
                                 showfeat 



Function

   Show features of a sequence

Description

   Showfeat reads a protein or nucleic sequence and its feature table,
   and writes a text representation of the features to standard output.

Usage

   Here is a sample session with showfeat


% showfeat 
Show features of a sequence.
Input sequence(s): tembl:hsfau1
Output file [hsfau1.showfeat]: 

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

   Example 2

   Display 'joined' features on one line with positions:


% showfeat -sort join -pos 
Show features of a sequence.
Input sequence(s): tembl:hsfau1
Output file [hsfau1.showfeat]: 

   Go to the output files for this example

   Example 3

   Display just positions and names of CDS features - this can be used as
   a regions file in showseq:


% showfeat -matchtype CDS -width 0 -noid -nodesc -noscale -pos  
Show features of a sequence.
Input sequence(s): tembl:hsfau1
Output file [hsfau1.showfeat]: 

   Go to the output files for this example

Command line arguments

   Standard (Mandatory) qualifiers:
  [-sequence]          seqall     Sequence database USA
  [-outfile]           outfile    Output file name

   Additional (Optional) qualifiers:
   -matchsource        string     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 '*'.
                                  If you wish to show more than one source,
                                  separate their names with the character '|',
                                  eg:
                                  gene* | embl
   -matchtype          string     By default any feature type in the feature
                                  table is shown. You can set this to match
                                  any feature type you wish to show.
                                  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 show more than one type,
                                  separate their names with the character '|',
                                  eg:
                                  *UTR | intron
   -matchtag           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 shown. You can set this to match
                                  any feature tag you wish to show.
                                  The tag may be wildcarded by using '*'.
                                  If you wish to show more than one tag,
                                  separate their names with the character '|',
                                  eg:
                                  gene | label
   -matchvalue         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
   -sort               menu       Sort features by Type, Start or Source,
                                  Nosort (don't sort - use input order) or
                                  join coding regions together and leave other
                                  features in the input order
   -annotation         range      Regions to annotate by marking.
                                  If this is left blank, then no annotation is
                                  added.
                                  A set of regions is specified by a set of
                                  pairs of positions followed by optional
                                  text.
                                  The positions are integers.
                                  They are followed by any text (but not
                                  digits when on the command-line).
                                  Examples of region specifications are:
                                  24-45 new domain 56-78 match to Mouse
                                  1-100 First part 120-156 oligo
                                  A file of ranges to annotate (one range per
                                  line) can be specified as '@filename'.

   Advanced (Unprompted) qualifiers:
   -html               boolean    Use HTML formatting
   -[no]id             boolean    Set this to be false if you do not wish to
                                  display the ID name of the sequence.
   -[no]description    boolean    Set this to be false if you do not wish to
                                  display the description of the sequence.
   -[no]scale          boolean    Set this to be false if you do not wish to
                                  display the scale line.
   -width              integer    You can expand (or contract) the width of
                                  the ASCII-character graphics display of the
                                  positions of the features using this value.
                                  For example, a width of 80 characters would
                                  cover a standard page width and a width a 10
                                  characters would be nearly unreadable.
                                  If the width is set to less than 4, the
                                  graphics lines and the scale line will not
                                  be displayed.
   -collapse           boolean    If this is set, then features from the same
                                  source and of the same type and sense are
                                  all printed on the same line. For instance
                                  if there are several features from the EMBL
                                  feature table (ie. the same source) which
                                  are all of type 'exon' in the same sense,
                                  then they will all be displayed on the same
                                  line. This makes it hard to distinguish
                                  overlapping features.
                                  If this is set to false then each feature is
                                  displayed on a separate line making it
                                  easier to distinguish where features start
                                  and end.
   -[no]forward        boolean    Set this to be false if you do not wish to
                                  display forward sense features.
   -[no]reverse        boolean    Set this to be false if you do not wish to
                                  display reverse sense features.
   -[no]unknown        boolean    Set this to be false if you do not wish to
                                  display unknown sense features. (ie.
                                  features with no directionality - all
                                  protein features are of this type and some
                                  nucleic features (for example, CG-rich
                                  regions)).
   -strand             boolean    Set this if you wish to display the strand
                                  of the features. Protein features are always
                                  directionless (indicated by '0'), forward
                                  is indicated by '+' and reverse is '-'.
   -source             boolean    Set this if you wish to display the source
                                  of the features.
                                  The source name is usually either the name
                                  of the program that detected the feature or
                                  it is the name of the feature table (eg:
                                  EMBL) that the feature came from.
   -position           boolean    Set this if you wish to display the start
                                  and end position of the features. If several
                                  features are being displayed on the same
                                  line, then the start and end positions will
                                  be joined by a comma, for example:
                                  '189-189,225-225'.
   -[no]type           boolean    Set this to be false if you do not wish to
                                  display the type of the features.
   -tags               boolean    Set this to be false if you do not wish to
                                  display the tags and values of the features.
   -[no]values         boolean    Set this to be false if you do not wish to
                                  display the tag values of the features. If
                                  this is set to be false, only the tag names
                                  will be displayed. If the tags are not
                                  displayed, then the values will not be
                                  displayed. The value of the 'translation'
                                  tag is never displayed as it is often
                                  extremely long.
   -stricttags         boolean    By default if any tag/value pair in a
                                  feature matches the specified tag and value,
                                  then all the tags/value pairs of that
                                  feature will be displayed. If this is set to
                                  be true, then only those tag/value pairs in
                                  a feature that match the specified tag and
                                  value will be displayed.

