                                  featmerge



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Function

   Merge two overlapping feature tables

Description

   featmerge reads two feature tables for the same sequence and combines
   them into a single table.

Algorithm

   The second feature table is appended to the first, retaining the
   original order.

Usage

   This run merges the GFF format output of one of the antigenic examples
   with the original feature table read from SwissProt. Here is a sample
   session with featmerge


% featmerge
Merge two overlapping feature tables
Input feature table: tsw:actb1_takru
Second input feature table: ../antigenic-keep/actb1_takru.antigenic
Features output [actb1_takru.gff]:


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

Command line arguments

Merge two overlapping feature tables
Version: EMBOSS:6.5.6.0

   Standard (Mandatory) qualifiers:
  [-afeatures]         features   (no help text) features value
  [-bfeatures]         features   (no help text) features value
  [-outfeat]           featout    [unknown.gff] Output features UFO

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers: (none)
   Associated qualifiers:

   "-afeatures" associated qualifiers
   -fformat1           string     Features format
   -iquery1            string     Input query fields or ID list
   -ioffset1           integer    Input start position offset
   -fopenfile1         string     Features file name
   -fask1              boolean    Prompt for begin/end/reverse
   -fbegin1            integer    Start of the features to be used
   -fend1              integer    End of the features to be used
   -freverse1          boolean    Reverse (if DNA)
   -fcircular1         boolean    Circular sequence features

   "-bfeatures" associated qualifiers
   -fformat2           string     Features format
   -iquery2            string     Input query fields or ID list
   -ioffset2           integer    Input start position offset
   -fopenfile2         string     Features file name
   -fask2              boolean    Prompt for begin/end/reverse
   -fbegin2            integer    Start of the features to be used
   -fend2              integer    End of the features to be used
   -freverse2          boolean    Reverse (if DNA)
   -fcircular2         boolean    Circular sequence features

   "-outfeat" associated qualifiers
   -offormat3          string     Output feature format
   -ofopenfile3        string     Features file name
   -ofextension3       string     File name extension
   -ofdirectory3       string     Output directory
   -ofname3            string     Base file name
   -ofsingle3          boolean    Separate file for each entry

   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write first file to standard output
   -filter             boolean    Read first file from standard input, write
                                  first file to 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 and exit. 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 dying program messages
   -version            boolean    Report version number and exit


Input file format

   The input is a standard EMBOSS feaure query.

   Data can also be read from feaure output in any supported format format
   written by an EMBOSS application. featmerge reads two feature UFOs.

  Input files for usage example

   'tsw:actb1_takru' is a sequence entry in the example protein database
   'tsw'

