'\" t
.\"     Title: TWOFEAT
.\"    Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
.\"      Date: 05/11/2012
.\"    Manual: EMBOSS Manual for Debian
.\"    Source: EMBOSS 6.4.0
.\"  Language: English
.\"
.TH "TWOFEAT" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
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.SH "NAME"
twofeat \- Finds neighbouring pairs of features in sequence(s)
.SH "SYNOPSIS"
.HP \w'\fBtwofeat\fR\ 'u
\fBtwofeat\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR [\fB\-asource\ \fR\fB\fIstring\fR\fR] \fB\-atype\ \fR\fB\fIstring\fR\fR [\fB\-asense\ \fR\fB\fIlist\fR\fR] [\fB\-aminscore\ \fR\fB\fIfloat\fR\fR] [\fB\-amaxscore\ \fR\fB\fIfloat\fR\fR] [\fB\-atag\ \fR\fB\fIstring\fR\fR] [\fB\-avalue\ \fR\fB\fIstring\fR\fR] [\fB\-bsource\ \fR\fB\fIstring\fR\fR] \fB\-btype\ \fR\fB\fIstring\fR\fR [\fB\-bsense\ \fR\fB\fIlist\fR\fR] [\fB\-bminscore\ \fR\fB\fIfloat\fR\fR] [\fB\-bmaxscore\ \fR\fB\fIfloat\fR\fR] [\fB\-btag\ \fR\fB\fIstring\fR\fR] [\fB\-bvalue\ \fR\fB\fIstring\fR\fR] [\fB\-overlap\ \fR\fB\fIlist\fR\fR] \fB\-minrange\ \fR\fB\fIinteger\fR\fR \fB\-maxrange\ \fR\fB\fIinteger\fR\fR [\fB\-rangetype\ \fR\fB\fIlist\fR\fR] [\fB\-sense\ \fR\fB\fIlist\fR\fR] [\fB\-order\ \fR\fB\fIlist\fR\fR] [\fB\-twoout\ \fR\fB\fItoggle\fR\fR] \fB\-typeout\ \fR\fB\fIstring\fR\fR \fB\-outfile\ \fR\fB\fIreport\fR\fR
.HP \w'\fBtwofeat\fR\ 'u
\fBtwofeat\fR \fB\-help\fR
.SH "DESCRIPTION"
.PP
\fBtwofeat\fR
is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Feature tables" command group(s)\&.
.SH "OPTIONS"
.SS "Input section"
.PP
\fB\-sequence\fR \fIseqall\fR
.RS 4
.RE
.SS "First feature options"
.PP
\fB\-asource\fR \fIstring\fR
.RS 4
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 \*(Aq*\*(Aq\&. If you wish to allow more than one source, separate their names with the character \*(Aq|\*(Aq, eg: gene* | embl Default value: *
.RE
.PP
\fB\-atype\fR \fIstring\fR
.RS 4
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 \*(Aq*\*(Aq\&. If you wish to allow more than one type, separate their names with the character \*(Aq|\*(Aq, eg: *UTR | intron Default value: *
.RE
.PP
\fB\-asense\fR \fIlist\fR
.RS 4
By default any feature sense is allowed\&. You can set this to match the required sense\&.
