featcopy |
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% featcopy Reads and writes a feature table Input feature table: paamir.gff3 Features output [x13776.gff]: |
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Reads and writes a feature table Version: EMBOSS:6.4.0.0 Standard (Mandatory) qualifiers: [-features] features (no help text) features value [-outfeat] featout [unknown.gff] Output features UFO Additional (Optional) qualifiers: (none) Advanced (Unprompted) qualifiers: (none) Associated qualifiers: "-features" associated qualifiers -fformat1 string Features format -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) "-outfeat" associated qualifiers -offormat2 string Output feature format -ofopenfile2 string Features file name -ofextension2 string File name extension -ofdirectory2 string Output directory -ofname2 string Base file name -ofsingle2 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 | ||||
[-features] (Parameter 1) |
features | (no help text) features value | Readable feature table | Required |
[-outfeat] (Parameter 2) |
featout | Output features UFO | Writeable feature table | unknown.gff |
Additional (Optional) qualifiers | ||||
(none) | ||||
Advanced (Unprompted) qualifiers | ||||
(none) | ||||
Associated qualifiers | ||||
"-features" associated features qualifiers | ||||
-fformat1 -fformat_features |
string | Features format | Any string | |
-fopenfile1 -fopenfile_features |
string | Features file name | Any string | |
-fask1 -fask_features |
boolean | Prompt for begin/end/reverse | Boolean value Yes/No | N |
-fbegin1 -fbegin_features |
integer | Start of the features to be used | Any integer value | 0 |
-fend1 -fend_features |
integer | End of the features to be used | Any integer value | 0 |
-freverse1 -freverse_features |
boolean | Reverse (if DNA) | Boolean value Yes/No | N |
"-outfeat" associated featout qualifiers | ||||
-offormat2 -offormat_outfeat |
string | Output feature format | Any string | |
-ofopenfile2 -ofopenfile_outfeat |
string | Features file name | Any string | |
-ofextension2 -ofextension_outfeat |
string | File name extension | Any string | |
-ofdirectory2 -ofdirectory_outfeat |
string | Output directory | Any string | |
-ofname2 -ofname_outfeat |
string | Base file name | Any string | |
-ofsingle2 -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 |
##gff-version 3 ##sequence-region X13776 1 2167 #!Date 2011-05-24 #!Type DNA #!Source-version EMBOSS 6.4.0.0 X13776 EMBL databank_entry 1 2167 . + . ID=X13776.1;organism=Pseudomonas aeruginosa;map=38 min;strain=PAC;isolate=PAC 1;mol_type=genomic DNA;db_xref=taxon:287 X13776 EMBL CDS 1289 1879 . + 0 ID=X13776.2;transl_table=11;gene=amiR;note=aliphatic amidase regulator%2C positive regulator of amiE;db_xref=GOA:P10932;db_xref=InterPro:IPR005561;db_xref=InterPro:IPR008327;db_xref=InterPro:IPR011006;db_xref=InterPro:IPR011991;db_xref=PDB:1QO0;db_xref=UniProtKB/Swiss-Prot:P10932;protein_id=CAA32023.1;translation=MSANSLLGSLRELQVLVLNPPGEVSDALVLQLIRIGCSVRQCWPPPEAFDVPVDVVFTSIFQNGHHDEIAALLAAGTPRTTLVALVEYESPAVLSQIIELECHGVITQPLDAHRVLPVLVSARRISEEMAKLKQKTEQLQDRIAGQARINQAKVLLMQRHGWDEREAHQHLSREAMKRREPILKIAQELLGNEPSA X13776 EMBL CDS 135 1292 . + 0 ID=X13776.3;transl_table=11;gene=amiC;note=negative regulator of amiR;db_xref=GOA:P27017;db_xref=InterPro:IPR000709;db_xref=PDB:1PEA;db_xref=PDB:1QNL;db_xref=PDB:1QO0;db_xref=UniProtKB/Swiss-Prot:P27017;protein_id=CAA32024.1;translation=MGSHQERPLIGLLFSETGVTADIERSHAYGALLAVEQLNREGGVGGRPIETLSQDPGGDPDRYRLCAEDFIRNRGVRFLVGCYMSHTRKAVMPVVERADALLCYPTPYEGFEYSPNIVYGGPAPNQNSAPLAAYLIRHYGERVVFIGSDYIYPRESNHVMRHLYRQHGGTVLEEIYIPLYPSDDDLQRAVERIYQARADVVFSTVVGTGTAELYRAIARRYGDGRRPPIASLTTSEAEVAKMESDVAEGQVVVAPYFSSIDTPASRAFVQACHGFFPENATITAWAEAAYWQTLLLGRAAQAAGNWRVEDVQRHLYDIDIDAPQGPVRVERQNNHSRLSSRIAEIDARGVFQVRWQSPEPIRPDPYVVVHNLDDWSASMGGGPLP X13776 EMBL promoter 8 24 . + . ID=X13776.4;note=proposed rpoN-dependent promoter X13776 EMBL promoter 65 81 . + . ID=X13776.5;note=proposed rpoN-dependent promoter X13776 EMBL ribosome_entry_site 121 126 . + . ID=X13776.6;note=proposed Shine-Dalgarno sequence X13776 EMBL sequence_variant 912 1167 . + . ID=X13776.7;gene=amiC;replace=;note=ClaI fragment deleted in pSW36%2C constitutive phenotype X13776 EMBL sequence_feature 1 1 . + . ID=X13776.8;note=last base of an XhoI site X13776 EMBL sequence_feature 648 653 . + . ID=X13776.9;note=end of 658bp XhoI fragment%2C deletion in pSW3 causes constitutive expression of amiE X13776 EMBL sequence_conflict 1281 1281 . + . ID=X13776.10;replace=g;citation=[3] |
