
                                textsearch 



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 [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 the textual description of sequence(s)
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 the textual description of sequence(s)

   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 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. 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

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 sympor
t).

  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 sympor
t).

  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

   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.)
   instead.

Diagnostic Error Messages

   None.

Exit status

   It always exits with status 0

Known bugs

   None.

See also

   Program name Description
   abiview Display the trace in an ABI sequencer file
   cirdna Draws circular maps of DNA constructs
   infoalign Display basic information about a multiple sequence
   alignment
   infobase Return information on a given nucleotide base
   inforesidue Return information on a given amino acid residue
   infoseq Display basic information about sequences
   lindna Draws linear maps of DNA constructs
   pepnet Draw a helical net for a protein sequence
   pepwheel Draw a helical wheel diagram for a protein sequence
   prettyplot Draw a sequence alignment with pretty formatting
   prettyseq Write a nucleotide sequence and its translation to file
   remap Display restriction enzyme binding sites in a nucleotide
   sequence
   seealso Finds programs with similar function to a specified program
   showalign Display a multiple sequence alignment in pretty format
   showdb Displays information on configured databases
   showfeat Display features of a sequence in pretty format
   showseq Displays sequences with features in pretty format
   sixpack Display a DNA sequence with 6-frame translation and ORFs
   tfm Displays full documentation for an application
   whichdb Search all sequence databases for an entry and retrieve it
   wossname Finds programs by keywords in their short description

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
