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featreport
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
Read and write a feature table
Description
featreport reads a sequence and a feature table and writes a standard
report output.
Usage
Here is a sample session with featreport
% featreport
Read and write a feature table
Input sequence: paamir.fasta
Input feature table: paamir.gff
Output report [x13776.featreport]: test.out
Go to the input files for this example
Go to the output files for this example
Command line arguments
Read and write a feature table
Version: EMBOSS:6.6.0.0
Standard (Mandatory) qualifiers:
[-sequence] sequence Sequence filename and optional format, or
reference (input USA)
[-features] features (no help text) features value
[-outfile] report [*.featreport] Output report file name
(default -rformat gff)
Additional (Optional) qualifiers: (none)
Advanced (Unprompted) qualifiers: (none)
Associated qualifiers:
"-sequence" associated qualifiers
-sbegin1 integer Start of the sequence to be used
-send1 integer End of the sequence to be used
-sreverse1 boolean Reverse (if DNA)
-sask1 boolean Ask for begin/end/reverse
-snucleotide1 boolean Sequence is nucleotide
-sprotein1 boolean Sequence is protein
-slower1 boolean Make lower case
-supper1 boolean Make upper case
-scircular1 boolean Sequence is circular
-squick1 boolean Read id and sequence only
-sformat1 string Input sequence format
-iquery1 string Input query fields or ID list
-ioffset1 integer Input start position offset
-sdbname1 string Database name
-sid1 string Entryname
-ufo1 string UFO features
-fformat1 string Features format
-fopenfile1 string Features file name
"-features" 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
"-outfile" associated qualifiers
-rformat3 string Report format
-rname3 string Base file name
-rextension3 string File name extension
-rdirectory3 string Output directory
-raccshow3 boolean Show accession number in the report
-rdesshow3 boolean Show description in the report
-rscoreshow3 boolean Show the score in the report
-rstrandshow3 boolean Show the nucleotide strand in the report
-rusashow3 boolean Show the full USA in the report
-rmaxall3 integer Maximum total hits to report
-rmaxseq3 integer Maximum hits to report for one sequence
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
featreport reads any nucleotide or protein sequences with features.
The input is a standard EMBOSS sequence query (also known as a 'USA')
with associated feature information.
Major sequence database sources defined as standard in EMBOSS
installations include srs:embl, srs:uniprot and ensembl
Data can also be read from sequence output in any supported format
written by an EMBOSS or third-party application.
The input format can be specified by using the command-line qualifier
-sformat xxx, where 'xxx' is replaced by the name of the required
format. The available format names are: text, html, xml (uniprotxml),
obo, embl (swissprot)
Where the sequence format has no feature information, a second file can
be read to load the feature data. The file is specified with the
qualifier -ufo xxx and the feature format is specified with the
qualifier -fformat xxx
See: http://emboss.sf.net/docs/themes/SequenceFormats.html for further
information on sequence formats.
See: http://emboss.sf.net/docs/themes/FeatureFormats.html for further
information on feature formats.
Input files for usage example
File: paamir.fasta
>X13776 X13776.1 Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase
regulation
ggtaccgctggccgagcatctgctcgatcaccaccagccgggcgacgggaactgcacgat
ctacctggcgagcctggagcacgagcgggttcgcttcgtacggcgctgagcgacagtcac
aggagaggaaacggatgggatcgcaccaggagcggccgctgatcggcctgctgttctccg
aaaccggcgtcaccgccgatatcgagcgctcgcacgcgtatggcgcattgctcgcggtcg
agcaactgaaccgcgagggcggcgtcggcggtcgcccgatcgaaacgctgtcccaggacc
ccggcggcgacccggaccgctatcggctgtgcgccgaggacttcattcgcaaccgggggg
tacggttcctcgtgggctgctacatgtcgcacacgcgcaaggcggtgatgccggtggtcg
