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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
Here is a sample session with infoseq
Display information on a sequence:
% infoseq tembl:x13776
Displays some simple information about sequences
USA Database Name Accession Type Length %G
C Description
tembl-id:X13776 tembl X13776 X13776 N 2167
66.54 Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase regul
ation
Go to the input files for this example
Example 2
Don't display the USA of a sequence:
% infoseq tembl:x13776 -nousa
Displays some simple information about sequences
Database Name Accession Type Length %GC Description
tembl X13776 X13776 N 2167 66.54 Pseudomonas aer
uginosa amiC and amiR gene for aliphatic amidase regulation
Example 3
Display only the name and length of a sequence:
% infoseq tembl:x13776 -only -name -length
Displays some simple information about sequences
Name Length
X13776 2167
Example 4
Display only the description of a sequence:
% infoseq tembl:x13776 -only -desc
Displays some simple information about sequences
Description
Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase regulation
Example 5
Display the type of a sequence:
% infoseq tembl:x13776 -only -type
Displays some simple information about sequences
Type
N
Example 6
Display information formatted with HTML:
% infoseq tembl:x13776 -html
Displays some simple information about sequences
USA Database Name Accession Type Length %GC Description
tembl-id:X13776 tembl X13776 X13776 N 2167 66.54 Pseudomonas aeruginosa amiC a
nd amiR gene for aliphatic amidase regulation
Command line arguments
Standard (Mandatory) qualifiers:
[-sequence] seqall (Gapped) sequence(s) filename and optional
format, or reference (input USA)
Additional (Optional) qualifiers:
-outfile outfile [stdout] If you enter the name of a file
here then this program will write the
sequence details into that file.
-html boolean [N] Format output as an HTML table
Advanced (Unprompted) qualifiers:
-[no]columns boolean [Y] Set this option on (Y) to print the
sequence information into neat, aligned
columns in the output file. Alternatively,
leave it unset (N), in which case the
information records will be delimited by a
character, which you may specify by using
the -delimiter option. In other words, if
-columns is set on, the -delimiter option is
overriden.
-delimiter string [|] This string, which is usually a single
character only, is used to delimit
individual records in the text output file.
It could be a space character, a tab
character, a pipe character or any other
character or string. (Any string is
accepted)
-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 -noacc -notype -nopgc
-nodesc'
to get only the length output, you can
specify
'-only -length'
-[no]heading boolean [Y] Display column headings
-usa boolean [@(!$(only))] Display the USA of the
sequence
-database boolean [@(!$(only))] Display 'database' column
-name boolean [@(!$(only))] Display 'name' column
-accession boolean [@(!$(only))] Display 'accession' column
-gi boolean [N] Display 'GI' column
-version boolean [N] Display 'version' column
-type boolean [@(!$(only))] Display 'type' column
-length boolean [@(!$(only))] Display 'length' column
-pgc boolean [@(!$(only))] Display 'percent GC content'
column
-description boolean [@(!$(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
-odirectory 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 dying program messages
Input file format
infoseq reads any sequence USAs.
Input files for usage example
'tembl:x13776' is a sequence entry in the example nucleic acid
database 'tembl'
Database entry: tembl:x13776
ID X13776; SV 1; linear; genomic DNA; STD; PRO; 2167 BP.
XX
AC X13776; M43175;
XX
DT 19-APR-1989 (Rel. 19, Created)
DT 14-NOV-2006 (Rel. 89, Last updated, Version 24)
XX
DE Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase regulation
XX
KW aliphatic amidase regulator; amiC gene; amiR gene.
XX
OS Pseudomonas aeruginosa
OC Bacteria; Proteobacteria; Gammaproteobacteria; Pseudomonadales;
OC Pseudomonadaceae; Pseudomonas.
XX
RN [1]
RP 1167-2167
RA Rice P.M.;
RT ;
RL Submitted (16-DEC-1988) to the EMBL/GenBank/DDBJ databases.
RL Rice P.M., EMBL, Postfach 10-2209, Meyerhofstrasse 1, 6900 Heidelberg, FRG
.
XX
RN [2]
RP 1167-2167
RX DOI; 10.1016/0014-5793(89)80249-2.
RX PUBMED; 2495988.
RA Lowe N., Rice P.M., Drew R.E.;
RT "Nucleotide sequence of the aliphatic amidase regulator gene of Pseudomona
s
RT aeruginosa";
RL FEBS Lett. 246(1-2):39-43(1989).
XX
RN [3]
RP 1-1292
RX PUBMED; 1907262.
RA Wilson S., Drew R.;
RT "Cloning and DNA seqence of amiC, a new gene regulating expression of the
RT Pseudomonas aeruginosa aliphatic amidase, and purification of the amiC
RT product.";
RL J. Bacteriol. 173(16):4914-4921(1991).
XX
RN [4]
RP 1-2167
RA Rice P.M.;
RT ;
RL Submitted (04-SEP-1991) to the EMBL/GenBank/DDBJ databases.
RL Rice P.M., EMBL, Postfach 10-2209, Meyerhofstrasse 1, 6900 Heidelberg, FRG
.
XX
DR GOA; Q51417.
