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showfeat |
Function
Show features of a sequenceDescription
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 |
|
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 60
ggcaaaacta aggccccaag taggaatgcc ttagttttcg gggttaacaa tgattaacac 120
tgagcctcac acccacgcga tgccctcagc tcctcgctca gcgctctcac caacagccgt 180
agcccgcagc cccgctggac accggttctc catccccgca gcgtagcccg gaacatggta 240
gctgccatct ttacctgcta cgccagcctt ctgtgcgcgc aactgtctgg tcccgccccg 300
tcctgcgcga gctgctgccc aggcaggttc gccggtgcga gcgtaaaggg gcggagctag 360
gactgccttg ggcggtacaa atagcaggga accgcgcggt cgctcagcag tgacgtgaca 420
cgcagcccac ggtctgtact gacgcgccct cgcttcttcc tctttctcga ctccatcttc 480
gcggtagctg ggaccgccgt tcaggtaaga atggggcctt ggctggatcc gaagggcttg 540
tagcaggttg gctgcggggt cagaaggcgc ggggggaacc gaagaacggg gcctgctccg 600
tggccctgct ccagtcccta tccgaactcc ttgggaggca ctggccttcc gcacgtgagc 660
cgccgcgacc accatcccgt cgcgatcgtt tctggaccgc tttccactcc caaatctcct 720
ttatcccaga gcatttcttg gcttctctta caagccgtct tttctttact cagtcgccaa 780
tatgcagctc tttgtccgcg cccaggagct acacaccttc gaggtgaccg gccaggaaac 840
ggtcgcccag atcaaggtaa ggctgcttgg tgcgccctgg gttccatttt cttgtgctct 900
tcactctcgc ggcccgaggg aacgcttacg agccttatct ttccctgtag gctcatgtag 960
cctcactgga gggcattgcc ccggaagatc aagtcgtgct cctggcaggc gcgcccctgg 1020
aggatgaggc cactctgggc cagtgcgggg tggaggccct gactaccctg gaagtagcag 1080
gccgcatgct tggaggtgag tgagagagga atgttctttg aagtaccggt aagcgtctag 1140
tgagtgtggg gtgcatagtc ctgacagctg agtgtcacac ctatggtaat agagtacttc 1200
tcactgtctt cagttcagag tgattcttcc tgtttacatc cctcatgttg aacacagacg 1260
tccatgggag actgagccag agtgtagttg tatttcagtc acatcacgag atcctagtct 1320
ggttatcagc ttccacacta aaaattaggt cagaccaggc cccaaagtgc tctataaatt 1380
agaagctgga agatcctgaa atgaaactta agatttcaag gtcaaatatc tgcaactttg 1440
ttctcattac ctattgggcg cagcttctct ttaaaggctt gaattgagaa aagaggggtt 1500
ctgctgggtg gcaccttctt gctcttacct gctggtgcct tcctttccca ctacaggtaa 1560
agtccatggt tccctggccc gtgctggaaa agtgagaggt cagactccta aggtgagtga 1620
gagtattagt ggtcatggtg ttaggacttt ttttcctttc acagctaaac caagtccctg 1680
ggctcttact cggtttgcct tctccctccc tggagatgag cctgagggaa gggatgctag 1740
gtgtggaaga caggaaccag ggcctgatta accttccctt ctccaggtgg ccaaacagga 1800
gaagaagaag aagaagacag gtcgggctaa gcggcggatg cagtacaacc ggcgctttgt 1860
caacgttgtg cccacctttg gcaagaagaa gggccccaat gccaactctt aagtcttttg 1920
taattctggc tttctctaat aaaaaagcca cttagttcag tcatcgcatt gtttcatctt 1980
tacttgcaag gcctcaggga gaggtgtgct tctcgg 2016
//
|
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
|--> |-> |---> |> |--> 408-504,774-856,951-1095,1557-1612,1787-1912 mRNA
|--> 408-504 exon
|-------> 505-773 intron
|-> 774-856 exon
|-> |---> |> |--> 782-856,951-1095,1557-1612,1787-1912 CDS
|--> 857-950 intron
|---> 951-1095 exon
|-------------> 1096-1556 intron
|> 1557-1612 exon
|----> 1613-1786 intron
|--> 1787-1912 exon
> 1938-1943 polyA_signal
|
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 sequence with restriction 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. Slow, use SRS and Entrez! |
| 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 WilliamsDec 2001 - added -sort nosort option to get the features in the input order