                                   cutseq



Wiki

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   http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki.

   Please help by correcting and extending the Wiki pages.

Function

   Remove a section from a sequence

Description

   This simple editing program allows you to cut out a region from your
   sequence by specifying the begin and end positions of the region to
   remove. It removes the sequence from the specified start to the end
   positions (inclusive) and writes the remaining sequence to the output
   file.

Usage

   Here is a sample session with cutseq

   To remove bases 10 to 12 from a database entry and write to the new
   sequence file 'gatta2.seq':


% cutseq tembl:x13776 gatta2.seq -from=10 -to=12
Remove a section from a sequence


   Go to the input files for this example
   Go to the output files for this example

   Example 2

   To remove the first 20 bases from 'tembl:x13776' and write it to
   'jsh.seq':


% cutseq tembl:x13776 -from=1 -to=20 -out=jsh.seq
Remove a section from a sequence


   Go to the output files for this example

   Example 3

   If the default start and end positions are accepted, then all of the
   sequence is removed!


% cutseq tembl:x13776 starta.seq -sbeg=-1000 -send=1290
Remove a section from a sequence
Start of region to delete [1168]:
End of region to delete [1290]:


   Go to the output files for this example

Command line arguments

Remove a section from a sequence
Version: EMBOSS:6.5.6.0

   Standard (Mandatory) qualifiers:
  [-sequence]          sequence   (Gapped) sequence filename and optional
                                  format, or reference (input USA)
   -from               integer    [Start of sequence (0)] This is the start
                                  position (inclusive) of the section of the
                                  sequence that you wish to remove. (Any
                                  integer value)
   -to                 integer    [End of sequence (0)] This is the end
                                  position (inclusive) of the section of the
                                  sequence that you wish to remove. (Any
                                  integer value)
  [-outseq]            seqout     [.] Sequence filename and
                                  optional format (output USA)

   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

   "-outseq" associated qualifiers
   -osformat2          string     Output seq format
   -osextension2       string     File name extension
   -osname2            string     Base file name
   -osdirectory2       string     Output directory
   -osdbname2          string     Database name to add
   -ossingle2          boolean    Separate file for each entry
   -oufo2              string     UFO features
   -offormat2          string     Features format
   -ofname2            string     Features file name
   -ofdirectory2       string     Output directory

   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

   cutseq reads a single nucleotide or protein sequence.

   The input is a standard EMBOSS sequence query (also known as a 'USA').

   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: 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/SequenceFormats.html for further
   information on sequence formats.

  Input files for usage example

   'tembl:x13776' is a sequence entry in the example nucleic acid database
   'tembl'

  Database entry: tembl:x13776

ID   X13776; SV 1; linear; genomic DNA; STD; PRO; 2167 BP.
XX
AC   X13776; M43175;
XX
DT   19-APR-1989 (Rel. 19, Created)
DT   14-NOV-2006 (Rel. 89, Last updated, Version 24)
XX
DE   Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase regulation
XX
KW   aliphatic amidase regulator; amiC gene; amiR gene.
XX
OS   Pseudomonas aeruginosa
OC   Bacteria; Proteobacteria; Gammaproteobacteria; Pseudomonadales;
OC   Pseudomonadaceae; Pseudomonas.
XX
RN   [1]
RP   1167-2167
RA   Rice P.M.;
RT   ;
RL   Submitted (16-DEC-1988) to the INSDC.
RL   Rice P.M., EMBL, Postfach 10-2209, Meyerhofstrasse 1, 6900 Heidelberg, FRG.
XX
RN   [2]
RP   1167-2167
RX   DOI; 10.1016/0014-5793(89)80249-2.
RX   PUBMED; 2495988.
RA   Lowe N., Rice P.M., Drew R.E.;
RT   "Nucleotide sequence of the aliphatic amidase regulator gene (amiR) of
RT   Pseudomonas aeruginosa";
RL   FEBS Lett. 246(1-2):39-43(1989).
XX
RN   [3]
RP   1-1292
RX   PUBMED; 1907262.
RA   Wilson S., Drew R.;
RT   "Cloning and DNA sequence of amiC, a new gene regulating expression of the
RT   Pseudomonas aeruginosa aliphatic amidase, and purification of the amiC
RT   product";
RL   J. Bacteriol. 173(16):4914-4921(1991).
XX
RN   [4]
RP   1-2167
RA   Rice P.M.;
RT   ;
RL   Submitted (04-SEP-1991) to the INSDC.
RL   Rice P.M., EMBL, Postfach 10-2209, Meyerhofstrasse 1, 6900 Heidelberg, FRG.
XX
DR   GOA; Q51417.
DR   InterPro; IPR003211; AmiSUreI_transpt.
DR   UniProtKB/Swiss-Prot; Q51417; AMIS_PSEAE.


  [Part of this file has been deleted for brevity]

FT                   /note="ClaI fragment deleted in pSW36,  constitutive
FT                   phenotype"
FT   misc_feature    1
FT                   /note="last base of an XhoI site"
FT   misc_feature    648..653
FT                   /note="end of 658bp XhoI fragment, deletion in  pSW3 causes
FT                   constitutive expression of amiE"
FT   misc_difference 1281
FT                   /replace="g"
FT                   /note="conflict"
FT                   /citation=[3]
XX
SQ   Sequence 2167 BP; 363 A; 712 C; 730 G; 362 T; 0 other;
     ggtaccgctg gccgagcatc tgctcgatca ccaccagccg ggcgacggga actgcacgat        60
     ctacctggcg agcctggagc acgagcgggt tcgcttcgta cggcgctgag cgacagtcac       120
     aggagaggaa acggatggga tcgcaccagg agcggccgct gatcggcctg ctgttctccg       180
     aaaccggcgt caccgccgat atcgagcgct cgcacgcgta tggcgcattg ctcgcggtcg       240
     agcaactgaa ccgcgagggc ggcgtcggcg gtcgcccgat cgaaacgctg tcccaggacc       300
     ccggcggcga cccggaccgc tatcggctgt gcgccgagga cttcattcgc aaccgggggg       360
     tacggttcct cgtgggctgc tacatgtcgc acacgcgcaa ggcggtgatg ccggtggtcg       420
     agcgcgccga cgcgctgctc tgctacccga ccccctacga gggcttcgag tattcgccga       480
     acatcgtcta cggcggtccg gcgccgaacc agaacagtgc gccgctggcg gcgtacctga       540
     ttcgccacta cggcgagcgg gtggtgttca tcggctcgga ctacatctat ccgcgggaaa       600
     gcaaccatgt gatgcgccac ctgtatcgcc agcacggcgg cacggtgctc gaggaaatct       660
     acattccgct gtatccctcc gacgacgact tgcagcgcgc cgtcgagcgc atctaccagg       720
     cgcgcgccga cgtggtcttc tccaccgtgg tgggcaccgg caccgccgag ctgtatcgcg       780
     ccatcgcccg tcgctacggc gacggcaggc ggccgccgat cgccagcctg accaccagcg       840
     aggcggaggt ggcgaagatg gagagtgacg tggcagaggg gcaggtggtg gtcgcgcctt       900
     acttctccag catcgatacg cccgccagcc gggccttcgt ccaggcctgc catggtttct       960
     tcccggagaa cgcgaccatc accgcctggg ccgaggcggc ctactggcag accttgttgc      1020
     tcggccgcgc cgcgcaggcc gcaggcaact ggcgggtgga agacgtgcag cggcacctgt      1080
     acgacatcga catcgacgcg ccacaggggc cggtccgggt ggagcgccag aacaaccaca      1140
     gccgcctgtc ttcgcgcatc gcggaaatcg atgcgcgcgg cgtgttccag gtccgctggc      1200
     agtcgcccga accgattcgc cccgaccctt atgtcgtcgt gcataacctc gacgactggt      1260
     ccgccagcat gggcggggga ccgctcccat gagcgccaac tcgctgctcg gcagcctgcg      1320
     cgagttgcag gtgctggtcc tcaacccgcc gggggaggtc agcgacgccc tggtcttgca      1380
     gctgatccgc atcggttgtt cggtgcgcca gtgctggccg ccgccggaag ccttcgacgt      1440
     gccggtggac gtggtcttca ccagcatttt ccagaatggc caccacgacg agatcgctgc      1500
     gctgctcgcc gccgggactc cgcgcactac cctggtggcg ctggtggagt acgaaagccc      1560
     cgcggtgctc tcgcagatca tcgagctgga gtgccacggc gtgatcaccc agccgctcga      1620
     tgcccaccgg gtgctgcctg tgctggtatc ggcgcggcgc atcagcgagg aaatggcgaa      1680
     gctgaagcag aagaccgagc agctccagga ccgcatcgcc ggccaggccc ggatcaacca      1740
     ggccaaggtg ttgctgatgc agcgccatgg ctgggacgag cgcgaggcgc accagcacct      1800
     gtcgcgggaa gcgatgaagc ggcgcgagcc gatcctgaag atcgctcagg agttgctggg      1860
     aaacgagccg tccgcctgag cgatccgggc cgaccagaac aataacaaga ggggtatcgt      1920
     catcatgctg ggactggttc tgctgtacgt tggcgcggtg ctgtttctca atgccgtctg      1980
     gttgctgggc aagatcagcg gtcgggaggt ggcggtgatc aacttcctgg tcggcgtgct      2040
     gagcgcctgc gtcgcgttct acctgatctt ttccgcagca gccgggcagg gctcgctgaa      2100
     ggccggagcg ctgaccctgc tattcgcttt tacctatctg tgggtggccg ccaaccagtt      2160
     cctcgag                                                                2167
//

Output file format

   The output is a standard EMBOSS sequence file.

   The results can be output in one of several styles by using the
   command-line qualifier -osformat 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,
   excel, feattable, motif, nametable, regions, seqtable, simple, srs,
   table, tagseq.

   See: http://emboss.sf.net/docs/themes/SequenceFormats.html for further
   information on sequence formats.

  Output files for usage example

  File: gatta2.seq

>X13776 X13776.1 Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase
 regulation
ggtaccgctcgagcatctgctcgatcaccaccagccgggcgacgggaactgcacgatcta
cctggcgagcctggagcacgagcgggttcgcttcgtacggcgctgagcgacagtcacagg
agaggaaacggatgggatcgcaccaggagcggccgctgatcggcctgctgttctccgaaa
ccggcgtcaccgccgatatcgagcgctcgcacgcgtatggcgcattgctcgcggtcgagc
aactgaaccgcgagggcggcgtcggcggtcgcccgatcgaaacgctgtcccaggaccccg
gcggcgacccggaccgctatcggctgtgcgccgaggacttcattcgcaaccggggggtac
ggttcctcgtgggctgctacatgtcgcacacgcgcaaggcggtgatgccggtggtcgagc
gcgccgacgcgctgctctgctacccgaccccctacgagggcttcgagtattcgccgaaca
tcgtctacggcggtccggcgccgaaccagaacagtgcgccgctggcggcgtacctgattc
gccactacggcgagcgggtggtgttcatcggctcggactacatctatccgcgggaaagca
accatgtgatgcgccacctgtatcgccagcacggcggcacggtgctcgaggaaatctaca
ttccgctgtatccctccgacgacgacttgcagcgcgccgtcgagcgcatctaccaggcgc
gcgccgacgtggtcttctccaccgtggtgggcaccggcaccgccgagctgtatcgcgcca
tcgcccgtcgctacggcgacggcaggcggccgccgatcgccagcctgaccaccagcgagg
cggaggtggcgaagatggagagtgacgtggcagaggggcaggtggtggtcgcgccttact
tctccagcatcgatacgcccgccagccgggccttcgtccaggcctgccatggtttcttcc
cggagaacgcgaccatcaccgcctgggccgaggcggcctactggcagaccttgttgctcg
gccgcgccgcgcaggccgcaggcaactggcgggtggaagacgtgcagcggcacctgtacg
acatcgacatcgacgcgccacaggggccggtccgggtggagcgccagaacaaccacagcc
gcctgtcttcgcgcatcgcggaaatcgatgcgcgcggcgtgttccaggtccgctggcagt
cgcccgaaccgattcgccccgacccttatgtcgtcgtgcataacctcgacgactggtccg
ccagcatgggcgggggaccgctcccatgagcgccaactcgctgctcggcagcctgcgcga
gttgcaggtgctggtcctcaacccgccgggggaggtcagcgacgccctggtcttgcagct
gatccgcatcggttgttcggtgcgccagtgctggccgccgccggaagccttcgacgtgcc
ggtggacgtggtcttcaccagcattttccagaatggccaccacgacgagatcgctgcgct
gctcgccgccgggactccgcgcactaccctggtggcgctggtggagtacgaaagccccgc
ggtgctctcgcagatcatcgagctggagtgccacggcgtgatcacccagccgctcgatgc
ccaccgggtgctgcctgtgctggtatcggcgcggcgcatcagcgaggaaatggcgaagct
gaagcagaagaccgagcagctccaggaccgcatcgccggccaggcccggatcaaccaggc
caaggtgttgctgatgcagcgccatggctgggacgagcgcgaggcgcaccagcacctgtc
gcgggaagcgatgaagcggcgcgagccgatcctgaagatcgctcaggagttgctgggaaa
cgagccgtccgcctgagcgatccgggccgaccagaacaataacaagaggggtatcgtcat
catgctgggactggttctgctgtacgttggcgcggtgctgtttctcaatgccgtctggtt
gctgggcaagatcagcggtcgggaggtggcggtgatcaacttcctggtcggcgtgctgag
cgcctgcgtcgcgttctacctgatcttttccgcagcagccgggcagggctcgctgaaggc
cggagcgctgaccctgctattcgcttttacctatctgtgggtggccgccaaccagttcct
cgag