   Associated qualifiers:

   "-sequence" associated qualifiers
   -sbegin1             integer    Start of each sequence to be used
   -send1               integer    End of each sequence to be used
   -sreverse1           boolean    Reverse (if DNA)
   -sask1               boolean    Ask for begin/end/reverse
   -snucleotide1        boolean    Sequence is nucleotide
   -sprotein1           boolean    Sequence is protein
   -slower1             boolean    Make lower case
   -supper1             boolean    Make upper case
   -sformat1            string     Input sequence format
   -sdbname1            string     Database name
   -sid1                string     Entryname
   -ufo1                string     UFO features
   -fformat1            string     Features format
   -fopenfile1          string     Features file name

   "-outfile" associated qualifiers
   -odirectory2         string     Output directory

   General qualifiers:
   -auto                boolean    Turn off prompts
   -stdout              boolean    Write standard output
   -filter              boolean    Read standard input, write standard output
   -options             boolean    Prompt for standard and additional values
   -debug               boolean    Write debug output to program.dbg
   -verbose             boolean    Report some/full command line options
   -help                boolean    Report command line options. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   -warning             boolean    Report warnings
   -error               boolean    Report errors
   -fatal               boolean    Report fatal errors
   -die                 boolean    Report deaths


   Standard (Mandatory) qualifiers Allowed values Default
   [-sequence]
   (Parameter 1) Sequence database USA Readable sequence(s) Required
   [-outfile]
   (Parameter 2) Output file name Output file <sequence>.showfeat
   Additional (Optional) qualifiers Allowed values Default
   -matchsource 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 '*'. If you
   wish to show more than one source, separate their names with the
   character '|', eg: gene* | embl Any string is accepted *
   -matchtype By default any feature type in the feature table is shown.
   You can set this to match any feature type you wish to show. 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
   show more than one type, separate their names with the character '|',
   eg: *UTR | intron Any string is accepted *
   -matchtag 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 shown. You can set this to match any feature tag you
   wish to show. The tag may be wildcarded by using '*'. If you wish to
   show more than one tag, separate their names with the character '|',
   eg: gene | label Any string is accepted *
   -matchvalue 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 *
   -sort Sort features by Type, Start or Source, Nosort (don't sort - use
   input order) or join coding regions together and leave other features
   in the input order
   source (Sort by Source)
   start  (Sort by Start position)
   type   (Sort by Type)
   nosort (No sorting done)
   join   (Join coding regions together)
   start
   -annotation Regions to annotate by marking. If this is left blank,
   then no annotation is added. A set of regions is specified by a set of
   pairs of positions followed by optional text. The positions are
   integers. They are followed by any text (but not digits when on the
   command-line). Examples of region specifications are: 24-45 new domain
   56-78 match to Mouse 1-100 First part 120-156 oligo A file of ranges
   to annotate (one range per line) can be specified as '@filename'.
   Sequence range If this is left blank, then no annotation is added.
   Advanced (Unprompted) qualifiers Allowed values Default
   -html Use HTML formatting Boolean value Yes/No No
   -[no]id Set this to be false if you do not wish to display the ID name
   of the sequence. Boolean value Yes/No Yes
   -[no]description Set this to be false if you do not wish to display
   the description of the sequence. Boolean value Yes/No Yes
   -[no]scale Set this to be false if you do not wish to display the
   scale line. Boolean value Yes/No Yes
   -width You can expand (or contract) the width of the ASCII-character
   graphics display of the positions of the features using this value.
   For example, a width of 80 characters would cover a standard page
   width and a width a 10 characters would be nearly unreadable. If the