.RE
.PP
\fB\-aminscore\fR \fIfloat\fR
.RS 4
If this is greater than or equal to the maximum score, then any score is allowed\&. Default value: 0\&.0
.RE
.PP
\fB\-amaxscore\fR \fIfloat\fR
.RS 4
If this is less than or equal to the maximum score, then any score is permitted\&. Default value: 0\&.0
.RE
.PP
\fB\-atag\fR \fIstring\fR
.RS 4
Tags are the types of extra values that a feature may have\&. For example in the EMBL feature table, a \*(AqCDS\*(Aq type of feature may have the tags \*(Aq/codon\*(Aq, \*(Aq/codon_start\*(Aq, \*(Aq/db_xref\*(Aq, \*(Aq/EC_number\*(Aq, \*(Aq/evidence\*(Aq, \*(Aq/exception\*(Aq, \*(Aq/function\*(Aq, \*(Aq/gene\*(Aq, \*(Aq/label\*(Aq, \*(Aq/map\*(Aq, \*(Aq/note\*(Aq, \*(Aq/number\*(Aq, \*(Aq/partial\*(Aq, \*(Aq/product\*(Aq, \*(Aq/protein_id\*(Aq, \*(Aq/pseudo\*(Aq, \*(Aq/standard_name\*(Aq, \*(Aq/translation\*(Aq, \*(Aq/transl_except\*(Aq, \*(Aq/transl_table\*(Aq, or \*(Aq/usedin\*(Aq\&. Some of these tags also have values, for example \*(Aq/gene\*(Aq 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 \*(Aq*\*(Aq\&. If you wish to allow more than one tag, separate their names with the character \*(Aq|\*(Aq, eg: gene | label Default value: *
.RE
.PP
\fB\-avalue\fR \fIstring\fR
.RS 4
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 \*(AqCDS\*(Aq type of feature may have the tags \*(Aq/codon\*(Aq, \*(Aq/codon_start\*(Aq, \*(Aq/db_xref\*(Aq, \*(Aq/EC_number\*(Aq, \*(Aq/evidence\*(Aq, \*(Aq/exception\*(Aq, \*(Aq/function\*(Aq, \*(Aq/gene\*(Aq, \*(Aq/label\*(Aq, \*(Aq/map\*(Aq, \*(Aq/note\*(Aq, \*(Aq/number\*(Aq, \*(Aq/partial\*(Aq, \*(Aq/product\*(Aq, \*(Aq/protein_id\*(Aq, \*(Aq/pseudo\*(Aq, \*(Aq/standard_name\*(Aq, \*(Aq/translation\*(Aq, \*(Aq/transl_except\*(Aq, \*(Aq/transl_table\*(Aq, or \*(Aq/usedin\*(Aq\&. Only some of these tags can have values, for example \*(Aq/gene\*(Aq 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 \*(Aq*\*(Aq\&. If you wish to allow more than one tag value, separate their names with the character \*(Aq|\*(Aq, eg: pax* | 10 Default value: *
.RE
.SS "Second feature options"
.PP
\fB\-bsource\fR \fIstring\fR
.RS 4
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 \*(Aq*\*(Aq\&. If you wish to allow more than one source, separate their names with the character \*(Aq|\*(Aq, eg: gene* | embl Default value: *
.RE
.PP
\fB\-btype\fR \fIstring\fR
.RS 4
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 \*(Aq*\*(Aq\&. If you wish to allow more than one type, separate their names with the character \*(Aq|\*(Aq, eg: *UTR | intron Default value: *
.RE
.PP
\fB\-bsense\fR \fIlist\fR
.RS 4
By default any feature sense is allowed\&. You can set this to match the required sense\&.
