
                                featreport 



Function

   Reads and writes 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 
Reads and writes a feature table
Input sequence: paamir.fasta
Input features: 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

   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

   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
   -sformat1           string     Input sequence format
   -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
   -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)

   "-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. 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

Input file format

   featreport reads any normal sequence USAs and features UFOs.

  Input files for usage example

  File: paamir.fasta

>X13776 X13776.1 Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidas
e 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 "PAAMI
R.1" ; db_xref "taxon:287" ; organism "Pseudomonas aeruginosa" ; strain "PAC" ;
 isolate "PAC 1" ; map "38 min"
PAAMIR  EMBL    CDS     1289    1879    0.000   +       .       Sequence "PAAMI
R.2" ; db_xref "SWISS-PROT:P10932" ; note "aliphatic amidase regulator, positiv
e regulator of amiE" ; transl_table 11 ; gene "amiR" ; protein_id "CAA32023.1"
; translation "MSANSLLGSLRELQVLVLNPPGEVSDALVLQLIRIGCSVRQCWPPPEAFDVPVDVVFTSIFQNG
HHDEIAALLAAGTPRTTLVALVEYESPAVLSQIIELECHGVITQPLDAHRVLPVLVSARRISEEMAKLKQKTEQLQDRI
AGQARINQAKVLLMQRHGWDEREAHQHLSREAMKRREPILKIAQELLGNEPSA"
PAAMIR  EMBL    CDS     135     1292    0.000   +       .       Sequence "PAAMI
R.3" ; db_xref "SWISS-PROT:P27017" ; note "negative regulator of amiR" ; transl
_table 11 ; gene "amiC" ; protein_id "CAA32024.1" ; translation "MGSHQERPLIGLLF
SETGVTADIERSHAYGALLAVEQLNREGGVGGRPIETLSQDPGGDPDRYRLCAEDFIRNRGVRFLVGCYMSHTRKAVMP
VVERADALLCYPTPYEGFEYSPNIVYGGPAPNQNSAPLAAYLIRHYGERVVFIGSDYIYPRESNHVMRHLYRQHGGTVL
EEIYIPLYPSDDDLQRAVERIYQARADVVFSTVVGTGTAELYRAIARRYGDGRRPPIASLTTSEAEVAKMESDVAEGQV
VVAPYFSSIDTPASRAFVQACHGFFPENATITAWAEAAYWQTLLLGRAAQAAGNWRVEDVQRHLYDIDIDAPQGPVRVE
RQNNHSRLSSRIAEIDARGVFQVRWQSPEPIRPDPYVVVHNLDDWSASMGGGPLP"
PAAMIR  EMBL    promoter        8       24      0.000   +       .       Sequenc
e "PAAMIR.4" ; note "proposed rpoN-dependent promoter"
PAAMIR  EMBL    promoter        65      81      0.000   +       .       Sequenc
e "PAAMIR.5" ; note "proposed rpoN-dependent promoter"
PAAMIR  EMBL    RBS     121     126     0.000   +       .       Sequence "PAAMI
R.6" ; note "proposed Shine-Dalgarno sequence"
PAAMIR  EMBL    variation       912     1167    0.000   +       .       Sequenc
e "PAAMIR.7" ; note "ClaI fragment deleted in pSW36, constitutive phenotype" ;
replace "" ; gene "amiC"
PAAMIR  EMBL    misc_feature    1       1       0.000   +       .       Sequenc
e "PAAMIR.8" ; FeatFlags "0x40" ; note "last base of an XhoI site"
PAAMIR  EMBL    misc_feature    648     653     0.000   +       .       Sequenc
e "PAAMIR.9" ; note "end of 658bp XhoI fragment, deletion in pSW3 causes consti
tutive expression of amiE"
PAAMIR  EMBL    conflict        1281    1281    0.000   +       .       Sequenc
e "PAAMIR.10" ; FeatFlags "0x40" ; replace "g" ; citation [3]

Output file format

   featreport outputs a report format file.

  Output files for usage example

  File: test.out

##gff-version 3
##sequence-region PAAMIR 1 2167
#!Date 2008-07-15
#!Type DNA
#!Source-version EMBOSS 6.0.0
PAAMIR  EMBL    databank_entry  1       2167    0.000   +       .       ID="PAA
MIR.1";db_xref="taxon:287";organism="Pseudomonas aeruginosa";strain="PAC";isola
te="PAC 1";map="38 min"
PAAMIR  EMBL    CDS     1289    1879    0.000   +       0       ID="PAAMIR.2";d
b_xref="SWISS-PROT:P10932";note="aliphatic amidase regulator, positive regulato
r of amiE";transl_table=11;gene="amiR";protein_id="CAA32023.1";translation="MSA
NSLLGSLRELQVLVLNPPGEVSDALVLQLIRIGCSVRQCWPPPEAFDVPVDVVFTSIFQNGHHDEIAALLAAGTPRTTL
VALVEYESPAVLSQIIELECHGVITQPLDAHRVLPVLVSARRISEEMAKLKQKTEQLQDRIAGQARINQAKVLLMQRHG
WDEREAHQHLSREAMKRREPILKIAQELLGNEPSA"
PAAMIR  EMBL    CDS     135     1292    0.000   +       0       ID="PAAMIR.3";d
b_xref="SWISS-PROT:P27017";note="negative regulator of amiR";transl_table=11;ge
ne="amiC";protein_id="CAA32024.1";translation="MGSHQERPLIGLLFSETGVTADIERSHAYGAL
LAVEQLNREGGVGGRPIETLSQDPGGDPDRYRLCAEDFIRNRGVRFLVGCYMSHTRKAVMPVVERADALLCYPTPYEGF
EYSPNIVYGGPAPNQNSAPLAAYLIRHYGERVVFIGSDYIYPRESNHVMRHLYRQHGGTVLEEIYIPLYPSDDDLQRAV
ERIYQARADVVFSTVVGTGTAELYRAIARRYGDGRRPPIASLTTSEAEVAKMESDVAEGQVVVAPYFSSIDTPASRAFV
QACHGFFPENATITAWAEAAYWQTLLLGRAAQAAGNWRVEDVQRHLYDIDIDAPQGPVRVERQNNHSRLSSRIAEIDAR
GVFQVRWQSPEPIRPDPYVVVHNLDDWSASMGGGPLP"
PAAMIR  EMBL    promoter        8       24      0.000   +       .       ID="PAA
MIR.4";note="proposed rpoN-dependent promoter"
PAAMIR  EMBL    promoter        65      81      0.000   +       .       ID="PAA
MIR.5";note="proposed rpoN-dependent promoter"
PAAMIR  EMBL    ribosome_entry_site     121     126     0.000   +       .
ID="PAAMIR.6";note="proposed Shine-Dalgarno sequence"
PAAMIR  EMBL    sequence_variant        912     1167    0.000   +       .
ID="PAAMIR.7";note="ClaI fragment deleted in pSW36, constitutive phenotype";rep
lace="";gene="amiC"
PAAMIR  EMBL    located_sequence_feature        1       1       0.000   +
.       ID="PAAMIR.8";featflags="0x40";note="last base of an XhoI site"
PAAMIR  EMBL    located_sequence_feature        648     653     0.000   +
.       ID="PAAMIR.9";note="end of 658bp XhoI fragment, deletion in pSW3 causes
 constitutive expression of amiE"
PAAMIR  EMBL    sequence_conflict       1281    1281    0.000   +       .
ID="PAAMIR.10";featflags="0x40";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 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
   featcopy Reads and writes a feature table
   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 all 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
   pasteseq Insert one sequence into another
   revseq Reverse and complement a nucleotide sequence
   seqret Reads and writes (returns) 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
   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

Author(s)

   Peter Rice (pmr © ebi.ac.uk)
   Informatics Division, 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
