cutseq

 

Function

Removes a specified 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 sequence to remove.

It removes the sequence from the specified start to the end positions (inclusive) and returns the rest of the sequence in 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:paamir gatta2.seq -from=10 -to=12 
Removes a specified 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:paamir' and write it to 'jsh.seq':


% cutseq tembl:paamir -from=1 -to=20 -out=jsh.seq 
Removes a specified 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:paamir starta.seq -sbeg=-1000 -send=1290 
Removes a specified 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   Sequence USA
   -from               integer    This is the start position (inclusive) of
                                  the section of the sequence that you wish to
                                  remove.
   -to                 integer    This is the end position (inclusive) of the
                                  section of the sequence that you wish to
                                  remove.
  [-outseq]            seqout     Output sequence 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 standard output
   -filter              boolean    Read standard input, write 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 deaths


Standard (Mandatory) qualifiers Allowed values Default
[-sequence]
(Parameter 1)
Sequence USA Readable sequence Required
-from This is the start position (inclusive) of the section of the sequence that you wish to remove. Any integer value Start of sequence (0)
-to This is the end position (inclusive) of the section of the sequence that you wish to remove. Any integer value End of sequence (0)
[-outseq]
(Parameter 2)
Output sequence USA Writeable sequence <sequence>.format
Additional (Optional) qualifiers Allowed values Default
(none)
Advanced (Unprompted) qualifiers Allowed values Default
(none)

Input file format

cutseq reads a single sequence USA.

Input files for usage example

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

Database entry: tembl:paamir

ID   PAAMIR     standard; DNA; PRO; 2167 BP.
XX
AC   X13776; M43175;
XX
SV   X13776.1
XX
DT   19-APR-1989 (Rel. 19, Created)
DT   17-FEB-1997 (Rel. 50, Last updated, Version 22)
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; gamma subdivision; 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   MEDLINE; 89211409.
RA   Lowe N., Rice P.M., Drew R.E.;
RT   "Nucleotide sequence of the aliphatic amidase regulator gene of Pseudomonas
RT   aeruginosa";
RL   FEBS Lett. 246:39-43(1989).
XX
RN   [3]
RP   1-1292
RX   MEDLINE; 91317707.
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. 173:4914-4921(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   SWISS-PROT; P10932; AMIR_PSEAE.
DR   SWISS-PROT; P27017; AMIC_PSEAE.
DR   SWISS-PROT; Q51417; AMIS_PSEAE.


  [Part of this file has been deleted for brevity]

FT                   phenotype"
FT                   /replace=""
FT                   /gene="amiC"
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   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        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

cutseq writes a single sequence file.

Output files for usage example

File: gatta2.seq

>PAAMIR 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

>PAAMIR 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

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

Data files

None.

Notes

This can be used as a simple sequence editor.

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 nameDescription
biosedReplace or delete sequence sections
codcopyReads and writes a codon usage table
degapseqRemoves gap characters from sequences
descseqAlter the name or description of a sequence
entretReads and writes (returns) flatfile entries
extractfeatExtract features from a sequence
extractseqExtract regions from a sequence
listorWrite a list file of the logical OR of two sets of sequences
maskfeatMask off features of a sequence
maskseqMask off regions of a sequence
newseqType in a short new sequence
noreturnRemoves carriage return from ASCII files
notseqExclude a set of sequences and write out the remaining ones
nthseqWrites one sequence from a multiple set of sequences
pasteseqInsert one sequence into another
revseqReverse and complement a sequence
seqretReads and writes (returns) sequences
seqretsplitReads and writes (returns) sequences in individual files
skipseqReads and writes (returns) sequences, skipping first few
splitterSplit a sequence into (overlapping) smaller sequences
trimestTrim poly-A tails off EST sequences
trimseqTrim ambiguous bits off the ends of sequences
unionReads sequence fragments and builds one sequence
vectorstripStrips out DNA between a pair of vector sequences
yankReads a sequence range, appends the 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