  File: ../antigenic-keep/actb1_takru.antigenic

##gff-version 3
##sequence-region ACTB1_TAKRU 1 375
#!Date 2012-07-15
#!Type Protein
#!Source-version EMBOSS 6.5.6.0
ACTB1_TAKRU     antigenic       epitope 214     222     1.207   .       .
ID=ACTB1_TAKRU.1;note=*pos 218
ACTB1_TAKRU     antigenic       epitope 131     145     1.187   .       .
ID=ACTB1_TAKRU.2;note=*pos 137
ACTB1_TAKRU     antigenic       epitope 5       12      1.166   .       .
ID=ACTB1_TAKRU.3;note=*pos 8
ACTB1_TAKRU     antigenic       epitope 27      38      1.164   .       .
ID=ACTB1_TAKRU.4;note=*pos 32
ACTB1_TAKRU     antigenic       epitope 160     183     1.136   .       .
ID=ACTB1_TAKRU.5;note=*pos 173
ACTB1_TAKRU     antigenic       epitope 367     372     1.135   .       .
ID=ACTB1_TAKRU.6;note=*pos 372
ACTB1_TAKRU     antigenic       epitope 93      108     1.116   .       .
ID=ACTB1_TAKRU.7;note=*pos 103
ACTB1_TAKRU     antigenic       epitope 295     301     1.113   .       .
ID=ACTB1_TAKRU.8;note=*pos 296
ACTB1_TAKRU     antigenic       epitope 256     266     1.11    .       .
ID=ACTB1_TAKRU.9;note=*pos 264
ACTB1_TAKRU     antigenic       epitope 336     352     1.107   .       .
ID=ACTB1_TAKRU.10;note=*pos 347
ACTB1_TAKRU     antigenic       epitope 62      76      1.102   .       .
ID=ACTB1_TAKRU.11;note=*pos 68
ACTB1_TAKRU     antigenic       epitope 232     250     1.086   .       .
ID=ACTB1_TAKRU.12;note=*pos 245
ACTB1_TAKRU     antigenic       epitope 327     332     1.083   .       .
ID=ACTB1_TAKRU.13;note=*pos 330
ACTB1_TAKRU     antigenic       epitope 317     323     1.074   .       .
ID=ACTB1_TAKRU.14;note=*pos 320
ACTB1_TAKRU     antigenic       epitope 186     192     1.068   .       .
ID=ACTB1_TAKRU.15;note=*pos 191
ACTB1_TAKRU     antigenic       epitope 40      46      1.066   .       .
ID=ACTB1_TAKRU.16;note=*pos 43
ACTB1_TAKRU     antigenic       epitope 269     275     1.045   .       .
ID=ACTB1_TAKRU.17;note=*pos 269
ACTB1_TAKRU     antigenic       epitope 51      57      1.034   .       .
ID=ACTB1_TAKRU.18;note=*pos 52

  Database entry: tsw:actb1_takru

ID   ACTB1_TAKRU             Reviewed;         375 AA.
AC   P68142; P53484;
DT   25-OCT-2004, integrated into UniProtKB/Swiss-Prot.
DT   25-OCT-2004, sequence version 1.
DT   16-MAY-2012, entry version 49.
DE   RecName: Full=Actin, cytoplasmic 1;
DE   AltName: Full=Beta-actin A;
DE   Contains:
DE     RecName: Full=Actin, cytoplasmic 1, N-terminally processed;
GN   Name=actba;
OS   Takifugu rubripes (Japanese pufferfish) (Fugu rubripes).
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC   Actinopterygii; Neopterygii; Teleostei; Euteleostei; Neoteleostei;
OC   Acanthomorpha; Acanthopterygii; Percomorpha; Tetraodontiformes;
OC   Tetradontoidea; Tetraodontidae; Takifugu.
OX   NCBI_TaxID=31033;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND TISSUE SPECIFICITY.
RX   MEDLINE=96275651; PubMed=8683572; DOI=10.1006/jmbi.1996.0347;
RA   Venkatesh B., Tay B.H., Elgar G., Brenner S.;
RT   "Isolation, characterization and evolution of nine pufferfish (Fugu
RT   rubripes) actin genes.";
RL   J. Mol. Biol. 259:655-665(1996).
CC   -!- FUNCTION: Actins are highly conserved proteins that are involved
CC       in various types of cell motility and are ubiquitously expressed
CC       in all eukaryotic cells.
CC   -!- SUBUNIT: Polymerization of globular actin (G-actin) leads to a
CC       structural filament (F-actin) in the form of a two-stranded helix.
CC       Each actin can bind to 4 others.
CC   -!- SUBCELLULAR LOCATION: Cytoplasm, cytoskeleton.
CC   -!- TISSUE SPECIFICITY: Widely distributed. Not expressed in skeletal
CC       muscle.
CC   -!- PTM: Oxidation of Met-44 by MICALs (MICAL1, MICAL2 or MICAL3) to
CC       form methionine sulfoxide promotes actin filament
CC       depolymerization. Methionine sulfoxide is produced
CC       stereospecifically, but it is not known whether the (S)-S-oxide or
CC       the (R)-S-oxide is produced (By similarity).
CC   -!- MISCELLANEOUS: In vertebrates 3 main groups of actin isoforms,
CC       alpha, beta and gamma have been identified. The alpha actins are
CC       found in muscle tissues and are a major constituent of the
CC       contractile apparatus. The beta and gamma actins coexist in most
CC       cell types as components of the cytoskeleton and as mediators of
CC       internal cell motility.
CC   -!- MISCELLANEOUS: There are three different beta-cytoplasmic actins
CC       in Fugu rubripes.
CC   -!- SIMILARITY: Belongs to the actin family.
CC   -----------------------------------------------------------------------
CC   Copyrighted by the UniProt Consortium, see http://www.uniprot.org/terms
CC   Distributed under the Creative Commons Attribution-NoDerivs License
CC   -----------------------------------------------------------------------
DR   EMBL; U37499; AAC59889.1; -; Genomic_DNA.
DR   PIR; S71124; S71124.
DR   ProteinModelPortal; P68142; -.
DR   SMR; P68142; 2-375.
DR   Ensembl; ENSTRUT00000013141; ENSTRUP00000013080; ENSTRUG00000005447.
DR   eggNOG; COG5277; -.
DR   GeneTree; ENSGT00630000089629; -.
DR   InParanoid; P68142; -.
DR   OMA; IKNLMER; -.
DR   OrthoDB; EOG41JZC9; -.
DR   GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-KW.
DR   GO; GO:0005856; C:cytoskeleton; IEA:UniProtKB-SubCell.
DR   GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR   InterPro; IPR004000; Actin-like.
DR   InterPro; IPR020902; Actin/actin-like_CS.
DR   InterPro; IPR004001; Actin_CS.
DR   PANTHER; PTHR11937; Actin_like; 1.
DR   Pfam; PF00022; Actin; 1.
DR   PRINTS; PR00190; ACTIN.
DR   SMART; SM00268; ACTIN; 1.
DR   PROSITE; PS00406; ACTINS_1; 1.
DR   PROSITE; PS00432; ACTINS_2; 1.
DR   PROSITE; PS01132; ACTINS_ACT_LIKE; 1.
PE   2: Evidence at transcript level;
KW   Acetylation; ATP-binding; Complete proteome; Cytoplasm; Cytoskeleton;
KW   Methylation; Nucleotide-binding; Oxidation; Reference proteome.
FT   CHAIN         1    375       Actin, cytoplasmic 1.
FT                                /FTId=PRO_0000367094.
FT   INIT_MET      1      1       Removed; alternate (By similarity).
FT   CHAIN         2    375       Actin, cytoplasmic 1, N-terminally
FT                                processed.
FT                                /FTId=PRO_0000000809.
FT   MOD_RES       1      1       N-acetylmethionine; in Actin, cytoplasmic
FT                                1; alternate (By similarity).
FT   MOD_RES       2      2       N-acetylglutamate; in Actin, cytoplasmic
FT                                1, N-terminally processed (By
FT                                similarity).
FT   MOD_RES      44     44       Methionine sulfoxide (By similarity).
FT   MOD_RES      73     73       Tele-methylhistidine (By similarity).
SQ   SEQUENCE   375 AA;  41767 MW;  9C505616D33E9495 CRC64;
     MEDEIAALVV DNGSGMCKAG FAGDDAPRAV FPSIVGRPRH QGVMVGMGQK DSYVGDEAQS
     KRGILTLKYP IEHGIVTNWD DMEKIWHHTF YNELRVAPEE HPVLLTEAPL NPKANREKMT
     QIMFETFNTP AMYVAIQAVL SLYASGRTTG IVMDSGDGVT HTVPIYEGYA LPHAILRLDL
     AGRDLTDYLM KILTERGYSF TTTAEREIVR DIKEKLCYVA LDFEQEMGTA ASSSSLEKSY
     ELPDGQVITI GNERFRCPEA LFQPSFLGME SCGIHETTYN SIMKCDVDIR KDLYANTVLS
     GGTTMYPGIA DRMQKEITAL APSTMKIKII APPERKYSVW IGGSILASLS TFQQMWISKQ
     EYDESGPSIV HRKCF
//

Output file format

   The output is a standard EMBOSS feature file.

   The results can be output in one of several styles by using the
   command-line qualifier -offormat xxx, where 'xxx' is replaced by the
   name of the required format. The available format names are: gff
   (gff3), gff2, embl (em), genbank (gb, refseq), ddbj, refseqp, pir
   (nbrf), swissprot (swiss, sw), dasgff and debug.

   See: http://emboss.sf.net/docs/themes/FeatureFormats.html for further
   information on feature formats.

   featmerge writes a single feature table. By default the output is in
   'gff' feature format.

  Output files for usage example

  File: actb1_takru.gff

##gff-version 3
##sequence-region ACTB1_TAKRU 1 375
#!Date 2012-07-15
#!Type Protein
#!Source-version EMBOSS 6.5.6.0
ACTB1_TAKRU     SWISSPROT       mature_protein_region   1       375     .
.       .       ID=ACTB1_TAKRU.1;note=Actin%2C cytoplasmic 1;ftid=PRO_0000367094
ACTB1_TAKRU     SWISSPROT       cleaved_initiator_methionine    1       1
.       .       .       ID=ACTB1_TAKRU.2;note=Removed%3B alternate;comment=By si
milarity
ACTB1_TAKRU     SWISSPROT       mature_protein_region   2       375     .
.       .       ID=ACTB1_TAKRU.3;note=Actin%2C cytoplasmic 1%2C N-terminally pro
cessed;ftid=PRO_0000000809
ACTB1_TAKRU     SWISSPROT       post_translationally_modified_region    1
1       .       .       .       ID=ACTB1_TAKRU.4;note=N-acetylmethionine%3B in A
ctin%2C cytoplasmic 1%3B alternate;comment=By similarity
ACTB1_TAKRU     SWISSPROT       post_translationally_modified_region    2
2       .       .       .       ID=ACTB1_TAKRU.5;note=N-acetylglutamate%3B in Ac
tin%2C cytoplasmic 1%2C N-terminally processed;comment=By similarity
ACTB1_TAKRU     SWISSPROT       post_translationally_modified_region    44
44      .       .       .       ID=ACTB1_TAKRU.6;note=Methionine sulfoxide;comme
nt=By similarity
ACTB1_TAKRU     SWISSPROT       post_translationally_modified_region    73
73      .       .       .       ID=ACTB1_TAKRU.7;note=Tele-methylhistidine;comme
nt=By similarity
ACTB1_TAKRU     antigenic       epitope 214     222     1.207   .       .
ID=ACTB1_TAKRU.1;note=*pos 218
ACTB1_TAKRU     antigenic       epitope 131     145     1.187   .       .
ID=ACTB1_TAKRU.2;note=*pos 137
ACTB1_TAKRU     antigenic       epitope 5       12      1.166   .       .
ID=ACTB1_TAKRU.3;note=*pos 8
ACTB1_TAKRU     antigenic       epitope 27      38      1.164   .       .
ID=ACTB1_TAKRU.4;note=*pos 32
ACTB1_TAKRU     antigenic       epitope 160     183     1.136   .       .
ID=ACTB1_TAKRU.5;note=*pos 173
ACTB1_TAKRU     antigenic       epitope 367     372     1.135   .       .
ID=ACTB1_TAKRU.6;note=*pos 372
ACTB1_TAKRU     antigenic       epitope 93      108     1.116   .       .
ID=ACTB1_TAKRU.7;note=*pos 103
ACTB1_TAKRU     antigenic       epitope 295     301     1.113   .       .
ID=ACTB1_TAKRU.8;note=*pos 296
ACTB1_TAKRU     antigenic       epitope 256     266     1.11    .       .
ID=ACTB1_TAKRU.9;note=*pos 264
ACTB1_TAKRU     antigenic       epitope 336     352     1.107   .       .
ID=ACTB1_TAKRU.10;note=*pos 347
ACTB1_TAKRU     antigenic       epitope 62      76      1.102   .       .
ID=ACTB1_TAKRU.11;note=*pos 68
ACTB1_TAKRU     antigenic       epitope 232     250     1.086   .       .
ID=ACTB1_TAKRU.12;note=*pos 245
ACTB1_TAKRU     antigenic       epitope 327     332     1.083   .       .
ID=ACTB1_TAKRU.13;note=*pos 330
ACTB1_TAKRU     antigenic       epitope 317     323     1.074   .       .
ID=ACTB1_TAKRU.14;note=*pos 320
ACTB1_TAKRU     antigenic       epitope 186     192     1.068   .       .
ID=ACTB1_TAKRU.15;note=*pos 191
ACTB1_TAKRU     antigenic       epitope 40      46      1.066   .       .
ID=ACTB1_TAKRU.16;note=*pos 43
ACTB1_TAKRU     antigenic       epitope 269     275     1.045   .       .
ID=ACTB1_TAKRU.17;note=*pos 269
ACTB1_TAKRU     antigenic       epitope 51      57      1.034   .       .
ID=ACTB1_TAKRU.18;note=*pos 52

Data files

   None.

Notes

   None.

References

   None.

Warnings

   None.

Diagnostic Error Messages

   None.

Exit status

   It always exits with status 0.

Known bugs

   None.

See also

   Program name     Description
   aligncopy        Read and write alignments
   aligncopypair    Read and write pairs from alignments
   biosed           Replace or delete sequence sections
   codcopy          Copy and reformat a codon usage table
   cutseq           Remove a section from a sequence
   degapseq         Remove non-alphabetic (e.g. gap) characters from sequences
   descseq          Alter the name or description of a sequence
   entret           Retrieve sequence entries from flatfile databases and files
   extractalign     Extract regions from a sequence alignment
   extractfeat      Extract features from sequence(s)
   extractseq       Extract regions from a sequence
   featcopy         Read and write a feature table
   featreport       Read and write a feature table
   feattext         Return a feature table original text
   listor           Write a list file of the logical OR of two sets of sequences
   makenucseq       Create random nucleotide sequences
   makeprotseq      Create random protein sequences
   maskambignuc     Mask all ambiguity characters in nucleotide sequences with
                    N
   maskambigprot    Mask all ambiguity characters in protein sequences with X
   maskfeat         Write a sequence with masked features
   maskseq          Write a sequence with masked regions
   newseq           Create a sequence file from a typed-in sequence
   nohtml           Remove mark-up (e.g. HTML tags) from an ASCII text file
   noreturn         Remove carriage return from ASCII files
   nospace          Remove whitespace from an ASCII text file
   notab            Replace tabs with spaces in an ASCII text file
   notseq           Write to file a subset of an input stream of sequences
   nthseq           Write to file a single sequence from an input stream of
                    sequences
   nthseqset        Read and write (return) one set of sequences from many
   pasteseq         Insert one sequence into another
   revseq           Reverse and complement a nucleotide sequence
   seqcount         Read and count sequences
   seqret           Read and write (return) sequences
   seqretsetall     Read and write (return) many sets of sequences
   seqretsplit      Read sequences and write them to individual files
   sizeseq          Sort sequences by size
   skipredundant    Remove redundant sequences from an input set
   skipseq          Read and write (return) sequences, skipping first few
   splitsource      Split sequence(s) into original source sequences
   splitter         Split sequence(s) into smaller sequences
   trimest          Remove poly-A tails from nucleotide sequences
   trimseq          Remove unwanted characters from start and end of sequence(s)
   trimspace        Remove extra whitespace from an ASCII text file
   union            Concatenate multiple sequences into a single sequence
   vectorstrip      Remove vectors from the ends of nucleotide sequence(s)
   yank             Add a sequence reference (a full USA) to a list file

Author(s)

   Peter Rice
   European Bioinformatics Institute, Wellcome Trust Genome Campus,
   Hinxton, Cambridge CB10 1SD, UK

   Please report all bugs to the EMBOSS bug team
   (emboss-bug (c) emboss.open-bio.org) not to the original author.

History

Target users

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

Comments

   None
