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'\" t
.\" Title: EXTRACTFEAT
.\" 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 "EXTRACTFEAT" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
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.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
.\" http://bugs.debian.org/507673
.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
.ie \n(.g .ds Aq \(aq
.el .ds Aq '
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.\" * set default formatting
.\" -----------------------------------------------------------------
.\" disable hyphenation
.nh
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.ad l
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.\" * MAIN CONTENT STARTS HERE *
.\" -----------------------------------------------------------------
.SH "NAME"
extractfeat \- Extract features from sequence(s)
.SH "SYNOPSIS"
.HP \w'\fBextractfeat\fR\ 'u
\fBextractfeat\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR [\fB\-before\ \fR\fB\fIinteger\fR\fR] [\fB\-after\ \fR\fB\fIinteger\fR\fR] [\fB\-source\ \fR\fB\fIstring\fR\fR] [\fB\-type\ \fR\fB\fIstring\fR\fR] [\fB\-sense\ \fR\fB\fIinteger\fR\fR] [\fB\-minscore\ \fR\fB\fIfloat\fR\fR] [\fB\-maxscore\ \fR\fB\fIfloat\fR\fR] [\fB\-tag\ \fR\fB\fIstring\fR\fR] [\fB\-value\ \fR\fB\fIstring\fR\fR] [\fB\-join\ \fR\fB\fIboolean\fR\fR] [\fB\-featinname\ \fR\fB\fIboolean\fR\fR] [\fB\-describe\ \fR\fB\fIstring\fR\fR] \fB\-outseq\ \fR\fB\fIseqout\fR\fR
.HP \w'\fBextractfeat\fR\ 'u
\fBextractfeat\fR \fB\-help\fR
.SH "DESCRIPTION"
.PP
\fBextractfeat\fR
is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit,Feature tables" command group(s)\&.
.SH "OPTIONS"
.SS "Input section"
.PP
\fB\-sequence\fR \fIseqall\fR
.RS 4
.RE
.SS "Additional section"
.PP
\fB\-before\fR \fIinteger\fR
.RS 4
If 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 \*(Aq10\*(Aq will start the extraction 10 bases/residues before the start of the sequence, and a value of \*(Aq\-10\*(Aq will start the extraction 10 bases/residues before the end of the feature\&. The output sequence will be padded with \*(AqN\*(Aq or \*(AqX\*(Aq characters if the sequence starts after the required start of the extraction\&.
.RE
.PP
\fB\-after\fR \fIinteger\fR
.RS 4
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 \*(Aq10\*(Aq will end the extraction 10 bases/residues after the end of the sequence, and a value of \*(Aq\-10\*(Aq will end the extraction 10 bases/residues after the start of the feature\&. The output sequence will be padded with \*(AqN\*(Aq or \*(AqX\*(Aq characters if the sequence ends before the required end of the extraction\&.
.RE
.PP
\fB\-source\fR \fIstring\fR
.RS 4
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 \*(Aq*\*(Aq\&. If you wish to show more than one source, separate their names with the character \*(Aq|\*(Aq, eg: gene* | embl Default value: *
.RE
.PP
\fB\-type\fR \fIstring\fR
.RS 4
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 \*(Aq*\*(Aq\&. If you wish to extract more than one type, separate their names with the character \*(Aq|\*(Aq, eg: *UTR | intron Default value: *
.RE
.PP
\fB\-sense\fR \fIinteger\fR
.RS 4
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
.RE
.PP
\fB\-minscore\fR \fIfloat\fR
.RS 4
Minimum score of feature to extract (see also maxscore) Default value: 0\&.0
.RE
.PP
\fB\-maxscore\fR \fIfloat\fR
.RS 4
Maximum score of feature to extract\&. If both minscore and maxscore are zero (the default), then any score is ignored Default value: 0\&.0
.RE
.PP
\fB\-tag\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 extracted\&. You can set this to match any feature tag you wish to show\&. The tag may be wildcarded by using \*(Aq*\*(Aq\&. If you wish to extract more than one tag, separate their names with the character \*(Aq|\*(Aq, eg: gene | label Default value: *
.RE
.PP
\fB\-value\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 shown\&. You can set this to match any feature tag value you wish to show\&. The tag value may be wildcarded by using \*(Aq*\*(Aq\&. If you wish to show more than one tag value, separate their names with a space or the character \*(Aq|\*(Aq, eg: pax* | 10 Default value: *
.RE
.SS "Output section"
.PP
\fB\-join\fR \fIboolean\fR
.RS 4
Some features, such as CDS (coding sequence) and mRNA are composed of introns concatenated together\&. There may be other forms of \*(Aqjoined\*(Aq 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 \*(Aqbefore\*(Aq and \*(Aqafter\*(Aq qualifiers have been set, then only the sequence before the first feature and after the last feature are added\&. Default value: N
.RE
.PP
\fB\-featinname\fR \fIboolean\fR
.RS 4
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
.RE
.PP
\fB\-describe\fR \fIstring\fR
.RS 4
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 \*(Aqgene\*(Aq, then if any output feature has the tag (for example) \*(Aq/gene=BRCA1\*(Aq associated with it, then the text \*(Aq(gene=BRCA1)\*(Aq 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 \*(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 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 \*(Aq*\*(Aq\&. If you wish to extract more than one tag, separate their names with the character \*(Aq|\*(Aq, eg: gene | label
.RE
.PP
\fB\-outseq\fR \fIseqout\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
extractfeat 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\&.
.sp
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