EMBOSS: infoseq

| ## EMBOSS: infoseq

# Program infoseq

## Function

Displays some simple information about sequences

## Description

This is a small utility to list the sequences' USA, name, accession number, type (nucleic or protein), length, percentage C+G, and/or description.

Any combination of these types of information can be easily selected or unselected.

By default, the output file starts each line with the USA of the sequence being described, so the output file is a list file that can be manually edited and read in by any other EMBOSS program that can read in one or more sequence to be analysed.

## Usage

Display information on a sequence

    % infoseq embl:paamir

Don't display the USA of a sequence

    % infoseq embl:paamir -nousa

Display only the name and length of a sequence

    % infoseq embl:paamir -only -name -length

Display only the description of a sequence

    % infoseq embl:paamir -only -desc

Display the type of a sequence

    % infoseq embl:paamir -only -type

Display information formatted with HTML

    % infoseq embl:paamir -html

## Command line arguments

       Mandatory qualifiers:
      [-sequence]          seqall     Sequence database USA

       Optional qualifiers:
       -outfile            outfile    If you enter the name of a file here then
                                      this program will write the sequence details
                                      into that file.
       -html               bool       Format output as an HTML table

       Advanced qualifiers:
       -only               bool       This is a way of shortening the command line
                                      if you only want a few things to be
                                      displayed. Instead of specifying:
                                      '-nohead -noname -noacc -notype -nopgc
                                      -nodesc'
                                      to get only the length output, you can
                                      specify
                                      '-only -length'
       -heading            bool       Display column headings
       -usa                bool       Display the USA of the sequence
       -name               bool       Display 'name' column
       -accession          bool       Display 'accession' column
       -type               bool       Display 'type' column
       -length             bool       Display 'length' column
       -pgc                bool       Display 'percent GC content' column
       -description        bool       Display 'description' column

       General qualifiers:
      -help                bool       report command line options. More
                                      information on associated and general
                                      qualifiers can be found with -help -verbose

Mandatory qualifiers | Allowed values | Default
--- | --- | ---
[-sequence] (Parameter 1) | Sequence database USA | Readable sequence(s) | Required
Optional qualifiers | Allowed values | Default
-outfile | If you enter the name of a file here then this program will write the sequence details into that file. | Output file | stdout
-html | Format output as an HTML table | Yes/No | No
Advanced 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 -noacc -notype -nopgc -nodesc' to get only the length output, you can specify '-only -length' | Yes/No | No
-heading | Display column headings | Yes/No | @(!$(only))
-usa | Display the USA of the sequence | Yes/No | @(!$(only))
-name | Display 'name' column | Yes/No | @(!$(only))
-accession | Display 'accession' column | Yes/No | @(!$(only))
-type | Display 'type' column | Yes/No | @(!$(only))
-length | Display 'length' column | Yes/No | @(!$(only))
-pgc | Display 'percent GC content' column | Yes/No | @(!$(only))
-description | Display 'description' column | Yes/No | @(!$(only))

## Input file format

Any sequence(s).

## Output file format

The output is displayed on the screen (stdout) by default.

A typical output file is:

    # USA             Name        Accession Type Length     Description
    tsw-id:5H1D_FUGRU 5H1D_FUGRU    P79748  P    379        5-HYDROXYTRYPTAMINE 1D RECEPTOR (5-HT-1D) (SEROTONIN RECEPTOR).
    tsw-id:ACT1_FUGRU ACT1_FUGRU    P53484  P    375        ACTIN, CYTOPLASMIC 1 (BETA-ACTIN 1).
    tsw-id:ACT2_FUGRU ACT2_FUGRU    P53485  P    375        ACTIN, CYTOPLASMIC 2 (BETA-ACTIN 2).
    tsw-id:ACT3_FUGRU ACT3_FUGRU    P53486  P    375        ACTIN, CYTOPLASMIC 3 (BETA-ACTIN 3).
    tsw-id:ACTC_FUGRU ACTC_FUGRU    P53480  P    377        ACTIN, ALPHA CARDIAC.
    tsw-id:ACTS_FUGRU ACTS_FUGRU    P53481  P    377        ACTIN, ALPHA SKELETAL MUSCLE 1.
    tsw-id:ACTT_FUGRU ACTT_FUGRU    P53482  P    377        ACTIN, ALPHA SKELETAL MUSCLE 2.
    tsw-id:ACTX_FUGRU ACTX_FUGRU    P53483  P    376        ACTIN, ALPHA ANOMALOUS.
    tsw-id:ARF3_HUMAN ARF3_HUMAN    P16587  P    180        ADP-RIBOSYLATION FACTOR 3.

The first non-blank line is the heading. This is followed by one line per sequence containing the following columns of data separated by one of more space or TAB characters:

- The USA (Uniform Sequence Address) that EMBOSS can use to read in the sequence.
- The name or ID of the sequence. If this is not known then '-' is output.
- The accession number. If this is not known then '-' is output.
- The type ('N' is nucleic, 'P' is protein).
- The sequence length.
- The description line of the sequence. This may be blank.

If qualifiers to inhibit various columns of information are used, then the remaining columns of information are output in the same order as shown above, so if '-nolength' is used, the order of output is: usa, name, accession, type, description.

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> and <BODY> 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.

## Data files

None.

## Notes

This program was written to make it easier to get some specific bits of information on a sequence for use in small perl scripts. This Perl code fragment to get the type of a sequence is typical:

    $type = `$PATH_TO_EMBOSS/infoseq $sequence -auto -only -type`;
    chomp $type;

You may find other uses for it, of course.

By default, the output file starts each line with the USA of the sequence being described, so the output file is a list file that can be manually edited and read in by other EMBOSS programs using the list-file specification of '@filename'.

## References

None.

## Warnings

None.

## Diagnostic Error Messages

None.

## Exit status

It always exits with status 0

## Known bugs

None noted.

## See also

Program name | Description
--- | ---
infoalign | Information on a multiple sequence alignment
seealso | Finds programs sharing group names
showdb | Displays information on the currently available databases
textsearch | Search sequence documentation text. SRS and Entrez are faster!
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

- geecee - Calculates the fractional GC content of a nucleic acid sequence

## Author(s)

This application was written by Gary Williams (gwilliam@hgmp.mrc.ac.uk)

## History

Finished.

## Target users

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

## Comments