pasteseq.txt

emboss的linux版本的源代码

                                 pasteseq 



Function

   Insert one sequence into another

Description

   This simple editing program allows you to insert one sequence into
   another sequence after a specified position and to then write out the
   results to a sequence file.

Usage

   Here is a sample session with pasteseq

   To insert the sequence 'tsw:flav_nossm' after position 67 in sequence
   'tsw:amir_pseae' and write the results to the file 'amir_pseae.fasta':


% pasteseq tsw:amir_pseae tsw:flav_nossm -pos=67 
Insert one sequence into another
output sequence [amir_pseae.fasta]: 

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

   Example 2

   This does the same thing, but the output qualifier is explicitly used:


% pasteseq tsw:amir_pseae tsw:flav_nossm -out=amirplus.seq -pos=67 
Insert one sequence into another

   Go to the output files for this example

   Example 3

   To insert the sequence 'tsw:flav_nossm' before the start of sequence
   'tsw:amir_pseae' use -pos=0:


% pasteseq tsw:amir_pseae tsw:flav_nossm -out=amirplus.seq -pos=0 
Insert one sequence into another

   Go to the output files for this example

Command line arguments

   Standard (Mandatory) qualifiers:
  [-asequence]         sequence   (Gapped) sequence filename and optional
                                  format, or reference (input USA)
  [-bsequence]         sequence   Sequence to insert
   -pos                integer    [$(asequence.end)] The position in the main
                                  input sequence to insert after.
                                  To insert before the start use the position
                                  0. (Integer 0 or more)
  [-outseq]            seqout     [.] Sequence filename and
                                  optional format (output USA)

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers: (none)
   Associated qualifiers:

   "-asequence" 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

   "-bsequence" associated qualifiers
   -sbegin2            integer    Start of the sequence to be used
   -send2              integer    End of the sequence to be used
   -sreverse2          boolean    Reverse (if DNA)
   -sask2              boolean    Ask for begin/end/reverse
   -snucleotide2       boolean    Sequence is nucleotide
   -sprotein2          boolean    Sequence is protein
   -slower2            boolean    Make lower case
   -supper2            boolean    Make upper case
   -sformat2           string     Input sequence format
   -sdbname2           string     Database name
   -sid2               string     Entryname
   -ufo2               string     UFO features
   -fformat2           string     Features format
   -fopenfile2         string     Features file name

   "-outseq" associated qualifiers
   -osformat3          string     Output seq format
   -osextension3       string     File name extension
   -osname3            string     Base file name
   -osdirectory3       string     Output directory
   -osdbname3          string     Database name to add
   -ossingle3          boolean    Separate file for each entry
   -oufo3              string     UFO features
   -offormat3          string     Features format
   -ofname3            string     Features file name
   -ofdirectory3       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 dying program messages

Input file format

   pasteseq reads 2 normal sequence USAs.

  Input files for usage example

   'tsw:amir_pseae' is a sequence entry in the example protein database
   'tsw'

