                                 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:6.6.0.0

   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
   -squick1            boolean    Read id and sequence only
   -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

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
   , ,  and  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
                    xmltext      Get XML document original full text

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 (c) 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
