EMBOSS: featmerge manual

featmerge

Wiki

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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:6.6.0.0

   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 2013-07-15
#!Type Protein
#!Source-version EMBOSS 6.6.0.0
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 2013-07-15
#!Type Protein
#!Source-version EMBOSS 6.6.0.0
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.

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

History

Target users

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

Comments

None

Wiki

Function

Description

Algorithm

Usage

Command line arguments

Input file format

Input files for usage example

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

Database entry: tsw:actb1_takru

Output file format

Output files for usage example

File: actb1_takru.gff

Data files

Notes

References

Warnings

Diagnostic Error Messages

Exit status

Known bugs

See also

Author(s)

History

Target users

Comments