EMBOSS: featmerge

| featmerge

## Wiki

The master copies of EMBOSS documentation are available at http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki.

Please help by correcting and extending the Wiki pages.

## 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

Qualifier | Type | Description | Allowed values | Default
--- | --- | --- | --- | ---
Standard (Mandatory) qualifiers
[-afeatures] (Parameter 1) | features | (no help text) features value | Readable feature table | Required
[-bfeatures] (Parameter 2) | features | (no help text) features value | Readable feature table | Required
[-outfeat] (Parameter 3) | featout | Output features UFO | Writeable feature table | unknown.gff
Additional (Optional) qualifiers
(none)
Advanced (Unprompted) qualifiers
(none)
Associated qualifiers
"-afeatures" associated features qualifiers
-fformat1 -fformat_afeatures | string | Features format | Any string |
-iquery1 -iquery_afeatures | string | Input query fields or ID list | Any string |
-ioffset1 -ioffset_afeatures | integer | Input start position offset | Any integer value | 0
-fopenfile1 -fopenfile_afeatures | string | Features file name | Any string |
-fask1 -fask_afeatures | boolean | Prompt for begin/end/reverse | Boolean value Yes/No | N
-fbegin1 -fbegin_afeatures | integer | Start of the features to be used | Any integer value | 0
-fend1 -fend_afeatures | integer | End of the features to be used | Any integer value | 0
-freverse1 -freverse_afeatures | boolean | Reverse (if DNA) | Boolean value Yes/No | N
-fcircular1 -fcircular_afeatures | boolean | Circular sequence features | Boolean value Yes/No | N
"-bfeatures" associated features qualifiers
-fformat2 -fformat_bfeatures | string | Features format | Any string |
-iquery2 -iquery_bfeatures | string | Input query fields or ID list | Any string |
-ioffset2 -ioffset_bfeatures | integer | Input start position offset | Any integer value | 0
-fopenfile2 -fopenfile_bfeatures | string | Features file name | Any string |
-fask2 -fask_bfeatures | boolean | Prompt for begin/end/reverse | Boolean value Yes/No | N
-fbegin2 -fbegin_bfeatures | integer | Start of the features to be used | Any integer value | 0
-fend2 -fend_bfeatures | integer | End of the features to be used | Any integer value | 0
-freverse2 -freverse_bfeatures | boolean | Reverse (if DNA) | Boolean value Yes/No | N
-fcircular2 -fcircular_bfeatures | boolean | Circular sequence features | Boolean value Yes/No | N
"-outfeat" associated featout qualifiers
-offormat3 -offormat_outfeat | string | Output feature format | Any string |
-ofopenfile3 -ofopenfile_outfeat | string | Features file name | Any string |
-ofextension3 -ofextension_outfeat | string | File name extension | Any string |
-ofdirectory3 -ofdirectory_outfeat | string | Output directory | Any string |
-ofname3 -ofname_outfeat | string | Base file name | Any string |
-ofsingle3 -ofsingle_outfeat | boolean | Separate file for each entry | Boolean value Yes/No | N
General qualifiers
-auto | boolean | Turn off prompts | Boolean value Yes/No | N
-stdout | boolean | Write first file to standard output | Boolean value Yes/No | N
-filter | boolean | Read first file from standard input, write first file to standard output | Boolean value Yes/No | N
-options | boolean | Prompt for standard and additional values | Boolean value Yes/No | N
-debug | boolean | Write debug output to program.dbg | Boolean value Yes/No | N
-verbose | boolean | Report some/full command line options | Boolean value Yes/No | Y
-help | boolean | Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose | Boolean value Yes/No | N
-warning | boolean | Report warnings | Boolean value Yes/No | Y
-error | boolean | Report errors | Boolean value Yes/No | Y
-fatal | boolean | Report fatal errors | Boolean value Yes/No | Y
-die | boolean | Report dying program messages | Boolean value Yes/No | Y
-version | boolean | Report version number and exit | Boolean value Yes/No | N

## 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 similarity
    ACTB1_TAKRU	SWISSPROT	mature_protein_region	2	375	.	.	.	ID=ACTB1_TAKRU.3;note=Actin%2C cytoplasmic 1%2C N-terminally processed;ftid=PRO_0000000809
    ACTB1_TAKRU	SWISSPROT	post_translationally_modified_region	1	1	.	.	.	ID=ACTB1_TAKRU.4;note=N-acetylmethionine%3B in Actin%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 Actin%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;comment=By similarity
    ACTB1_TAKRU	SWISSPROT	post_translationally_modified_region	73	73	.	.	.	ID=ACTB1_TAKRU.7;note=Tele-methylhistidine;comment=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 © 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