EXTRACTFEAT(1e) | EMBOSS Manual for Debian | EXTRACTFEAT(1e) |
NAME¶
extractfeat - Extract features from sequence(s)SYNOPSIS¶
extractfeat
-sequence seqall
[-before integer] [
-after integer] [
-source string] [
-type string] [
-sense integer] [
-minscore float] [
-maxscore float] [
-tag string] [
-value string] [
-join boolean] [
-featinname boolean] [
-describe string]
-outseq seqout
extractfeat
-help
DESCRIPTION¶
extractfeat is a command line program from EMBOSS (“the European Molecular Biology Open Software Suite”). It is part of the "Edit,Feature tables" command group(s).OPTIONS¶
Input section¶
-sequence seqallAdditional section¶
-before integerIf this value is greater than 0 then that
number of bases or residues before the feature are included in the extracted
sequence. This allows you to get the context of the feature. If this value is
negative then the start of the extracted sequence will be this number of
bases/residues before the end of the feature. So a value of '10' will start
the extraction 10 bases/residues before the start of the sequence, and a value
of '-10' will start the extraction 10 bases/residues before the end of the
feature. The output sequence will be padded with 'N' or 'X' characters if the
sequence starts after the required start of the extraction.
-after integer
If this value is greater than 0 then that
number of bases or residues after the feature are included in the extracted
sequence. This allows you to get the context of the feature. If this value is
negative then the end of the extracted sequence will be this number of
bases/residues after the start of the feature. So a value of '10' will end the
extraction 10 bases/residues after the end of the sequence, and a value of
'-10' will end the extraction 10 bases/residues after the start of the
feature. The output sequence will be padded with 'N' or 'X' characters if the
sequence ends before the required end of the extraction.
-source string
By default any feature source in the feature
table is shown. You can set this to match any feature source you wish to show.
The source name is usually either the name of the program that detected the
feature or it is the feature table (eg: EMBL) that the feature came from. The
source may be wildcarded by using '*'. If you wish to show more than one
source, separate their names with the character '|', eg: gene* | embl Default
value: *
-type string
By default every feature in the feature table
is extracted. You can set this to be any feature type you wish to extract. See
http://www.ebi.ac.uk/embl/WebFeat/ for a list of the EMBL feature types and
see the Uniprot user manual in
http://www.uniprot.org/manual/sequence_annotation for a list of the Uniprot
feature types. The type may be wildcarded by using '*'. If you wish to extract
more than one type, separate their names with the character '|', eg: *UTR |
intron Default value: *
-sense integer
By default any feature type in the feature
table is extracted. You can set this to match any feature sense you wish. 0 -
any sense, 1 - forward sense, -1 - reverse sense
-minscore float
Minimum score of feature to extract (see also
maxscore) Default value: 0.0
-maxscore float
Maximum score of feature to extract. If both
minscore and maxscore are zero (the default), then any score is ignored
Default value: 0.0
-tag string
Tags are the types of extra values that a
feature may have. For example in the EMBL feature table, a 'CDS' type of
feature may have the tags '/codon', '/codon_start', '/db_xref', '/EC_number',
'/evidence', '/exception', '/function', '/gene', '/label', '/map', '/note',
'/number', '/partial', '/product', '/protein_id', '/pseudo', '/standard_name',
'/translation', '/transl_except', '/transl_table', or '/usedin'. Some of these
tags also have values, for example '/gene' can have the value of the gene
name. By default any feature tag in the feature table is extracted. You can
set this to match any feature tag you wish to show. The tag may be wildcarded
by using '*'. If you wish to extract more than one tag, separate their names
with the character '|', eg: gene | label Default value: *
-value string
Tag values are the values associated with a
feature tag. Tags are the types of extra values that a feature may have. For
example in the EMBL feature table, a 'CDS' type of feature may have the tags
'/codon', '/codon_start', '/db_xref', '/EC_number', '/evidence', '/exception',
'/function', '/gene', '/label', '/map', '/note', '/number', '/partial',
'/product', '/protein_id', '/pseudo', '/standard_name', '/translation',
'/transl_except', '/transl_table', or '/usedin'. Only some of these tags can
have values, for example '/gene' can have the value of the gene name. By
default any feature tag value in the feature table is shown. You can set this
to match any feature tag value you wish to show. The tag value may be
wildcarded by using '*'. If you wish to show more than one tag value, separate
their names with a space or the character '|', eg: pax* | 10 Default value:
*
Output section¶
-join booleanSome features, such as CDS (coding sequence)
and mRNA are composed of introns concatenated together. There may be other
forms of 'joined' sequence, depending on the feature table. If this option is
set TRUE, then any group of these features will be output as a single
sequence. If the 'before' and 'after' qualifiers have been set, then only the
sequence before the first feature and after the last feature are added.
Default value: N
-featinname boolean
To aid you in identifying the type of feature
that has been output, the type of feature is added to the start of the
description of the output sequence. Sometimes the description of a sequence is
lost in subsequent processing of the sequences file, so it is useful for the
type to be a part of the sequence ID name. If you set this to be TRUE then the
name is added to the ID name of the output sequence. Default value: N
-describe string
To aid you in identifying some further
properties of a feature that has been output, this lets you specify one or
more tag names that should be added to the output sequence Description text,
together with their values (if any). For example, if this is set to be 'gene',
then if any output feature has the tag (for example) '/gene=BRCA1' associated
with it, then the text '(gene=BRCA1)' will be added to the Description line.
Tags are the types of extra values that a feature may have. For example in the
EMBL feature table, a 'CDS' type of feature may have the tags '/codon',
'/codon_start', '/db_xref', '/EC_number', '/evidence', '/exception',
'/function', '/gene', '/label', '/map', '/note', '/number', '/partial',
'/product', '/protein_id', '/pseudo', '/standard_name', '/translation',
'/transl_except', '/transl_table', or '/usedin'. Some of these tags also have
values, for example '/gene' can have the value of the gene name. By default no
feature tag is displayed. You can set this to match any feature tag you wish
to show. The tag may be wildcarded by using '*'. If you wish to extract more
than one tag, separate their names with the character '|', eg: gene |
label
-outseq seqout
BUGS¶
Bugs can be reported to the Debian Bug Tracking system (http://bugs.debian.org/emboss), or directly to the EMBOSS developers (http://sourceforge.net/tracker/?group_id=93650&atid=605031).SEE ALSO¶
extractfeat is fully documented via the tfm(1) system.AUTHOR¶
Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>Wrote the script used to autogenerate this
manual page.
COPYRIGHT¶
This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package. It can be redistributed under the same terms as EMBOSS itself.05/11/2012 | EMBOSS 6.4.0 |