agcgcgccgacgcgctgctctgctacccgaccccctacgagggcttcgagtattcgccga
acatcgtctacggcggtccggcgccgaaccagaacagtgcgccgctggcggcgtacctga
ttcgccactacggcgagcgggtggtgttcatcggctcggactacatctatccgcgggaaa
gcaaccatgtgatgcgccacctgtatcgccagcacggcggcacggtgctcgaggaaatct
acattccgctgtatccctccgacgacgacttgcagcgcgccgtcgagcgcatctaccagg
cgcgcgccgacgtggtcttctccaccgtggtgggcaccggcaccgccgagctgtatcgcg
ccatcgcccgtcgctacggcgacggcaggcggccgccgatcgccagcctgaccaccagcg
aggcggaggtggcgaagatggagagtgacgtggcagaggggcaggtggtggtcgcgcctt
acttctccagcatcgatacgcccgccagccgggccttcgtccaggcctgccatggtttct
tcccggagaacgcgaccatcaccgcctgggccgaggcggcctactggcagaccttgttgc
tcggccgcgccgcgcaggccgcaggcaactggcgggtggaagacgtgcagcggcacctgt
acgacatcgacatcgacgcgccacaggggccggtccgggtggagcgccagaacaaccaca
gccgcctgtcttcgcgcatcgcggaaatcgatgcgcgcggcgtgttccaggtccgctggc
agtcgcccgaaccgattcgccccgacccttatgtcgtcgtgcataacctcgacgactggt
ccgccagcatgggcgggggaccgctcccatgagcgccaactcgctgctcggcagcctgcg
cgagttgcaggtgctggtcctcaacccgccgggggaggtcagcgacgccctggtcttgca
gctgatccgcatcggttgttcggtgcgccagtgctggccgccgccggaagccttcgacgt
gccggtggacgtggtcttcaccagcattttccagaatggccaccacgacgagatcgctgc
gctgctcgccgccgggactccgcgcactaccctggtggcgctggtggagtacgaaagccc
cgcggtgctctcgcagatcatcgagctggagtgccacggcgtgatcacccagccgctcga
tgcccaccgggtgctgcctgtgctggtatcggcgcggcgcatcagcgaggaaatggcgaa
gctgaagcagaagaccgagcagctccaggaccgcatcgccggccaggcccggatcaacca
ggccaaggtgttgctgatgcagcgccatggctgggacgagcgcgaggcgcaccagcacct
gtcgcgggaagcgatgaagcggcgcgagccgatcctgaagatcgctcaggagttgctggg
aaacgagccgtccgcctgagcgatccgggccgaccagaacaataacaagaggggtatcgt
catcatgctgggactggttctgctgtacgttggcgcggtgctgtttctcaatgccgtctg
gttgctgggcaagatcagcggtcgggaggtggcggtgatcaacttcctggtcggcgtgct
gagcgcctgcgtcgcgttctacctgatcttttccgcagcagccgggcagggctcgctgaa
ggccggagcgctgaccctgctattcgcttttacctatctgtgggtggccgccaaccagtt
cctcgag
File: paamir.gff
##gff-version 2.0
##date 2003-02-14
##Type DNA PAAMIR
PAAMIR EMBL source 1 2167 0.000 + . Sequence "PAAMIR
.1" ; db_xref "taxon:287" ; organism "Pseudomonas aeruginosa" ; strain "PAC" ; i
solate "PAC 1" ; map "38 min"
PAAMIR EMBL CDS 1289 1879 0.000 + . Sequence "PAAMIR
.2" ; db_xref "SWISS-PROT:P10932" ; note "aliphatic amidase regulator, positive
regulator of amiE" ; transl_table 11 ; gene "amiR" ; protein_id "CAA32023.1" ; t
ranslation "MSANSLLGSLRELQVLVLNPPGEVSDALVLQLIRIGCSVRQCWPPPEAFDVPVDVVFTSIFQNGHHDE
IAALLAAGTPRTTLVALVEYESPAVLSQIIELECHGVITQPLDAHRVLPVLVSARRISEEMAKLKQKTEQLQDRIAGQAR
INQAKVLLMQRHGWDEREAHQHLSREAMKRREPILKIAQELLGNEPSA"
PAAMIR EMBL CDS 135 1292 0.000 + . Sequence "PAAMIR
.3" ; db_xref "SWISS-PROT:P27017" ; note "negative regulator of amiR" ; transl_t
able 11 ; gene "amiC" ; protein_id "CAA32024.1" ; translation "MGSHQERPLIGLLFSET
GVTADIERSHAYGALLAVEQLNREGGVGGRPIETLSQDPGGDPDRYRLCAEDFIRNRGVRFLVGCYMSHTRKAVMPVVER
ADALLCYPTPYEGFEYSPNIVYGGPAPNQNSAPLAAYLIRHYGERVVFIGSDYIYPRESNHVMRHLYRQHGGTVLEEIYI
PLYPSDDDLQRAVERIYQARADVVFSTVVGTGTAELYRAIARRYGDGRRPPIASLTTSEAEVAKMESDVAEGQVVVAPYF
SSIDTPASRAFVQACHGFFPENATITAWAEAAYWQTLLLGRAAQAAGNWRVEDVQRHLYDIDIDAPQGPVRVERQNNHSR
LSSRIAEIDARGVFQVRWQSPEPIRPDPYVVVHNLDDWSASMGGGPLP"
PAAMIR EMBL promoter 8 24 0.000 + . Sequence
"PAAMIR.4" ; note "proposed rpoN-dependent promoter"
PAAMIR EMBL promoter 65 81 0.000 + . Sequence
"PAAMIR.5" ; note "proposed rpoN-dependent promoter"
PAAMIR EMBL RBS 121 126 0.000 + . Sequence "PAAMIR
.6" ; note "proposed Shine-Dalgarno sequence"
PAAMIR EMBL variation 912 1167 0.000 + . Sequence
"PAAMIR.7" ; note "ClaI fragment deleted in pSW36, constitutive phenotype" ; re
place "" ; gene "amiC"
PAAMIR EMBL misc_feature 1 1 0.000 + . Sequence
"PAAMIR.8" ; FeatFlags "0x40" ; note "last base of an XhoI site"
PAAMIR EMBL misc_feature 648 653 0.000 + . Sequence
"PAAMIR.9" ; note "end of 658bp XhoI fragment, deletion in pSW3 causes constitu
tive expression of amiE"
PAAMIR EMBL conflict 1281 1281 0.000 + . Sequence
"PAAMIR.10" ; FeatFlags "0x40" ; replace "g" ; citation [3]
Output file format
The output is a standard EMBOSS report file.
