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EMBOSS: infoseq |
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.
% 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
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 |
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)) |
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:
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.
$type = `$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'.
Program name | Description |
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