EMBOSS: textsearch

| textsearch

## Wiki

The master copies of EMBOSS documentation are available at http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki.

Please help by correcting and extending the Wiki pages.

## Function

Search the textual description of sequence(s)

## Description

textsearch searches for words (specified as a regular expression) in the description text of one or more input sequences. It writes an output file with optional contents such as the name, description and accession number of any sequence whose description line from the annotation matches the search term. Optionally, the search is case-sensitive and the results output as an HTML table. textsearch is convenient for small input files but will be slow for larger files and databases; you should use use SRS or Entrez instead.

## Algorithm

textsearch searches only the description line, not the full sequence annotation.

## Usage

Here is a sample session with textsearch

Search for 'lactose':

    % textsearch "tsw:*" "lactose"
    Search the textual description of sequence(s)
    Output file [cru4_arath.textsearch]:

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 the textual description of sequence(s)
    Output file [bgal_ecoli.textsearch]:

Go to the input files for this example
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 the textual description of sequence(s)

Go to the output files for this example

## Command line arguments

    Search the textual description of sequence(s)
    Version: EMBOSS:6.5.6.0

       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)
      [-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
       -scircular1         boolean    Sequence is circular
       -sformat1           string     Input sequence format
       -iquery1            string     Input query fields or ID list
       -ioffset1           integer    Input start position offset
       -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 first file to standard output
       -filter             boolean    Read first file from standard input, write
                                      first file to 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 and exit. 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
       -version            boolean    Report version number and exit

Qualifier | Type | Description | Allowed values | Default
--- | --- | --- | --- | ---
Standard (Mandatory) qualifiers
[-sequence] (Parameter 1) | seqall | (Gapped) sequence(s) filename and optional format, or reference (input USA) | Readable sequence(s) | Required
[-pattern] (Parameter 2) | 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 |
[-outfile] (Parameter 3) | outfile | Output file name | Output file | <*>.textsearch
Additional (Optional) qualifiers
-casesensitive | boolean | Do a case-sensitive search | Boolean value Yes/No | No
-html | boolean | Format output as an HTML table | Boolean value Yes/No | No
Advanced (Unprompted) qualifiers
-only | boolean | 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 | boolean | Display column headings | Boolean value Yes/No | @(!$(only))
-usa | boolean | Display the USA of the sequence | Boolean value Yes/No | @(!$(only))
-accession | boolean | Display 'accession' column | Boolean value Yes/No | @(!$(only))
-name | boolean | Display 'name' column | Boolean value Yes/No | @(!$(only))
-description | boolean | Display 'description' column | Boolean value Yes/No | @(!$(only))
Associated qualifiers
"-sequence" associated seqall qualifiers
-sbegin1 -sbegin_sequence | integer | Start of each sequence to be used | Any integer value | 0
-send1 -send_sequence | integer | End of each sequence to be used | Any integer value | 0
-sreverse1 -sreverse_sequence | boolean | Reverse (if DNA) | Boolean value Yes/No | N
-sask1 -sask_sequence | boolean | Ask for begin/end/reverse | Boolean value Yes/No | N
-snucleotide1 -snucleotide_sequence | boolean | Sequence is nucleotide | Boolean value Yes/No | N
-sprotein1 -sprotein_sequence | boolean | Sequence is protein | Boolean value Yes/No | N
-slower1 -slower_sequence | boolean | Make lower case | Boolean value Yes/No | N
-supper1 -supper_sequence | boolean | Make upper case | Boolean value Yes/No | N
-scircular1 -scircular_sequence | boolean | Sequence is circular | Boolean value Yes/No | N
-sformat1 -sformat_sequence | string | Input sequence format | Any string |
-iquery1 -iquery_sequence | string | Input query fields or ID list | Any string |
-ioffset1 -ioffset_sequence | integer | Input start position offset | Any integer value | 0
-sdbname1 -sdbname_sequence | string | Database name | Any string |
-sid1 -sid_sequence | string | Entryname | Any string |
-ufo1 -ufo_sequence | string | UFO features | Any string |
-fformat1 -fformat_sequence | string | Features format | Any string |
-fopenfile1 -fopenfile_sequence | string | Features file name | Any string |
"-outfile" associated outfile qualifiers
-odirectory3 -odirectory_outfile | string | Output directory | Any string |
General qualifiers
-auto | boolean | Turn off prompts | Boolean value Yes/No | N
-stdout | boolean | Write first file to standard output | Boolean value Yes/No | N
-filter | boolean | Read first file from standard input, write first file to standard output | Boolean value Yes/No | N
-options | boolean | Prompt for standard and additional values | Boolean value Yes/No | N
-debug | boolean | Write debug output to program.dbg | Boolean value Yes/No | N
-verbose | boolean | Report some/full command line options | Boolean value Yes/No | Y
-help | boolean | Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose | Boolean value Yes/No | N
-warning | boolean | Report warnings | Boolean value Yes/No | Y
-error | boolean | Report errors | Boolean value Yes/No | Y
-fatal | boolean | Report fatal errors | Boolean value Yes/No | Y
-die | boolean | Report dying program messages | Boolean value Yes/No | Y
-version | boolean | Report version number and exit | Boolean value Yes/No | N

## Input file format

textsearch reads one or more nucleotide or protein sequences.

The input is a standard EMBOSS sequence query (also known as a 'USA').

Major sequence database sources defined as standard in EMBOSS installations include srs:embl, srs:uniprot and ensembl

Data can also be read from sequence output in any supported format written by an EMBOSS or third-party application.

The input format can be specified by using the command-line qualifier `-sformat xxx`, where 'xxx' is replaced by the name of the required format. The available format names are: gff (gff3), gff2, embl (em), genbank (gb, refseq), ddbj, refseqp, pir (nbrf), swissprot (swiss, sw), dasgff and debug.

See: http://emboss.sf.net/docs/themes/SequenceFormats.html for further information on sequence formats.

### Input files for usage example 2

'|' is a sequence entry in the example protein database '|'

## Output file format

### Output files for usage example

### File: cru4_arath.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: bgal_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 SRS (http://srs.ebi.ac.uk/) or Entrez ( http://www.ncbi.nlm.nih.gov/Entrez/)

## References

None.

## Warnings

## Diagnostic Error Messages

None.

## Exit status

It always exits with status 0

## Known bugs

None.

## See also

Program name | Description
--- | ---
drtext | Get data resource entries complete text
entret | Retrieve sequence entries from flatfile databases and files
ontotext | Get ontology term(s) original full text
textget | Get text data entries

## Author(s)

Gary Williams formerly at:
MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK

Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.

## History

## Target users

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

## Comments

None