.RE
.PP
\fB\-bminscore\fR \fIfloat\fR
.RS 4
If this is greater than or equal to the maximum score, then any score is allowed\&. Default value: 0\&.0
.RE
.PP
\fB\-bmaxscore\fR \fIfloat\fR
.RS 4
If this is less than or equal to the maximum score, then any score is permitted\&. Default value: 0\&.0
.RE
.PP
\fB\-btag\fR \fIstring\fR
.RS 4
Tags are the types of extra values that a feature may have\&. For example in the EMBL feature table, a \*(AqCDS\*(Aq type of feature may have the tags \*(Aq/codon\*(Aq, \*(Aq/codon_start\*(Aq, \*(Aq/db_xref\*(Aq, \*(Aq/EC_number\*(Aq, \*(Aq/evidence\*(Aq, \*(Aq/exception\*(Aq, \*(Aq/function\*(Aq, \*(Aq/gene\*(Aq, \*(Aq/label\*(Aq, \*(Aq/map\*(Aq, \*(Aq/note\*(Aq, \*(Aq/number\*(Aq, \*(Aq/partial\*(Aq, \*(Aq/product\*(Aq, \*(Aq/protein_id\*(Aq, \*(Aq/pseudo\*(Aq, \*(Aq/standard_name\*(Aq, \*(Aq/translation\*(Aq, \*(Aq/transl_except\*(Aq, \*(Aq/transl_table\*(Aq, or \*(Aq/usedin\*(Aq\&. Some of these tags also have values, for example \*(Aq/gene\*(Aq 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 \*(Aq*\*(Aq\&. If you wish to allow more than one tag, separate their names with the character \*(Aq|\*(Aq, eg: gene | label Default value: *
.RE
.PP
\fB\-bvalue\fR \fIstring\fR
.RS 4
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 \*(AqCDS\*(Aq type of feature may have the tags \*(Aq/codon\*(Aq, \*(Aq/codon_start\*(Aq, \*(Aq/db_xref\*(Aq, \*(Aq/EC_number\*(Aq, \*(Aq/evidence\*(Aq, \*(Aq/exception\*(Aq, \*(Aq/function\*(Aq, \*(Aq/gene\*(Aq, \*(Aq/label\*(Aq, \*(Aq/map\*(Aq, \*(Aq/note\*(Aq, \*(Aq/number\*(Aq, \*(Aq/partial\*(Aq, \*(Aq/product\*(Aq, \*(Aq/protein_id\*(Aq, \*(Aq/pseudo\*(Aq, \*(Aq/standard_name\*(Aq, \*(Aq/translation\*(Aq, \*(Aq/transl_except\*(Aq, \*(Aq/transl_table\*(Aq, or \*(Aq/usedin\*(Aq\&. Only some of these tags can have values, for example \*(Aq/gene\*(Aq 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 \*(Aq*\*(Aq\&. If you wish to allow more than one tag value, separate their names with the character \*(Aq|\*(Aq, eg: pax* | 10 Default value: *
.RE
.SS "Feature relation options"
.PP
\fB\-overlap\fR \fIlist\fR
.RS 4
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
.RE
.PP
\fB\-minrange\fR \fIinteger\fR
.RS 4
If this is greater or equal to \*(Aqmaxrange\*(Aq, then no min or max range is specified
.RE
.PP
\fB\-maxrange\fR \fIinteger\fR
.RS 4
If this is less than or equal to \*(Aqminrange\*(Aq, then no min or max range is specified
.RE
.PP
\fB\-rangetype\fR \fIlist\fR
.RS 4
This allows you to specify the positions from which the allowed minimum or maximum distance between the features is measured Default value: N
.RE
.PP
\fB\-sense\fR \fIlist\fR
.RS 4
This allows you to specify the required sense that the two features must be on\&. This is ignored (always \*(AqAny\*(Aq) when looking at protein sequence features\&. Default value: A
.RE
.PP
\fB\-order\fR \fIlist\fR
.RS 4
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
.RE
.SS "Output section"
.PP
\fB\-twoout\fR \fItoggle\fR
.RS 4
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
.RE
.PP
\fB\-typeout\fR \fIstring\fR
.RS 4
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 \*(Aqtype\*(Aq 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 \*(Aqmisc_feature\*(Aq is used\&. Default value: misc_feature
.RE
.PP
\fB\-outfile\fR \fIreport\fR
.RS 4
.RE
.SH "BUGS"
.PP
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)\&.
.SH "SEE ALSO"
.PP
twofeat is fully documented via the
\fBtfm\fR(1)
system\&.
.SH "AUTHOR"
.PP
\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
.RS 4
Wrote the script used to autogenerate this manual page\&.
.RE
.SH "COPYRIGHT"
.br
.PP
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\&.
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