twofeat.txt

emboss的linux版本的源代码

                                  twofeat 



Function

   Finds neighbouring pairs of features in sequences

Description

   twofeat reads in the feature tables of sequences and reports
   occurances of pairs of specified features.

   This is intended for use as a simple data-mining tool to enable you to
   look for instances of pairs of features that occur near to each other
   in the same sequence entry.

   For each of the pair of features, you can specify its type name, its
   sense, its score and any tag/value pairs, amongst other things.

   You can then specify the type of relationship that the two features
   should have. You can specify the minimum and maximum distance between
   them. You can specify the type of overlap allowed: Any type of overlap
   or no overlap is allowed, Overlap required, No overlaps are allowed,
   Overlap required but one feature must not be completely within the
   other, Feature A must be completely enclosed within feature B, Feature
   B must be completely enclosed within feature A. You can specify that
   the distance should be measured from the nearest ends of the two
   features, From the left ends, From right ends, From the furthest ends.
   You can specify that the features should be in any sense, in the same
   sense or in opposite senses. You can specify that the features should
   be in any order, Feature A then feature B, Feature B then feature A.

   By default the resulting pairs of features found are then written to a
   report file as a single feature from the first postion of the
   left-most feature to the last position of the right-most feature. You
   can modify the output to report the pairs of features with no changes
   made to them.

Algorithm

For each sequence:
        identify the features that match the criteria for Feature A
        identify the features that match the criteria for Feature B
        compare all pairs of features
        if they satisfy the requirements output them to the report file

Usage

   Here is a sample session with twofeat

   Without the -twoout option the output report contains just one feature
   for every pair of features found.


% twofeat tembl:hsfau 
Finds neighbouring pairs of features in sequences
Type of first feature [*]: polyA_signal
Type of second feature [*]: polyA_site
The minimum distance between the features [0]: 10
The maximum distance between the features [0]: 50
Output report [hsfau.twofeat]: 

   Go to the input files for this example
   Go to the output files for this example

   Example 2

   The -twoout option makes the output report give the pairs of features
   found. The output report format type has been changed to display the
   full original pairs of features in GFF format.


% twofeat -twoout -rformat gff tembl:hsfau 
Finds neighbouring pairs of features in sequences
Type of first feature [*]: polyA_signal
Type of second feature [*]: polyA_site
The minimum distance between the features [0]: 10
The maximum distance between the features [0]: 50
Output report [hsfau.twofeat]: 

   Go to the output files for this example

Command line arguments

   Standard (Mandatory) qualifiers:
  [-sequence]          seqall     Sequence(s) filename and optional format, or
                                  reference (input USA)
   -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://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 allow more than one type,
                                  separate their names with the character '|',
                                  eg:
                                  *UTR | intron (Any string is accepted)
   -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://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 allow more than one type,
                                  separate their names with the character '|',
                                  eg:
                                  *UTR | intron (Any string is accepted)
   -minrange           integer    [0] If this is greater or equal to
                                  'maxrange', then no min or max range is
                                  specified (Any integer value)
   -maxrange           integer    [0] If this is less than or equal to
                                  'minrange', then no min or max range is
                                  specified (Any integer value)
  [-outfile]           report     [*.twofeat] Output report file name

   Additional (Optional) qualifiers (* if not always prompted):
   -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 (Any string is accepted)
   -asense             menu       [0] By default any feature sense is allowed.
                                  You can set this to match the required
                                  sense. (Values: 0 (Any sense); + (Forward
                                  sense); - (Reverse sense))
   -aminscore          float      [0.0] If this is greater than or equal to
                                  the maximum score, then any score is
                                  allowed. (Any numeric value)
   -amaxscore          float      [0.0] If this is less than or equal to the
                                  maximum score, then any score is permitted.
                                  (Any numeric value)
   -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 (Any string is accepted)
   -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 (Any string is accepted)
   -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 (Any string is accepted)
   -bsense             menu       [0] By default any feature sense is allowed.
                                  You can set this to match the required
                                  sense. (Values: 0 (Any sense); + (Forward
                                  sense); - (Reverse sense))
   -bminscore          float      [0.0] If this is greater than or equal to
                                  the maximum score, then any score is
                                  allowed. (Any numeric value)
   -bmaxscore          float      [0.0] If this is less than or equal to the
                                  maximum score, then any score is permitted.
                                  (Any numeric value)
   -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 (Any string is accepted)
   -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 (Any string is accepted)
   -overlap            menu       [A] 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. (Values: A (Any); O
                                  (Overlap required); NO (No overlaps are
                                  allowed); NW (Overlap required but not
                                  within); AW (A must be all within B); BW (B
                                  must be all within A))
   -rangetype          menu       [N] This allows you to specify the positions
                                  from which the allowed minimum or maximum
                                  distance between the features is measured
                                  (Values: N (From nearest ends); L (From left
                                  ends); R (From right ends); F (From
                                  furthest ends))
   -sense              menu       [A] This allows you to specify the required
                                  sense that the two features must be on. This