  Output files for usage example 2

  File: jsh.seq

>X13776 X13776.1 Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase
 regulation
tgctcgatcaccaccagccgggcgacgggaactgcacgatctacctggcgagcctggagc
acgagcgggttcgcttcgtacggcgctgagcgacagtcacaggagaggaaacggatggga
tcgcaccaggagcggccgctgatcggcctgctgttctccgaaaccggcgtcaccgccgat
atcgagcgctcgcacgcgtatggcgcattgctcgcggtcgagcaactgaaccgcgagggc
ggcgtcggcggtcgcccgatcgaaacgctgtcccaggaccccggcggcgacccggaccgc
tatcggctgtgcgccgaggacttcattcgcaaccggggggtacggttcctcgtgggctgc
tacatgtcgcacacgcgcaaggcggtgatgccggtggtcgagcgcgccgacgcgctgctc
tgctacccgaccccctacgagggcttcgagtattcgccgaacatcgtctacggcggtccg
gcgccgaaccagaacagtgcgccgctggcggcgtacctgattcgccactacggcgagcgg
gtggtgttcatcggctcggactacatctatccgcgggaaagcaaccatgtgatgcgccac
ctgtatcgccagcacggcggcacggtgctcgaggaaatctacattccgctgtatccctcc
gacgacgacttgcagcgcgccgtcgagcgcatctaccaggcgcgcgccgacgtggtcttc
tccaccgtggtgggcaccggcaccgccgagctgtatcgcgccatcgcccgtcgctacggc
gacggcaggcggccgccgatcgccagcctgaccaccagcgaggcggaggtggcgaagatg
gagagtgacgtggcagaggggcaggtggtggtcgcgccttacttctccagcatcgatacg
cccgccagccgggccttcgtccaggcctgccatggtttcttcccggagaacgcgaccatc
accgcctgggccgaggcggcctactggcagaccttgttgctcggccgcgccgcgcaggcc
gcaggcaactggcgggtggaagacgtgcagcggcacctgtacgacatcgacatcgacgcg
ccacaggggccggtccgggtggagcgccagaacaaccacagccgcctgtcttcgcgcatc
gcggaaatcgatgcgcgcggcgtgttccaggtccgctggcagtcgcccgaaccgattcgc
cccgacccttatgtcgtcgtgcataacctcgacgactggtccgccagcatgggcggggga
ccgctcccatgagcgccaactcgctgctcggcagcctgcgcgagttgcaggtgctggtcc
tcaacccgccgggggaggtcagcgacgccctggtcttgcagctgatccgcatcggttgtt
cggtgcgccagtgctggccgccgccggaagccttcgacgtgccggtggacgtggtcttca
ccagcattttccagaatggccaccacgacgagatcgctgcgctgctcgccgccgggactc
cgcgcactaccctggtggcgctggtggagtacgaaagccccgcggtgctctcgcagatca
tcgagctggagtgccacggcgtgatcacccagccgctcgatgcccaccgggtgctgcctg
tgctggtatcggcgcggcgcatcagcgaggaaatggcgaagctgaagcagaagaccgagc
agctccaggaccgcatcgccggccaggcccggatcaaccaggccaaggtgttgctgatgc
agcgccatggctgggacgagcgcgaggcgcaccagcacctgtcgcgggaagcgatgaagc
ggcgcgagccgatcctgaagatcgctcaggagttgctgggaaacgagccgtccgcctgag
cgatccgggccgaccagaacaataacaagaggggtatcgtcatcatgctgggactggttc
tgctgtacgttggcgcggtgctgtttctcaatgccgtctggttgctgggcaagatcagcg
gtcgggaggtggcggtgatcaacttcctggtcggcgtgctgagcgcctgcgtcgcgttct
acctgatcttttccgcagcagccgggcagggctcgctgaaggccggagcgctgaccctgc
tattcgcttttacctatctgtgggtggccgccaaccagttcctcgag

  Output files for usage example 3

  File: starta.seq

>X13776 X13776.1 Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidase
 regulation

Data files

   None.

Notes

   Qualifiers that are in-built for sequence datatypes allow the input and
   output files to be specified in more detail, for example, the format
   for the output files.

References

   None.

Warnings

   You can delete a complete sequence and write out an empty sequence
   file.

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
   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
   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

Author(s)

   Gary Williams formerly at:
   MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust
   Genome Campus, Hinxton, Cambridge, CB10 1SB, UK

   Please report all bugs to the EMBOSS bug team
   (emboss-bug (c) emboss.open-bio.org) not to the original author.

History

   Completed 26 Jan 1999

Target users

   This program is intended to be used by everyone and everything, from
   naive users to embedded scripts.

Comments

   None
