textsearch

 

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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:6.5.0.0

   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
   -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:J01636J01636J01636 E.coli lactose operon with lacI, lacZ, lacY and lacA genes.
tembl-id:V00296V00296V00296 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