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textsearch |
Function
Search sequence documentation. Slow, use SRS and Entrez!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
Here is a sample session with textsearchSearch for 'lactose':
% textsearch tsw:* 'lactose' Search sequence documentation. Slow, use SRS and Entrez! Output file [100k_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 sequence documentation. Slow, use SRS and Entrez! 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 sequence documentation. Slow, use SRS and Entrez! |
Go to the input files for this example
Go to the output files for this example
Command line arguments
Standard (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
[-outfile] outfile Output file name
Additional (Optional) qualifiers:
-casesensitive boolean Do a case-sensitive search
-html boolean Format output as an HTML table
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'
-heading boolean Display column headings
-usa boolean Display the USA of the sequence
-accession boolean Display 'accession' column
-name boolean Display 'name' column
-description boolean 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 standard output
-filter boolean Read standard input, write 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 deaths
|
| Standard (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 |
| [-outfile] (Parameter 3) |
Output file name | Output file | <sequence>.textsearch |
| Additional (Optional) qualifiers | Allowed values | Default | |
| -casesensitive | Do a case-sensitive search | Boolean value Yes/No | No |
| -html | Format output as an HTML table | Boolean value Yes/No | No |
| Advanced (Unprompted) 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' | Boolean value Yes/No | No |
| -heading | Display column headings | Boolean value Yes/No | @(!$(only)) |
| -usa | Display the USA of the sequence | Boolean value Yes/No | @(!$(only)) |
| -accession | Display 'accession' column | Boolean value Yes/No | @(!$(only)) |
| -name | Display 'name' column | Boolean value Yes/No | @(!$(only)) |
| -description | Display 'description' column | Boolean value Yes/No | @(!$(only)) |
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: 100k_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 SYMPORT). |
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 SYMPORT). |
Output files for usage example 3
File: embl.lacz.html
|
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
None.Diagnostic Error Messages
None.Exit status
It always exits with status 0Known bugs
None.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 sequence with restriction 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 |
| sixpack | Display a DNA sequence with 6-frame translation and ORFs |
| 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)
Gary Williams (gwilliam © rfcgr.mrc.ac.uk)MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK