EMBOSS: featreport

| 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:6.5.6.0

       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
       -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

Qualifier | Type | Description | Allowed values | Default
--- | --- | --- | --- | ---
Standard (Mandatory) qualifiers
[-sequence] (Parameter 1) | sequence | Sequence filename and optional format, or reference (input USA) | Readable sequence | Required
[-features] (Parameter 2) | features | (no help text) features value | Readable feature table | Required
[-outfile] (Parameter 3) | report | Output report file name | (default -rformat gff) | <*>.featreport
Additional (Optional) qualifiers
(none)
Advanced (Unprompted) qualifiers
(none)
Associated qualifiers
"-sequence" associated sequence qualifiers
-sbegin1 -sbegin_sequence | integer | Start of the sequence to be used | Any integer value | 0
-send1 -send_sequence | integer | End of the sequence to be used | Any integer value | 0
-sreverse1 -sreverse_sequence | boolean | Reverse (if DNA) | Boolean value Yes/No | N
-sask1 -sask_sequence | boolean | Ask for begin/end/reverse | Boolean value Yes/No | N
-snucleotide1 -snucleotide_sequence | boolean | Sequence is nucleotide | Boolean value Yes/No | N
-sprotein1 -sprotein_sequence | boolean | Sequence is protein | Boolean value Yes/No | N
-slower1 -slower_sequence | boolean | Make lower case | Boolean value Yes/No | N
-supper1 -supper_sequence | boolean | Make upper case | Boolean value Yes/No | N
-scircular1 -scircular_sequence | boolean | Sequence is circular | Boolean value Yes/No | N
-sformat1 -sformat_sequence | string | Input sequence format | Any string |
-iquery1 -iquery_sequence | string | Input query fields or ID list | Any string |
-ioffset1 -ioffset_sequence | integer | Input start position offset | Any integer value | 0
-sdbname1 -sdbname_sequence | string | Database name | Any string |
-sid1 -sid_sequence | string | Entryname | Any string |
-ufo1 -ufo_sequence | string | UFO features | Any string |
-fformat1 -fformat_sequence | string | Features format | Any string |
-fopenfile1 -fopenfile_sequence | string | Features file name | Any string |
"-features" associated features qualifiers
-fformat2 -fformat_features | string | Features format | Any string |
-iquery2 -iquery_features | string | Input query fields or ID list | Any string |
-ioffset2 -ioffset_features | integer | Input start position offset | Any integer value | 0
-fopenfile2 -fopenfile_features | string | Features file name | Any string |
-fask2 -fask_features | boolean | Prompt for begin/end/reverse | Boolean value Yes/No | N
-fbegin2 -fbegin_features | integer | Start of the features to be used | Any integer value | 0
-fend2 -fend_features | integer | End of the features to be used | Any integer value | 0
-freverse2 -freverse_features | boolean | Reverse (if DNA) | Boolean value Yes/No | N
-fcircular2 -fcircular_features | boolean | Circular sequence features | Boolean value Yes/No | N
"-outfile" associated report qualifiers
-rformat3 -rformat_outfile | string | Report format | Any string | gff
-rname3 -rname_outfile | string | Base file name | Any string |
-rextension3 -rextension_outfile | string | File name extension | Any string |
-rdirectory3 -rdirectory_outfile | string | Output directory | Any string |
-raccshow3 -raccshow_outfile | boolean | Show accession number in the report | Boolean value Yes/No | N
-rdesshow3 -rdesshow_outfile | boolean | Show description in the report | Boolean value Yes/No | N
-rscoreshow3 -rscoreshow_outfile | boolean | Show the score in the report | Boolean value Yes/No | Y
-rstrandshow3 -rstrandshow_outfile | boolean | Show the nucleotide strand in the report | Boolean value Yes/No | Y
-rusashow3 -rusashow_outfile | boolean | Show the full USA in the report | Boolean value Yes/No | N
-rmaxall3 -rmaxall_outfile | integer | Maximum total hits to report | Any integer value | 0
-rmaxseq3 -rmaxseq_outfile | integer | Maximum hits to report for one sequence | Any integer value | 0
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

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" ; isolate "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" ; translation "MSANSLLGSLRELQVLVLNPPGEVSDALVLQLIRIGCSVRQCWPPPEAFDVPVDVVFTSIFQNGHHDEIAALLAAGTPRTTLVALVEYESPAVLSQIIELECHGVITQPLDAHRVLPVLVSARRISEEMAKLKQKTEQLQDRIAGQARINQAKVLLMQRHGWDEREAHQHLSREAMKRREPILKIAQELLGNEPSA"
    PAAMIR	EMBL	CDS	135	1292	0.000	+	.	Sequence "PAAMIR.3" ; db_xref "SWISS-PROT:P27017" ; note "negative regulator of amiR" ; transl_table 11 ; gene "amiC" ; protein_id "CAA32024.1" ; translation "MGSHQERPLIGLLFSETGVTADIERSHAYGALLAVEQLNREGGVGGRPIETLSQDPGGDPDRYRLCAEDFIRNRGVRFLVGCYMSHTRKAVMPVVERADALLCYPTPYEGFEYSPNIVYGGPAPNQNSAPLAAYLIRHYGERVVFIGSDYIYPRESNHVMRHLYRQHGGTVLEEIYIPLYPSDDDLQRAVERIYQARADVVFSTVVGTGTAELYRAIARRYGDGRRPPIASLTTSEAEVAKMESDVAEGQVVVAPYFSSIDTPASRAFVQACHGFFPENATITAWAEAAYWQTLLLGRAAQAAGNWRVEDVQRHLYDIDIDAPQGPVRVERQNNHSRLSSRIAEIDARGVFQVRWQSPEPIRPDPYVVVHNLDDWSASMGGGPLP"
    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" ; replace "" ; 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 constitutive 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 2012-07-15
    #!Type DNA
    #!Source-version EMBOSS 6.5.6.0
    PAAMIR	EMBL	databank_entry	1	2167	.	+	.	ID=PAAMIR.1;db_xref=taxon:287;organism=Pseudomonas aeruginosa;strain=PAC;isolate=PAC 1;map=38 min
    PAAMIR	EMBL	CDS	1289	1879	.	+	0	ID=PAAMIR.2;db_xref=SWISS-PROT:P10932;note=aliphatic amidase regulator%2C positive regulator of amiE;transl_table=11;gene=amiR;protein_id=CAA32023.1;translation=MSANSLLGSLRELQVLVLNPPGEVSDALVLQLIRIGCSVRQCWPPPEAFDVPVDVVFTSIFQNGHHDEIAALLAAGTPRTTLVALVEYESPAVLSQIIELECHGVITQPLDAHRVLPVLVSARRISEEMAKLKQKTEQLQDRIAGQARINQAKVLLMQRHGWDEREAHQHLSREAMKRREPILKIAQELLGNEPSA
    PAAMIR	EMBL	CDS	135	1292	.	+	0	ID=PAAMIR.3;db_xref=SWISS-PROT:P27017;note=negative regulator of amiR;transl_table=11;gene=amiC;protein_id=CAA32024.1;translation=MGSHQERPLIGLLFSETGVTADIERSHAYGALLAVEQLNREGGVGGRPIETLSQDPGGDPDRYRLCAEDFIRNRGVRFLVGCYMSHTRKAVMPVVERADALLCYPTPYEGFEYSPNIVYGGPAPNQNSAPLAAYLIRHYGERVVFIGSDYIYPRESNHVMRHLYRQHGGTVLEEIYIPLYPSDDDLQRAVERIYQARADVVFSTVVGTGTAELYRAIARRYGDGRRPPIASLTTSEAEVAKMESDVAEGQVVVAPYFSSIDTPASRAFVQACHGFFPENATITAWAEAAYWQTLLLGRAAQAAGNWRVEDVQRHLYDIDIDAPQGPVRVERQNNHSRLSSRIAEIDARGVFQVRWQSPEPIRPDPYVVVHNLDDWSASMGGGPLP
    PAAMIR	EMBL	promoter	8	24	.	+	.	ID=PAAMIR.4;note=proposed rpoN-dependent promoter
    PAAMIR	EMBL	promoter	65	81	.	+	.	ID=PAAMIR.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;replace=;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 constitutive 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 © 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