EMBOSS: extractfeat

| ## EMBOSS: extractfeat

# Program extractfeat

## Function

Extract features from a sequence

## Description

extractfeat is a simple utility for extracting parts of a sequence that have been annotated as being a specific type of feature. These sub-sequences are writen to the output sequence file.

If the feature is annotated as being in the reverse sense of a nucleic acid sequence, then that feature's sub-sequence is reverse-complemented before being written out.

It is often useful to have some information on the context of the feature. extractfeat allows you to specify a number of bases or residues before and/or after the feature to write out.

If you are interested in extracting the sequence of the region around the start or end of the feature, then this can also be specified.

Please remember that the output feature sequence is only as good as the annotation. If you rely upon other people's, or other program's annotation of features, then some of these will be incorrect.

## Usage

Here is a sample session with extractfeat to write out the exons of a sequence:

    % extractfeat embl:hsfau1 -type exon stdout

To write out the exons with 10 extra bases at the start and end so that you can inspect the splice sites:

    % extractfeat embl:hsfau1 -type exon -before 10 -after 10 stdout

To write out the 10 bases around the start of all 'exon' features in the embl database:

    % extractfeat embl:\*  -type exon -before 5 -after -5 stdout

To write out the 7 residues around all phosphorylated residues in swissprot:

    % extractfeat sw:\*  -type mod_res -value phosphorylation -before 3 -after -4 stdout

## Command line arguments

       Mandatory qualifiers:
      [-sequence]          seqall     Sequence database USA
      [-outseq]            seqout     Output sequence USA

       Optional qualifiers:
       -before             integer    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 '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 se t this to match
                                      any feature source you wish to show.
                                      The source name is usuall y 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 u sing '*'.
                                      If you wish to show more than one source,
                                      separate their names with the character '|',
                                      eg:
                                      gene* | embl
       -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://www3.ebi.ac.uk/Services/WebFeat/
                                      for a list of the EMBL feature types and see
                                      Appendix A of the Swissprot user manual in
                                      http://www.expasy.ch/txt/userman.txt for a
                                      list of the Swissprot 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
       -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      If this is greater than or equal to the
                                      maximum score, then any score is permitted
       -maxscore           float      If this is less than or equal to the maximum
                                      score, then any score is permitted
       -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
       -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 valueyou 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 the character
                                      '|', eg:
                                      pax* | 10

       Advanced qualifiers: (none)
       General qualifiers:
      -help                bool       report command line options. More
                                      information on associated and general
                                      qualifiers can be found with -help -verbose

Mandatory qualifiers | Allowed values | Default
--- | --- | ---
[-sequence] (Parameter 1) | Sequence database USA | Readable sequence(s) | Required
[-outseq] (Parameter 2) | Output sequence USA | Writeable sequence | <sequence>.format
Optional qualifiers | Allowed values | Default
-before | 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 '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. | Any integer value | 0
-after | 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. | Any integer value | 0
-source | By default any feature source in the feature table is shown. You can se t this to match any feature source you wish to show. The source name is usuall y 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 u sing '*'. If you wish to show more than one source, separate their names with the character '|', eg: gene* | embl | Any string is accepted | *
-type | 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://www3.ebi.ac.uk/Services/WebFeat/ for a list of the EMBL feature types and see Appendix A of the Swissprot user manual in http://www.expasy.ch/txt/userman.txt for a list of the Swissprot 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 | Any string is accepted | *
-sense | 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 | Any integer value | 0 - any sense, 1 - forward sense, -1 - reverse sense
-minscore | If this is greater than or equal to the maximum score, then any score is permitted | Any integer value | 0.0
-maxscore | If this is less than or equal to the maximum score, then any score is permitted | Any integer value | 0.0
-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'. 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 | Any string is accepted | *
-value | 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 valueyou 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 the character '|', eg: pax* | 10 | Any string is accepted | *
Advanced qualifiers | Allowed values | Default
(none)

## Input file format

Normal sequence with features.

Feature tables in Swissprot, EMBL, GFF, etc. format can be added using '-ufo featurefile' on the command line.

## Output file format

The sequences of the specified features are written out.

The ID name of the sequence is formed from the original sequence anme with the start and end positions of the feature appended to it. So if the feature came from a sequence with an ID name of 'XYZ' from positions 10 to 22, then the resulting ID name of the feature sequence will be 'XYZ_10_22'

The name of the type of feature is added to the start of the description of the sequence in brackets, e.g.: '[exon]'.

The sequence is written out as a normal sequence.

If the feature is in the reverse sense of a nucleic acid sequence, then it is reverse-complemented before being written.

## Data files

None.

## Notes

None.

## References

None.

## Warnings

None.

## Diagnostic Error Messages

If the end position of the sequence to be written is less than the start position, then the warning message "Extraction region end less than start for feature type [start-end] in ID name" is written and no sequence is output.

## Exit status

It always exits with status 0.

## Known bugs

None.

## See also

Program name | Description
--- | ---
biosed | Replace or delete sequence sections
coderet | Extract CDS, mRNA and translations from feature tables
cutseq | Removes a specified section from a sequence
degapseq | Removes gap characters from sequences
descseq | Alter the name or description of a sequence
entret | Reads and writes (returns) flatfile entries
extractseq | Extract regions from a sequence
listor | Writes a list file of the logical OR of two sets of sequences
maskfeat | Mask off features of a sequence
maskseq | Mask off regions of a sequence
newseq | Type in a short new sequence
noreturn | Removes carriage return from ASCII files
notseq | Excludes a set of sequences and writes out the remaining ones
nthseq | Writes one sequence from a multiple set of sequences
pasteseq | Insert one sequence into another
revseq | Reverse and complement a sequence
seqret | Reads and writes (returns) sequences
seqretsplit | Reads and writes (returns) sequences in individual files
showfeat | Show features of a sequence
splitter | Split a sequence into (overlapping) smaller sequences
swissparse | Retrieves sequences from swissprot using keyword search
trimest | Trim poly-A tails off EST sequences
trimseq | Trim ambiguous bits off the ends of sequences
union | Reads sequence fragments and builds one sequence
vectorstrip | Strips out DNA between a pair of vector sequences
yank | Reads a sequence range, appends the full USA to a list file

## Author(s)

This application was written by Gary Williams (gwilliam@hgmp.mrc.ac.uk)

## History

Written (Dec 12 2001) - Gary Williams

## Target users

This program is intended to be used by everyone and everything, from naive users to embedded scripts.

## Comments