DR UniProtKB/Swiss-Prot; Q51417; AMIS_PSEAE.
XX
[Part of this file has been deleted for brevity]
FT /replace=""
FT /note="ClaI fragment deleted in pSW36, constitutive
FT phenotype"
FT misc_feature 1
FT /note="last base of an XhoI site"
FT misc_feature 648..653
FT /note="end of 658bp XhoI fragment, deletion in pSW3 cause
s
FT constitutive expression of amiE"
FT conflict 1281
FT /replace="g"
FT /citation=[3]
XX
SQ Sequence 2167 BP; 363 A; 712 C; 730 G; 362 T; 0 other;
ggtaccgctg gccgagcatc tgctcgatca ccaccagccg ggcgacggga actgcacgat 6
0
ctacctggcg agcctggagc acgagcgggt tcgcttcgta cggcgctgag cgacagtcac 12
0
aggagaggaa acggatggga tcgcaccagg agcggccgct gatcggcctg ctgttctccg 18
0
aaaccggcgt caccgccgat atcgagcgct cgcacgcgta tggcgcattg ctcgcggtcg 24
0
agcaactgaa ccgcgagggc ggcgtcggcg gtcgcccgat cgaaacgctg tcccaggacc 30
0
ccggcggcga cccggaccgc tatcggctgt gcgccgagga cttcattcgc aaccgggggg 36
0
tacggttcct cgtgggctgc tacatgtcgc acacgcgcaa ggcggtgatg ccggtggtcg 42
0
agcgcgccga cgcgctgctc tgctacccga ccccctacga gggcttcgag tattcgccga 48
0
acatcgtcta cggcggtccg gcgccgaacc agaacagtgc gccgctggcg gcgtacctga 54
0
ttcgccacta cggcgagcgg gtggtgttca tcggctcgga ctacatctat ccgcgggaaa 60
0
gcaaccatgt gatgcgccac ctgtatcgcc agcacggcgg cacggtgctc gaggaaatct 66
0
acattccgct gtatccctcc gacgacgact tgcagcgcgc cgtcgagcgc atctaccagg 72
0
cgcgcgccga cgtggtcttc tccaccgtgg tgggcaccgg caccgccgag ctgtatcgcg 78
0
ccatcgcccg tcgctacggc gacggcaggc ggccgccgat cgccagcctg accaccagcg 84
0
aggcggaggt ggcgaagatg gagagtgacg tggcagaggg gcaggtggtg gtcgcgcctt 90
0
acttctccag catcgatacg cccgccagcc gggccttcgt ccaggcctgc catggtttct 96
0
tcccggagaa cgcgaccatc accgcctggg ccgaggcggc ctactggcag accttgttgc 102
0
tcggccgcgc cgcgcaggcc gcaggcaact ggcgggtgga agacgtgcag cggcacctgt 108
0
acgacatcga catcgacgcg ccacaggggc cggtccgggt ggagcgccag aacaaccaca 114
0
gccgcctgtc ttcgcgcatc gcggaaatcg atgcgcgcgg cgtgttccag gtccgctggc 120
0
agtcgcccga accgattcgc cccgaccctt atgtcgtcgt gcataacctc gacgactggt 126
0
ccgccagcat gggcggggga ccgctcccat gagcgccaac tcgctgctcg gcagcctgcg 132
0
cgagttgcag gtgctggtcc tcaacccgcc gggggaggtc agcgacgccc tggtcttgca 138
0
gctgatccgc atcggttgtt cggtgcgcca gtgctggccg ccgccggaag ccttcgacgt 144
0
gccggtggac gtggtcttca ccagcatttt ccagaatggc caccacgacg agatcgctgc 150
0
gctgctcgcc gccgggactc cgcgcactac cctggtggcg ctggtggagt acgaaagccc 156
0
cgcggtgctc tcgcagatca tcgagctgga gtgccacggc gtgatcaccc agccgctcga 162
0
tgcccaccgg gtgctgcctg tgctggtatc ggcgcggcgc atcagcgagg aaatggcgaa 168
0
gctgaagcag aagaccgagc agctccagga ccgcatcgcc ggccaggccc ggatcaacca 174
0
ggccaaggtg ttgctgatgc agcgccatgg ctgggacgag cgcgaggcgc accagcacct 180
0
gtcgcgggaa gcgatgaagc ggcgcgagcc gatcctgaag atcgctcagg agttgctggg 186
0
aaacgagccg tccgcctgag cgatccgggc cgaccagaac aataacaaga ggggtatcgt 192
0
catcatgctg ggactggttc tgctgtacgt tggcgcggtg ctgtttctca atgccgtctg 198
0
gttgctgggc aagatcagcg gtcgggaggt ggcggtgatc aacttcctgg tcggcgtgct 204
0
gagcgcctgc gtcgcgttct acctgatctt ttccgcagca gccgggcagg gctcgctgaa 210
0
ggccggagcg ctgaccctgc tattcgcttt tacctatctg tgggtggccg ccaaccagtt 216
0
cctcgag 216
7
//
Output file format
The output is displayed on the screen (stdout) by default.
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. Slow, use SRS and Entrez!
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)
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
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