EMBOSS: textsearch

| ## EMBOSS: textsearch

# Program textsearch

## Function

Search sequence documentation text. SRS and Entrez are faster!

## 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

Search for matches to 'lacZ'

    % textsearch swissprot:\*  'lacz'

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

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

Output a search for 'transport' formatted with HTML to a file

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

## Command line arguments

       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

       Optional qualifiers:
       -casesensitive      bool       Do a case-sensitive search
       -html               bool       Format output as an HTML table
       -outfile            outfile    If you enter the name of a file here then
                                      this program will write the sequence details
                                      into that file.

       Advanced qualifiers:
       -only               bool       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            bool       Display column headings
       -usa                bool       Display the USA of the sequence
       -accession          bool       Display 'accession' column
       -name               bool       Display 'name' column
       -description        bool       Display 'description' column

       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
[-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
Optional qualifiers | Allowed values | Default
-casesensitive | Do a case-sensitive search | Yes/No | No
-html | Format output as an HTML table | Yes/No | No
-outfile | If you enter the name of a file here then this program will write the sequence details into that file. | Output file | stdout
Advanced 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' | Yes/No | No
-heading | Display column headings | Yes/No | @(!$(only))
-usa | Display the USA of the sequence | Yes/No | @(!$(only))
-accession | Display 'accession' column | Yes/No | @(!$(only))
-name | Display 'name' column | Yes/No | @(!$(only))
-description | Display 'description' column | Yes/No | @(!$(only))

## Input file format

Normal sequence

## Output file format

The output is displayed on the screen (stdout) by default. A typical output file is:

    ---------------------------------------------------------------------------
    # Search for: TRANSPORT
    ANSP_SALTY    L-ASPARAGINE PERMEASE (L-ASPARAGINE TRANSPORT PROTEIN).
    CYST_SALTY    SULFATE TRANSPORT SYSTEM PERMEASE PROTEIN CYST (FRAGMENT).
    HISM_SALTY    HISTIDINE TRANSPORT SYSTEM PERMEASE PROTEIN HISM.
    HISQ_SALTY    HISTIDINE TRANSPORT SYSTEM PERMEASE PROTEIN HISQ.
    LIVH_SALTY    HIGH-AFFINITY BRANCHED-CHAIN AMINO ACID TRANSPORT PERMEASE ...
    LIVM_SALTY    HIGH-AFFINITY BRANCHED-CHAIN AMINO ACID TRANSPORT PERMEASE ...
    MALF_SALTY    MALTOSE TRANSPORT SYSTEM PERMEASE PROTEIN MALF.
    MALG_SALTY    MALTOSE TRANSPORT SYSTEM PERMEASE PROTEIN MALG.
    MELB_SALTY    MELIBIOSE CARRIER PROTEIN (THIOMETHYLGALACTOSIDE PERMEASE II) ...
    MGLC_SALTY    GALACTOSIDE TRANSPORT SYSTEM PERMEASE PROTEIN MGLC.
    OPPB_SALTY    OLIGOPEPTIDE TRANSPORT SYSTEM PERMEASE PROTEIN OPPB.
    OPPC_SALTY    OLIGOPEPTIDE TRANSPORT SYSTEM PERMEASE PROTEIN OPPC.
    POTB_SALTY    SPERMIDINE/PUTRESCINE TRANSPORT SYSTEM PERMEASE PROTEIN POTB ...
    PROW_SALTY    GLYCINE BETAINE/L-PROLINE TRANSPORT SYSTEM PERMEASE PROTEIN ...
    SAPB_SALTY    PEPTIDE TRANSPORT SYSTEM PERMEASE PROTEIN SAPB.
    SAPC_SALTY    PEPTIDE TRANSPORT SYSTEM PERMEASE PROTEIN SAPC.
    ---------------------------------------------------------------------------

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.hgmp.mrc.ac.uk/ or http://www.sanger.ac.uk/srs6/ etc.)

## References

## Warnings

## Diagnostic Error Messages

## Exit status

It always exits with status 0

## Known bugs

None noted.

## 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 a sequence with restriction cut 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
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)

This application was written by Gary Williams (gwilliam@hgmp.mrc.ac.uk)

## History

Finished.

## Target users

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

## Comments