  Database entry: tsw:amir_pseae

ID   AMIR_PSEAE     STANDARD;      PRT;   196 AA.
AC   P10932;
DT   01-JUL-1989 (Rel. 11, Created)
DT   01-JUL-1989 (Rel. 11, Last sequence update)
DT   15-DEC-1998 (Rel. 37, Last annotation update)
DE   ALIPHATIC AMIDASE REGULATOR.
GN   AMIR.
OS   Pseudomonas aeruginosa.
OC   Bacteria; Proteobacteria; gamma subdivision; Pseudomonas group;
OC   Pseudomonas.
RN   [1]
RP   SEQUENCE FROM N.A.
RC   STRAIN=PAC;
RX   MEDLINE; 89211409.
RA   LOWE N., RICE P.M., DREW R.E.;
RT   "Nucleotide sequence of the aliphatic amidase regulator gene (amiR)
RT   of Pseudomonas aeruginosa.";
RL   FEBS Lett. 246:39-43(1989).
RN   [2]
RP   CHARACTERIZATION.
RX   MEDLINE; 95286483.
RA   WILSON S.A., DREW R.E.;
RT   "Transcriptional analysis of the amidase operon from Pseudomonas
RT   aeruginosa.";
RL   J. Bacteriol. 177:3052-3057(1995).
CC   -!- FUNCTION: POSITIVE CONTROLLING ELEMENT OF AMIE, THE GENE FOR
CC       ALIPHATIC AMIDASE. ACTS AS A TRANSCRIPTIONAL ANTITERMINATION
CC       FACTOR. IT IS THOUGHT TO ALLOW RNA POLYMERASE READ THROUGH A RHO-
CC       INDEPENDENT TRANSCRIPTION TERMINATOR BETWEEN THE AMIE PROMOTER AND
CC       GENE.
CC   --------------------------------------------------------------------------
CC   This SWISS-PROT entry is copyright. It is produced through a collaboration
CC   between  the Swiss Institute of Bioinformatics  and the  EMBL outstation -
CC   the European Bioinformatics Institute.  There are no  restrictions on  its
CC   use  by  non-profit  institutions as long  as its content  is  in  no  way
CC   modified and this statement is not removed.  Usage  by  and for commercial
CC   entities requires a license agreement (See http://www.isb-sib.ch/announce/
CC   or send an email to [e-mail]).
CC   --------------------------------------------------------------------------
DR   EMBL; X13776; CAA32023.1; -.
DR   PIR; S03884; S03884.
KW   Transcription regulation; Activator.
SQ   SEQUENCE   196 AA;  21776 MW;  560A8AE3 CRC32;
     MSANSLLGSL RELQVLVLNP PGEVSDALVL QLIRIGCSVR QCWPPPEAFD VPVDVVFTSI
     FQNGHHDEIA ALLAAGTPRT TLVALVEYES PAVLSQIIEL ECHGVITQPL DAHRVLPVLV
     SARRISEEMA KLKQKTEQLQ DRIAGQARIN QAKVLLMQRH GWDEREAHQH LSREAMKRRE
     PILKIAQELL GNEPSA
//

  Database entry: tsw:flav_nossm

ID   FLAV_NOSSM     STANDARD;      PRT;    35 AA.
AC   P35707;
DT   01-JUN-1994 (Rel. 29, Created)
DT   01-JUN-1994 (Rel. 29, Last sequence update)
DT   15-DEC-1998 (Rel. 37, Last annotation update)
DE   FLAVODOXIN (FRAGMENT).
OS   Nostoc sp. (strain MAC).
OC   Bacteria; Cyanobacteria; Nostocales; Nostocaceae; Nostoc.
RN   [1]
RP   SEQUENCE.
RA   Takruri I.A.H., Boulter D., Fitzgerald M.P., Hutber G.N., Rogers L.J.;
RT   "N-terminal amino acid sequences of flavodoxins from Chondrus crispus
RT   and Nostoc strain MAC.";
RL   Phytochemistry 25:2113-2115(1986).
CC   -!- FUNCTION: LOW-POTENTIAL ELECTRON DONOR TO A NUMBER OF REDOX
CC       ENZYMES.
CC   -!- COFACTOR: FMN.
CC   -!- SIMILARITY: BELONGS TO THE FLAVODOXIN FAMILY.
DR   PIR; PA0004; PA0004.
DR   HSSP; P11241; 1RCF.
DR   INTERPRO; IPR001226; -.
DR   PFAM; PF00258; flavodoxin; 1.
DR   PROSITE; PS00201; FLAVODOXIN; 1.
KW   Electron transport; Flavoprotein; FMN.
FT   NON_TER      35     35
SQ   SEQUENCE   35 AA;  3820 MW;  B6EEB5CA7A45DDA6 CRC64;
     SKKIGLFYGT ZTGKTESVAE IIDEFGDEVV TLDID
//

Output file format

   pasteseq writes a normal sequence file.

