| TWOFEAT(1e) | EMBOSS Manual for Debian | TWOFEAT(1e) |
NAME¶
twofeat - Finds neighbouring pairs of features in sequence(s)
SYNOPSIS¶
twofeat -sequence seqall [-asource string] -atype string [-asense list] [-aminscore float] [-amaxscore float] [-atag string] [-avalue string] [-bsource string] -btype string [-bsense list] [-bminscore float] [-bmaxscore float] [-btag string] [-bvalue string] [-overlap list] -minrange integer -maxrange integer [-rangetype list] [-sense list] [-order list] [-twoout toggle] -typeout string -outfile report
twofeat -help
DESCRIPTION¶
twofeat is a command line program from EMBOSS (“the European Molecular Biology Open Software Suite”). It is part of the "Feature tables" command group(s).
OPTIONS¶
Input section¶
-sequence seqall
First feature options¶
-asource string
By default any feature source in the feature table is
allowed. You can set this to match any feature source you wish to allow. 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 allow more than one
source, separate their names with the character '|', eg: gene* | embl Default
value: *
-atype string
By default every feature in the feature table is allowed.
You can set this to be any feature type you wish to allow. See
http://www.ebi.ac.uk/embl/WebFeat/ for a list of the EMBL feature types and
see Appendix A of the Swissprot user manual in
http://www.expasy.org/sprot/userman.html for a list of the Swissprot feature
types. The type may be wildcarded by using '*'. If you wish to allow more than
one type, separate their names with the character '|', eg: *UTR | intron
Default value: *
-asense list
By default any feature sense is allowed. You can set this
to match the required sense.
-aminscore float
If this is greater than or equal to the maximum score,
then any score is allowed. Default value: 0.0
-amaxscore float
If this is less than or equal to the maximum score, then
any score is permitted. Default value: 0.0
-atag 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 allowed. You can set
this to match any feature tag you wish to allow. The tag may be wildcarded by
using '*'. If you wish to allow more than one tag, separate their names with
the character '|', eg: gene | label Default value: *
-avalue 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 allowed. You can set
this to match any feature tag value you wish to allow. The tag value may be
wildcarded by using '*'. If you wish to allow more than one tag value,
separate their names with the character '|', eg: pax* | 10 Default value:
*
Second feature options¶
-bsource string
By default any feature source in the feature table is
allowed. You can set this to match any feature source you wish to allow. 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 allow more than one
source, separate their names with the character '|', eg: gene* | embl Default
value: *
-btype string
By default every feature in the feature table is allowed.
You can set this to be any feature type you wish to allow. See
http://www.ebi.ac.uk/embl/WebFeat/ for a list of the EMBL feature types and
see Appendix A of the Swissprot user manual in
http://www.expasy.org/sprot/userman.html for a list of the Swissprot feature
types. The type may be wildcarded by using '*'. If you wish to allow more than
one type, separate their names with the character '|', eg: *UTR | intron
Default value: *
-bsense list
By default any feature sense is allowed. You can set this
to match the required sense.
-bminscore float
If this is greater than or equal to the maximum score,
then any score is allowed. Default value: 0.0
-bmaxscore float
If this is less than or equal to the maximum score, then
any score is permitted. Default value: 0.0
-btag 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 allowed. You can set
this to match any feature tag you wish to allow. The tag may be wildcarded by
using '*'. If you wish to allow more than one tag, separate their names with
the character '|', eg: gene | label Default value: *
-bvalue 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 allowed. You can set
this to match any feature tag value you wish to allow. The tag value may be
wildcarded by using '*'. If you wish to allow more than one tag value,
separate their names with the character '|', eg: pax* | 10 Default value:
*
Feature relation options¶
-overlap list
This allows you to specify the allowed overlaps of the
features A and B. You can allow any or no overlaps, specify that they must or
must not overlap, that one must or must not be wholly enclosed within another
feature. Default value: A
-minrange integer
If this is greater or equal to 'maxrange', then no min or
max range is specified
-maxrange integer
If this is less than or equal to 'minrange', then no min
or max range is specified
-rangetype list
This allows you to specify the positions from which the
allowed minimum or maximum distance between the features is measured Default
value: N
-sense list
This allows you to specify the required sense that the
two features must be on. This is ignored (always 'Any') when looking at
protein sequence features. Default value: A
-order list
This allows you to specify the required order of the two
features. The order is measured from the start positions of the features. This
criterion is always applied despite the specified overlap type required.
Default value: A
Output section¶
-twoout toggle
If you set this to be true, then the two features
themselves will be written out. If it is left as false, then a single feature
will be written out covering the two features you found. Default value:
N
-typeout string
If you have specified that the pairs of features that are
found should be reported as one feature in the output, then you can specify
the 'type' name of the new feature here. By default every feature in the
feature table is allowed. See http://www.ebi.ac.uk/embl/WebFeat/ for a list of
the EMBL feature types and see Appendix A of the Swissprot user manual in
http://www.expasy.org/sprot/userman.html for a list of the Swissprot feature
types. If you specify an invalid feature type name, then the default name
'misc_feature' is used. Default value: misc_feature
-outfile report
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¶
twofeat 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 |