

| textsearch

## Function

Search sequence documentation. Slow, use SRS and Entrez!

## Description

This 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. NB. It only searches the description line of the annotation, not the full annotation.

## Usage

Here is a sample session with textsearch

Search for 'lactose':

    % textsearch tsw:* 'lactose'
    Search sequence documentation. Slow, use SRS and Entrez!
    Output file [edd1_rat.textsearch]:

Go to the input files for this example
Go to the output files for this example

Example 2

Search for 'lactose' or 'permease' in E.coli proteins:

    % textsearch tsw:*_ecoli 'lactose | permease'
    Search sequence documentation. Slow, use SRS and Entrez!
    Output file [laci_ecoli.textsearch]:

Go to the output files for this example

Example 3

Output a search for 'lacz' formatted with HTML to a file:

    % textsearch tembl:* 'lacz' -html -outfile embl.lacz.html
    Search sequence documentation. Slow, use SRS and Entrez!

Go to the input files for this example
Go to the output files for this example

## Command line arguments

       Standard (Mandatory) qualifiers:
      [-sequence]          seqall     (Gapped) sequence(s) filename and optional
                                      format, or reference (input 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 (Any string is accepted)
      [-outfile]           outfile    [*.textsearch] Output file name

       Additional (Optional) qualifiers:
       -casesensitive      boolean    [N] Do a case-sensitive search
       -html               boolean    [N] Format output as an HTML table

       Advanced (Unprompted) qualifiers:
       -only               boolean    [N] This is a way of shortening the command
                                      line if you only want a few things to be
                                      displayed. Instead of specifying:
                                      '-nohead -noname -nousa -noacc -nodesc'
                                      to get only the name output, you can specify
                                      '-only -name'
       -heading            boolean    [@(!$(only))] Display column headings
       -usa                boolean    [@(!$(only))] Display the USA of the
                                      sequence
       -accession          boolean    [@(!$(only))] Display 'accession' column
       -name               boolean    [@(!$(only))] Display 'name' column
       -description        boolean    [@(!$(only))] Display 'description' column

       Associated qualifiers:

       "-sequence" associated qualifiers
       -sbegin1            integer    Start of each sequence to be used
       -send1              integer    End of each sequence to be used
       -sreverse1          boolean    Reverse (if DNA)
       -sask1              boolean    Ask for begin/end/reverse
       -snucleotide1       boolean    Sequence is nucleotide
       -sprotein1          boolean    Sequence is protein
       -slower1            boolean    Make lower case
       -supper1            boolean    Make upper case
       -sformat1           string     Input sequence format
       -sdbname1           string     Database name
       -sid1               string     Entryname
       -ufo1               string     UFO features
       -fformat1           string     Features format
       -fopenfile1         string     Features file name

       "-outfile" associated qualifiers
       -odirectory3        string     Output directory

       General qualifiers:
       -auto               boolean    Turn off prompts
       -stdout             boolean    Write standard output
       -filter             boolean    Read standard input, write standard output
       -options            boolean    Prompt for standard and additional values
       -debug              boolean    Write debug output to program.dbg
       -verbose            boolean    Report some/full command line options
       -help               boolean    Report command line options. More
                                      information on associated and general
                                      qualifiers can be found with -help -verbose
       -warning            boolean    Report warnings
       -error              boolean    Report errors
       -fatal              boolean    Report fatal errors
       -die                boolean    Report dying program messages