##gff-version 3 ##sequence-region X13776 1 2167 #!Date 2011-07-15 #!Type DNA #!Source-version EMBOSS 6.4.0.0 X13776 EMBL databank_entry 1 2167 . + . ID=X13776.1;organism=Pseudomonas aeruginosa;map=38 min;strain=PAC;isolate=PAC 1;mol_type=genomic DNA;db_xref=taxon:287 X13776 EMBL CDS 1289 1879 . + 0 ID=X13776.2;transl_table=11;gene=amiR;note=aliphatic amidase regulator%2C positive regulator of amiE;db_xref=GOA:P10932;db_xref=InterPro:IPR005561;db_xref=InterPro:IPR008327;db_xref=InterPro:IPR011006;db_xref=InterPro:IPR011991;db_xref=PDB:1QO0;db_xref=UniProtKB/Swiss-Prot:P10932;protein_id=CAA32023.1;translation=MSANSLLGSLRELQVLVLNPPGEVSDALVLQLIRIGCSVRQCWPPPEAFDVPVDVVFTSIFQNGHHDEIAALLAAGTPRTTLVALVEYESPAVLSQIIELECHGVITQPLDAHRVLPVLVSARRISEEMAKLKQKTEQLQDRIAGQARINQAKVLLMQRHGWDEREAHQHLSREAMKRREPILKIAQELLGNEPSA X13776 EMBL CDS 135 1292 . + 0 ID=X13776.3;transl_table=11;gene=amiC;note=negative regulator of amiR;db_xref=GOA:P27017;db_xref=InterPro:IPR000709;db_xref=PDB:1PEA;db_xref=PDB:1QNL;db_xref=PDB:1QO0;db_xref=UniProtKB/Swiss-Prot:P27017;protein_id=CAA32024.1;translation=MGSHQERPLIGLLFSETGVTADIERSHAYGALLAVEQLNREGGVGGRPIETLSQDPGGDPDRYRLCAEDFIRNRGVRFLVGCYMSHTRKAVMPVVERADALLCYPTPYEGFEYSPNIVYGGPAPNQNSAPLAAYLIRHYGERVVFIGSDYIYPRESNHVMRHLYRQHGGTVLEEIYIPLYPSDDDLQRAVERIYQARADVVFSTVVGTGTAELYRAIARRYGDGRRPPIASLTTSEAEVAKMESDVAEGQVVVAPYFSSIDTPASRAFVQACHGFFPENATITAWAEAAYWQTLLLGRAAQAAGNWRVEDVQRHLYDIDIDAPQGPVRVERQNNHSRLSSRIAEIDARGVFQVRWQSPEPIRPDPYVVVHNLDDWSASMGGGPLP X13776 EMBL promoter 8 24 . + . ID=X13776.4;note=proposed rpoN-dependent promoter X13776 EMBL promoter 65 81 . + . ID=X13776.5;note=proposed rpoN-dependent promoter X13776 EMBL ribosome_entry_site 121 126 . + . ID=X13776.6;note=proposed Shine-Dalgarno sequence X13776 EMBL sequence_variant 912 1167 . + . ID=X13776.7;gene=amiC;replace=;note=ClaI fragment deleted in pSW36%2C constitutive phenotype X13776 EMBL sequence_feature 1 1 . + . ID=X13776.8;note=last base of an XhoI site X13776 EMBL sequence_feature 648 653 . + . ID=X13776.9;note=end of 658bp XhoI fragment%2C deletion in pSW3 causes constitutive expression of amiE X13776 EMBL sequence_conflict 1281 1281 . + . ID=X13776.10;replace=g;citation=[3] |
Program name | Description |
---|---|
aligncopy | Reads and writes alignments |
aligncopypair | Reads and writes pairs from alignments |
biosed | Replace or delete sequence sections |
codcopy | Copy and reformat a codon usage table |
cutseq | Removes a section from a sequence |
degapseq | Removes non-alphabetic (e.g. gap) characters from sequences |
descseq | Alter the name or description of a sequence |
entret | Retrieves 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 |
featreport | Reads and writes 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 | Masks all ambiguity characters in nucleotide sequences with N |
maskambigprot | Masks 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 | Reads and writes (returns) one set of sequences from many |
pasteseq | Insert one sequence into another |
revseq | Reverse and complement a nucleotide sequence |
seqcount | Reads and counts sequences |
seqret | Reads and writes (returns) sequences |
seqretsetall | Reads and writes (returns) many sets of sequences |
seqretsplit | Reads sequences and writes them to individual files |
sizeseq | Sort sequences by size |
skipredundant | Remove redundant sequences from an input set |
skipseq | Reads and writes (returns) 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 | Removes 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.