   width is set to less than 4, the graphics lines and the scale line
   will not be displayed. Integer 0 or more 60
   -collapse If this is set, then features from the same source and of
   the same type and sense are all printed on the same line. For instance
   if there are several features from the EMBL feature table (ie. the
   same source) which are all of type 'exon' in the same sense, then they
   will all be displayed on the same line. This makes it hard to
   distinguish overlapping features. If this is set to false then each
   feature is displayed on a separate line making it easier to
   distinguish where features start and end. Boolean value Yes/No No
   -[no]forward Set this to be false if you do not wish to display
   forward sense features. Boolean value Yes/No Yes
   -[no]reverse Set this to be false if you do not wish to display
   reverse sense features. Boolean value Yes/No Yes
   -[no]unknown Set this to be false if you do not wish to display
   unknown sense features. (ie. features with no directionality - all
   protein features are of this type and some nucleic features (for
   example, CG-rich regions)). Boolean value Yes/No Yes
   -strand Set this if you wish to display the strand of the features.
   Protein features are always directionless (indicated by '0'), forward
   is indicated by '+' and reverse is '-'. Boolean value Yes/No No
   -source Set this if you wish to display the source of the features.
   The source name is usually either the name of the program that
   detected the feature or it is the name of the feature table (eg: EMBL)
   that the feature came from. Boolean value Yes/No No
   -position Set this if you wish to display the start and end position
   of the features. If several features are being displayed on the same
   line, then the start and end positions will be joined by a comma, for
   example: '189-189,225-225'. Boolean value Yes/No No
   -[no]type Set this to be false if you do not wish to display the type
   of the features. Boolean value Yes/No Yes
   -tags Set this to be false if you do not wish to display the tags and
   values of the features. Boolean value Yes/No No
   -[no]values Set this to be false if you do not wish to display the tag
   values of the features. If this is set to be false, only the tag names
   will be displayed. If the tags are not displayed, then the values will
   not be displayed. The value of the 'translation' tag is never
   displayed as it is often extremely long. Boolean value Yes/No Yes
   -stricttags By default if any tag/value pair in a feature matches the
   specified tag and value, then all the tags/value pairs of that feature
   will be displayed. If this is set to be true, then only those
   tag/value pairs in a feature that match the specified tag and value
   will be displayed. Boolean value Yes/No No

Input file format

   The feature input is the feature table lines from a normal sequence
   USA.

  Input files for usage example

   'tembl:hsfau1' is a sequence entry in the example nucleic acid
   database 'tembl'

  Database entry: tembl:hsfau1

ID   HSFAU1     standard; DNA; HUM; 2016 BP.
XX
AC   X65921; S45242;
XX
SV   X65921.1
XX
DT   13-MAY-1992 (Rel. 31, Created)
DT   21-JUL-1993 (Rel. 36, Last updated, Version 5)
XX
DE   H.sapiens fau 1 gene
XX
KW   fau 1 gene.
XX
OS   Homo sapiens (human)
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia
;
OC   Eutheria; Primates; Catarrhini; Hominidae; Homo.
XX
RN   [1]
RP   1-2016
RA   Kas K.;
RT   ;
RL   Submitted (29-APR-1992) to the EMBL/GenBank/DDBJ databases.
RL   K. Kas, University of Antwerp, Dept of Biochemistry T3.22,
RL   Universiteitsplein 1, 2610 Wilrijk, BELGIUM
XX
RN   [2]
RP   1-2016
RX   MEDLINE; 92412144.
RA   Kas K., Michiels L., Merregaert J.;
RT   "Genomic structure and expression of the human fau gene: encoding the
RT   ribosomal protein S30 fused to a ubiquitin-like protein.";
RL   Biochem. Biophys. Res. Commun. 187:927-933(1992).
XX
DR   SWISS-PROT; P35544; UBIM_HUMAN.
DR   SWISS-PROT; Q05472; RS30_HUMAN.
XX
FH   Key             Location/Qualifiers
FH
FT   source          1..2016
FT                   /db_xref="taxon:9606"
FT                   /organism="Homo sapiens"
FT                   /clone_lib="CML cosmid"
FT                   /clone="15.1"
FT   mRNA            join(408..504,774..856,951..1095,1557..1612,1787..>1912)
FT                   /gene="fau 1"
FT   exon            408..504
FT                   /number=1
FT   intron          505..773
FT                   /number=1
FT   exon            774..856


