featmerge |
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% 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]: |
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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 |
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.
##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 |
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 // |
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.
##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 |
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 |
Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.