
                                  cutseq 



Function

   Removes 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 
Removes 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 
Removes 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 
Removes 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

   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
   -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

   "-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. 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

   cutseq reads a single sequence USA.

  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 EMBL/GenBank/DDBJ databases.
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 of Pseudomona
s
RT   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 seqence 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 EMBL/GenBank/DDBJ databases.
RL   Rice P.M., EMBL, Postfach 10-2209, Meyerhofstrasse 1, 6900 Heidelberg, FRG
.
XX
DR   GOA; Q51417.
DR   UniProtKB/Swiss-Prot; Q51417; AMIS_PSEAE.
XX


  [Part of this file has been deleted for brevity]

FT                   /replace=""
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 cause
s
FT                   constitutive expression of amiE"
FT   conflict        1281
FT                   /replace="g"
FT                   /citation=[3]
XX
SQ   Sequence 2167 BP; 363 A; 712 C; 730 G; 362 T; 0 other;
     ggtaccgctg gccgagcatc tgctcgatca ccaccagccg ggcgacggga actgcacgat        6
0
     ctacctggcg agcctggagc acgagcgggt tcgcttcgta cggcgctgag cgacagtcac       12
0
     aggagaggaa acggatggga tcgcaccagg agcggccgct gatcggcctg ctgttctccg       18
0
     aaaccggcgt caccgccgat atcgagcgct cgcacgcgta tggcgcattg ctcgcggtcg       24
0
     agcaactgaa ccgcgagggc ggcgtcggcg gtcgcccgat cgaaacgctg tcccaggacc       30
0
     ccggcggcga cccggaccgc tatcggctgt gcgccgagga cttcattcgc aaccgggggg       36
0
     tacggttcct cgtgggctgc tacatgtcgc acacgcgcaa ggcggtgatg ccggtggtcg       42
0
     agcgcgccga cgcgctgctc tgctacccga ccccctacga gggcttcgag tattcgccga       48
0
     acatcgtcta cggcggtccg gcgccgaacc agaacagtgc gccgctggcg gcgtacctga       54
0
     ttcgccacta cggcgagcgg gtggtgttca tcggctcgga ctacatctat ccgcgggaaa       60
0
     gcaaccatgt gatgcgccac ctgtatcgcc agcacggcgg cacggtgctc gaggaaatct       66
0
     acattccgct gtatccctcc gacgacgact tgcagcgcgc cgtcgagcgc atctaccagg       72
0
     cgcgcgccga cgtggtcttc tccaccgtgg tgggcaccgg caccgccgag ctgtatcgcg       78
0
     ccatcgcccg tcgctacggc gacggcaggc ggccgccgat cgccagcctg accaccagcg       84
0
     aggcggaggt ggcgaagatg gagagtgacg tggcagaggg gcaggtggtg gtcgcgcctt       90
0
     acttctccag catcgatacg cccgccagcc gggccttcgt ccaggcctgc catggtttct       96
0
     tcccggagaa cgcgaccatc accgcctggg ccgaggcggc ctactggcag accttgttgc      102
0
     tcggccgcgc cgcgcaggcc gcaggcaact ggcgggtgga agacgtgcag cggcacctgt      108
0
     acgacatcga catcgacgcg ccacaggggc cggtccgggt ggagcgccag aacaaccaca      114
0
     gccgcctgtc ttcgcgcatc gcggaaatcg atgcgcgcgg cgtgttccag gtccgctggc      120
0
     agtcgcccga accgattcgc cccgaccctt atgtcgtcgt gcataacctc gacgactggt      126
0
     ccgccagcat gggcggggga ccgctcccat gagcgccaac tcgctgctcg gcagcctgcg      132
0
     cgagttgcag gtgctggtcc tcaacccgcc gggggaggtc agcgacgccc tggtcttgca      138
0
     gctgatccgc atcggttgtt cggtgcgcca gtgctggccg ccgccggaag ccttcgacgt      144
0
     gccggtggac gtggtcttca ccagcatttt ccagaatggc caccacgacg agatcgctgc      150
0
     gctgctcgcc gccgggactc cgcgcactac cctggtggcg ctggtggagt acgaaagccc      156
0
     cgcggtgctc tcgcagatca tcgagctgga gtgccacggc gtgatcaccc agccgctcga      162
0
     tgcccaccgg gtgctgcctg tgctggtatc ggcgcggcgc atcagcgagg aaatggcgaa      168
0
     gctgaagcag aagaccgagc agctccagga ccgcatcgcc ggccaggccc ggatcaacca      174
0
     ggccaaggtg ttgctgatgc agcgccatgg ctgggacgag cgcgaggcgc accagcacct      180
0
     gtcgcgggaa gcgatgaagc ggcgcgagcc gatcctgaag atcgctcagg agttgctggg      186
0
     aaacgagccg tccgcctgag cgatccgggc cgaccagaac aataacaaga ggggtatcgt      192
0
     catcatgctg ggactggttc tgctgtacgt tggcgcggtg ctgtttctca atgccgtctg      198
0
     gttgctgggc aagatcagcg gtcgggaggt ggcggtgatc aacttcctgg tcggcgtgct      204
0
     gagcgcctgc gtcgcgttct acctgatctt ttccgcagca gccgggcagg gctcgctgaa      210
0
     ggccggagcg ctgaccctgc tattcgcttt tacctatctg tgggtggccg ccaaccagtt      216
0
     cctcgag                                                                216
7
//

Output file format

   cutseq writes a single sequence file.

  Output files for usage example

  File: gatta2.seq

>X13776 X13776.1 Pseudomonas aeruginosa amiC and amiR gene for aliphatic amidas
e 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 amidas
e 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 amidas
e 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 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
   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
   featreport 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)

   Gary Williams (gwilliam © rfcgr.mrc.ac.uk)
   MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust
   Genome Campus, Hinxton, Cambridge, CB10 1SB, UK

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