  Output files for usage example

  File: amir_pseae.fasta

>AMIR_PSEAE ALIPHATIC AMIDASE REGULATOR.
MSANSLLGSLRELQVLVLNPPGEVSDALVLQLIRIGCSVRQCWPPPEAFDVPVDVVFTSI
FQNGHHDSKKIGLFYGTZTGKTESVAEIIDEFGDEVVTLDIDEIAALLAAGTPRTTLVAL
VEYESPAVLSQIIELECHGVITQPLDAHRVLPVLVSARRISEEMAKLKQKTEQLQDRIAG
QARINQAKVLLMQRHGWDEREAHQHLSREAMKRREPILKIAQELLGNEPSA

  Output files for usage example 2

  File: amirplus.seq

>AMIR_PSEAE ALIPHATIC AMIDASE REGULATOR.
MSANSLLGSLRELQVLVLNPPGEVSDALVLQLIRIGCSVRQCWPPPEAFDVPVDVVFTSI
FQNGHHDSKKIGLFYGTZTGKTESVAEIIDEFGDEVVTLDIDEIAALLAAGTPRTTLVAL
VEYESPAVLSQIIELECHGVITQPLDAHRVLPVLVSARRISEEMAKLKQKTEQLQDRIAG
QARINQAKVLLMQRHGWDEREAHQHLSREAMKRREPILKIAQELLGNEPSA

  Output files for usage example 3

  File: amirplus.seq

>AMIR_PSEAE ALIPHATIC AMIDASE REGULATOR.
SKKIGLFYGTZTGKTESVAEIIDEFGDEVVTLDIDMSANSLLGSLRELQVLVLNPPGEVS
DALVLQLIRIGCSVRQCWPPPEAFDVPVDVVFTSIFQNGHHDEIAALLAAGTPRTTLVAL
VEYESPAVLSQIIELECHGVITQPLDAHRVLPVLVSARRISEEMAKLKQKTEQLQDRIAG
QARINQAKVLLMQRHGWDEREAHQHLSREAMKRREPILKIAQELLGNEPSA

Data files

   None.

Notes

   This can be used as a simple sequence editor.

References

   None.

Warnings

   None.

Diagnostic Error Messages

   None.

Exit status

   It always exits with status 0.

Known bugs

   None.

See also

   Program name                         Description
   biosed       Replace or delete sequence sections
   codcopy      Reads and writes a codon usage table
   cutseq       Removes a specified section from a sequence
   degapseq     Removes gap characters from sequences
   descseq      Alter the name or description of a sequence
   entret       Reads and writes (returns) flatfile entries
   extractalign Extract regions from a sequence alignment
   extractfeat  Extract features from a sequence
   extractseq   Extract regions from a sequence
   listor       Write a list file of the logical OR of two sets of sequences
   makenucseq   Creates random nucleotide sequences
   makeprotseq  Creates random protein sequences
   maskfeat     Mask off features of a sequence
   maskseq      Mask off regions of a sequence
   newseq       Type in a short new sequence
   noreturn     Removes carriage return from ASCII files
   notseq       Exclude a set of sequences and write out the remaining ones
   nthseq       Writes one sequence from a multiple set of sequences
   revseq       Reverse and complement a sequence
   seqret       Reads and writes (returns) sequences
   seqretsplit  Reads and writes (returns) sequences in individual files
   skipseq      Reads and writes (returns) sequences, skipping first few
   splitter     Split a sequence into (overlapping) smaller sequences
   trimest      Trim poly-A tails off EST sequences
   trimseq      Trim ambiguous bits off the ends of sequences
   union        Reads sequence fragments and builds one sequence
   vectorstrip  Strips out DNA between a pair of vector sequences
   yank         Reads a sequence range, appends the full USA to a list file

Author(s)

   Gary Williams (gwilliam