Standard (Mandatory) qualifiers | Allowed values | Default
--- | --- | ---
[-sequence] (Parameter 1) | (Gapped) sequence(s) filename and optional format, or reference (input USA) | Readable sequence(s) | Required
[-pattern] (Parameter 2) | 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 | Any string is accepted | An empty string is accepted
[-outfile] (Parameter 3) | Output file name | Output file | <*>.textsearch
Additional (Optional) qualifiers | Allowed values | Default
-casesensitive | Do a case-sensitive search | Boolean value Yes/No | No
-html | Format output as an HTML table | Boolean value Yes/No | No
Advanced (Unprompted) qualifiers | Allowed values | Default
-only | This is a way of shortening the command line if you only want a few things to be displayed. Instead of specifying: '-nohead -noname -nousa -noacc -nodesc' to get only the name output, you can specify '-only -name' | Boolean value Yes/No | No
-heading | Display column headings | Boolean value Yes/No | @(!$(only))
-usa | Display the USA of the sequence | Boolean value Yes/No | @(!$(only))
-accession | Display 'accession' column | Boolean value Yes/No | @(!$(only))
-name | Display 'name' column | Boolean value Yes/No | @(!$(only))
-description | Display 'description' column | Boolean value Yes/No | @(!$(only))

## Input file format

textsearch reads one or more normal sequence USAs.

### Input files for usage example

'tsw:*' is a sequence entry in the example protein database 'tsw'

### Input files for usage example 3

'tembl:*' is a sequence entry in the example nucleic acid database 'tembl'

## Output file format

### Output files for usage example

### File: edd1_rat.textsearch

    # Search for: lactose
    tsw-id:LACI_ECOLI LACI_ECOLI    P03023	Lactose operon repressor.
    tsw-id:LACY_ECOLI LACY_ECOLI    P02920	Lactose permease (Lactose-proton symport).

### Output files for usage example 2

### File: laci_ecoli.textsearch

    # Search for: lactose | permease
    tsw-id:LACI_ECOLI LACI_ECOLI    P03023	Lactose operon repressor.
    tsw-id:LACY_ECOLI LACY_ECOLI    P02920	Lactose permease (Lactose-proton symport).

### Output files for usage example 3

### File: embl.lacz.html

Search for: lacz
tembl-id:J01636 | J01636 | J01636 | E.coli lactose operon with lacI, lacZ, lacY and lacA genes.
tembl-id:V00296 | V00296 | V00296 | E. coli gene lacZ coding for beta-galactosidase (EC 3.2.1.23).

The first column in the name or ID of each sequence. The remaining text is the description line of the sequence.

When the -html qualifier is specified, then the output will be wrapped in HTML tags, ready for inclusion in a Web page. Note that tags such as <HTML>, <BODY>, </BODY> and </HTML> are not output by this program as the table of databases is expected to form only part of the contents of a web page - the rest of the web page must be supplier by the user.

The lines of out information are guaranteed not to have trailing white-space at the end. So if '-nodesc' is used, there will not be any whitespace after the ID name.

## Data files

None.

## Notes

This is a rather slow way to search for text in databases. If you are searching for text in public databases, you should consider using either Entrez (http://www.ncbi.nlm.nih.gov/Entrez/) or SRS (http://srs.rfcgr.mrc.ac.uk/ or http://www.sanger.ac.uk/srs6/ etc.)

## References

None.

## Warnings

None.

## Diagnostic Error Messages

None.

## Exit status

It always exits with status 0

## Known bugs

None.

## See also

Program name | Description
--- | ---
abiview | Reads ABI file and display the trace
cirdna | Draws circular maps of DNA constructs
infoalign | Information on a multiple sequence alignment
infoseq | Displays some simple information about sequences
lindna | Draws linear maps of DNA constructs
pepnet | Displays proteins as a helical net
pepwheel | Shows protein sequences as helices
prettyplot | Displays aligned sequences, with colouring and boxing
prettyseq | Output sequence with translated ranges
remap | Display sequence with restriction sites, translation etc
seealso | Finds programs sharing group names
showalign | Displays a multiple sequence alignment
showdb | Displays information on the currently available databases
showfeat | Show features of a sequence
showseq | Display a sequence with features, translation etc
sixpack | Display a DNA sequence with 6-frame translation and ORFs
tfm | Displays a program's help documentation manual
whichdb | Search all databases for an entry
wossname | Finds programs by keywords in their one-line documentation

## Author(s)

Gary Williams (gwilliam © rfcgr.mrc.ac.uk)
MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK

## History

## Target users

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

## Comments

None