  [Part of this file has been deleted for brevity]

FT                   RAKRRMQYNRRFVNVVPTFGKKKGPNANS"
FT   intron          857..950
FT                   /number=2
FT   exon            951..1095
FT                   /number=3
FT   intron          1096..1556
FT                   /number=3
FT   exon            1557..1612
FT                   /number=4
FT   intron          1613..1786
FT                   /number=4
FT   exon            1787..>1912
FT                   /number=5
FT   polyA_signal    1938..1943
XX
SQ   Sequence 2016 BP; 421 A; 562 C; 538 G; 495 T; 0 other;
     ctaccatttt ccctctcgat tctatatgta cactcgggac aagttctcct gatcgaaaac        6
0
     ggcaaaacta aggccccaag taggaatgcc ttagttttcg gggttaacaa tgattaacac       12
0
     tgagcctcac acccacgcga tgccctcagc tcctcgctca gcgctctcac caacagccgt       18
0
     agcccgcagc cccgctggac accggttctc catccccgca gcgtagcccg gaacatggta       24
0
     gctgccatct ttacctgcta cgccagcctt ctgtgcgcgc aactgtctgg tcccgccccg       30
0
     tcctgcgcga gctgctgccc aggcaggttc gccggtgcga gcgtaaaggg gcggagctag       36
0
     gactgccttg ggcggtacaa atagcaggga accgcgcggt cgctcagcag tgacgtgaca       42
0
     cgcagcccac ggtctgtact gacgcgccct cgcttcttcc tctttctcga ctccatcttc       48
0
     gcggtagctg ggaccgccgt tcaggtaaga atggggcctt ggctggatcc gaagggcttg       54
0
     tagcaggttg gctgcggggt cagaaggcgc ggggggaacc gaagaacggg gcctgctccg       60
0
     tggccctgct ccagtcccta tccgaactcc ttgggaggca ctggccttcc gcacgtgagc       66
0
     cgccgcgacc accatcccgt cgcgatcgtt tctggaccgc tttccactcc caaatctcct       72
0
     ttatcccaga gcatttcttg gcttctctta caagccgtct tttctttact cagtcgccaa       78
0
     tatgcagctc tttgtccgcg cccaggagct acacaccttc gaggtgaccg gccaggaaac       84
0
     ggtcgcccag atcaaggtaa ggctgcttgg tgcgccctgg gttccatttt cttgtgctct       90
0
     tcactctcgc ggcccgaggg aacgcttacg agccttatct ttccctgtag gctcatgtag       96
0
     cctcactgga gggcattgcc ccggaagatc aagtcgtgct cctggcaggc gcgcccctgg      102
0
     aggatgaggc cactctgggc cagtgcgggg tggaggccct gactaccctg gaagtagcag      108
0
     gccgcatgct tggaggtgag tgagagagga atgttctttg aagtaccggt aagcgtctag      114
0
     tgagtgtggg gtgcatagtc ctgacagctg agtgtcacac ctatggtaat agagtacttc      120
0
     tcactgtctt cagttcagag tgattcttcc tgtttacatc cctcatgttg aacacagacg      126
0
     tccatgggag actgagccag agtgtagttg tatttcagtc acatcacgag atcctagtct      132
0
     ggttatcagc ttccacacta aaaattaggt cagaccaggc cccaaagtgc tctataaatt      138
0
     agaagctgga agatcctgaa atgaaactta agatttcaag gtcaaatatc tgcaactttg      144
0
     ttctcattac ctattgggcg cagcttctct ttaaaggctt gaattgagaa aagaggggtt      150
0
     ctgctgggtg gcaccttctt gctcttacct gctggtgcct tcctttccca ctacaggtaa      156
0
     agtccatggt tccctggccc gtgctggaaa agtgagaggt cagactccta aggtgagtga      162
0
     gagtattagt ggtcatggtg ttaggacttt ttttcctttc acagctaaac caagtccctg      168
0
     ggctcttact cggtttgcct tctccctccc tggagatgag cctgagggaa gggatgctag      174
0
     gtgtggaaga caggaaccag ggcctgatta accttccctt ctccaggtgg ccaaacagga      180
0
     gaagaagaag aagaagacag gtcgggctaa gcggcggatg cagtacaacc ggcgctttgt      186
0
     caacgttgtg cccacctttg gcaagaagaa gggccccaat gccaactctt aagtcttttg      192
0
     taattctggc tttctctaat aaaaaagcca cttagttcag tcatcgcatt gtttcatctt      198
0
     tacttgcaag gcctcaggga gaggtgtgct tctcgg                                201
6
//