The results can be output in one of several styles by using the
command-line qualifier -rformat xxx, where 'xxx' is replaced by the
name of the required format. The available format names are: embl,
genbank, gff, pir, swiss, dasgff, debug, listfile, dbmotif, diffseq,
draw, restrict, excel, feattable, motif, nametable, regions, seqtable,
simple, srs, table, tagseq.
See: http://emboss.sf.net/docs/themes/ReportFormats.html for further
information on report formats.
By default the report is in 'gff' feature format.
Output files for usage example
File: test.out
##gff-version 3
##sequence-region PAAMIR 1 2167
#!Date 2013-07-15
#!Type DNA
#!Source-version EMBOSS 6.6.0.0
PAAMIR EMBL databank_entry 1 2167 . + . ID=PAAMI
R.1;db_xref=taxon:287;organism=Pseudomonas aeruginosa;strain=PAC;isolate=PAC 1;m
ap=38 min
PAAMIR EMBL CDS 1289 1879 . + 0 ID=PAAMIR.2;db_x
ref=SWISS-PROT:P10932;note=aliphatic amidase regulator%2C positive regulator of
amiE;transl_table=11;gene=amiR;protein_id=CAA32023.1;translation=MSANSLLGSLRELQV
LVLNPPGEVSDALVLQLIRIGCSVRQCWPPPEAFDVPVDVVFTSIFQNGHHDEIAALLAAGTPRTTLVALVEYESPAVLS
QIIELECHGVITQPLDAHRVLPVLVSARRISEEMAKLKQKTEQLQDRIAGQARINQAKVLLMQRHGWDEREAHQHLSREA
MKRREPILKIAQELLGNEPSA
PAAMIR EMBL CDS 135 1292 . + 0 ID=PAAMIR.3;db_x
ref=SWISS-PROT:P27017;note=negative regulator of amiR;transl_table=11;gene=amiC;
protein_id=CAA32024.1;translation=MGSHQERPLIGLLFSETGVTADIERSHAYGALLAVEQLNREGGVGG
RPIETLSQDPGGDPDRYRLCAEDFIRNRGVRFLVGCYMSHTRKAVMPVVERADALLCYPTPYEGFEYSPNIVYGGPAPNQ
NSAPLAAYLIRHYGERVVFIGSDYIYPRESNHVMRHLYRQHGGTVLEEIYIPLYPSDDDLQRAVERIYQARADVVFSTVV
GTGTAELYRAIARRYGDGRRPPIASLTTSEAEVAKMESDVAEGQVVVAPYFSSIDTPASRAFVQACHGFFPENATITAWA
EAAYWQTLLLGRAAQAAGNWRVEDVQRHLYDIDIDAPQGPVRVERQNNHSRLSSRIAEIDARGVFQVRWQSPEPIRPDPY
VVVHNLDDWSASMGGGPLP
PAAMIR EMBL promoter 8 24 . + . ID=PAAMI
R.4;note=proposed rpoN-dependent promoter
PAAMIR EMBL promoter 65 81 . + . ID=PAAMI
R.5;note=proposed rpoN-dependent promoter
PAAMIR EMBL ribosome_entry_site 121 126 . + .
ID=PAAMIR.6;note=proposed Shine-Dalgarno sequence
PAAMIR EMBL sequence_variant 912 1167 . + .
ID=PAAMIR.7;note=ClaI fragment deleted in pSW36%2C constitutive phenotype;replac
e=;gene=amiC
PAAMIR EMBL sequence_feature 1 1 . + .
ID=PAAMIR.8;note=last base of an XhoI site
PAAMIR EMBL sequence_feature 648 653 . + .
ID=PAAMIR.9;note=end of 658bp XhoI fragment%2C deletion in pSW3 causes constitut
ive expression of amiE
PAAMIR EMBL sequence_conflict 1281 1281 . + .
ID=PAAMIR.10;replace=g;citation=[3]
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
featmerge Merge two overlapping feature tables
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
|