Output file format

   The output is a text representation of the feature table.

  Output files for usage example

  File: hsfau1.showfeat

HSFAU1
H.sapiens fau 1 gene
|==========================================================| 2016
|----------------------------------------------------------> source
           |-->                                              exon
           |-->                                              mRNA
              |------->                                      intron
                      |->                                    exon
                      |->                                    mRNA
                      |->                                    CDS
                        |-->                                 intron
                           |--->                             CDS
                           |--->                             exon
                           |--->                             mRNA
                               |------------->               intron
                                             |>              CDS
                                             |>              exon
                                             |>              mRNA
                                               |---->        intron
                                                    |-->     CDS
                                                    |-->     exon
                                                    |-->     mRNA
                                                        >    polyA_signal

  Output files for usage example 2

  File: hsfau1.showfeat

HSFAU1
H.sapiens fau 1 gene
|==========================================================| 2016
|----------------------------------------------------------> 1-2016 source
           |-->       |->  |--->             |>     |-->     408-504,774-856,95
1-1095,1557-1612,1787-1912 mRNA
           |-->                                              408-504 exon
              |------->                                      505-773 intron
                      |->                                    774-856 exon
                      |->  |--->             |>     |-->     782-856,951-1095,1
557-1612,1787-1912 CDS
                        |-->                                 857-950 intron
                           |--->                             951-1095 exon
                               |------------->               1096-1556 intron
                                             |>              1557-1612 exon
                                               |---->        1613-1786 intron
                                                    |-->     1787-1912 exon
                                                        >    1938-1943 polyA_si
gnal

  Output files for usage example 3

  File: hsfau1.showfeat

782-856 CDS
951-1095 CDS
1557-1612 CDS
1787-1912 CDS

Data files

   None.

Notes

   None.

References

   None.

Warnings

   None.

Diagnostic Error Messages

   None.

Exit status

   It always exits with a status of 0.

Known bugs

   None.

See also

   Program name Description
   abiview Reads ABI file and display the trace
   cirdna Draws circular maps of DNA constructs
   coderet Extract CDS, mRNA and translations from feature tables
   extractfeat Extract features from a sequence
   lindna Draws linear maps of DNA constructs
   maskfeat Mask off features of a sequence
   pepnet Displays proteins as a helical net
   pepwheel Shows protein sequences as helices
   prettyplot Displays aligned sequences, with colouring and boxing
   prettyseq Output sequence with translated ranges
   remap Display a sequence with restriction cut sites, translation etc
   seealso Finds programs sharing group names
   showalign Displays a multiple sequence alignment
   showdb Displays information on the currently available databases
   showseq Display a sequence with features, translation etc
   sixpack Display a DNA sequence with 6-frame translation and ORFs
   textsearch Search sequence documentation text. SRS and Entrez are
   faster!
   twofeat Finds neighbouring pairs of features in sequences

Author(s)

   Gary Williams (gwilliam © rfcgr.mrc.ac.uk)
   MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust
   Genome Campus, Hinxton, Cambridge, CB10 1SB, UK

History

   Written 1999 - Gary Williams

   Dec 2001 - added -sort nosort option to get the features in the input
   order

Target users

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

Comments

   None
