
                                   yank 



Function

   Reads a sequence range, appends the full USA to a list file

Description

   yank is a simple utility to add a specified sequence name to a list
   file.

   In fact, it writes out not just the name of the sequence, but also the
   start and end position of a region within that sequence and, if the
   sequence is nucleic, if can specify whether the sequence is the
   reverse complement.

   Without the program yank you would need to use a text editor such as
   pico to create the appropriate list files. yank makes this process
   easy.

  List Files

   Many EMBOSS programs can read in a set of sequences. (Some examples
   are emma and union) There are many ways of specifying these sequences,
   including wildcarded sequence file names, wildcarded database entry
   names and list files. List files (files of file names) are the most
   flexible. yank is a utility to add sequences to a list file.

   Instead of containing the sequences themselves, a List file contains
   "references" to sequences - so, for example, you might include
   database entries, the names of files containing sequences, or even the
   names of other list files. For example, here's a valid list file,
   called seq.list:

unix % more seq.list

opsd_abyko.fasta
sw:opsd_xenla
sw:opsd_c*
@another_list

   This looks a bit odd, but it's really very straightforward; the file
   contains:

     * opsd_abyko.fasta - this is the name of a sequence file. The file
       is read in from the current directory.
     * sw:opsd_xenla - this is a reference to a specific sequence in the
       SwissProt database
     * sw:opsd_c* - this represents all the sequences in SwissProt whose
       identifiers start with ``opsd_c''
     * another_list - this is the name of a second list file

   Notice the @ in front of the last entry. This is the way you tell
   EMBOSS that this file is a list file, not a regular sequence file.

Usage

   Here is a sample session with yank

   This is an example of adding an entry for the part of tembl:x65921
   between positions 1913 and 1915 to the existing list file 'cds.list':


% yank 
Reads a sequence range, appends the full USA to a list file
Input (gapped) sequence: tembl:x65921
     Begin at position [start]: 1913
       End at position [end]: 1915
        Reverse strand [N]: 
List of USAs output file [x65921.yank]: cds.list

   Go to the input files for this example
   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)
  [-outfile]           outfile    [*.yank] List of USAs output file

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers:
   -newfile            boolean    [N] Overwrite existing output file

   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

   "-outfile" associated qualifiers
   -odirectory2        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

   yank reads any valid sequence USA.

   You will be prompted for the start and end positions you wish to use.

   If the sequence is nucleic, you will be prompted whether you wish to
   use the reverse complement of the sequence.

  Input files for usage example

   'tembl:x65921' is a sequence entry in the example nucleic acid
   database 'tembl'

  Database entry: tembl:x65921

ID   X65921; SV 1; linear; genomic DNA; STD; HUM; 2016 BP.
XX
AC   X65921; S45242;
XX
DT   13-MAY-1992 (Rel. 31, Created)
DT   14-NOV-2006 (Rel. 89, Last updated, Version 7)
XX
DE   H.sapiens fau 1 gene
XX
KW   fau 1 gene.
XX
OS   Homo sapiens (human)
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia
;
OC   Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae;
OC   Homo.
XX
RN   [1]
RP   1-2016
RA   Kas K.;
RT   ;
RL   Submitted (29-APR-1992) to the EMBL/GenBank/DDBJ databases.
RL   K. Kas, University of Antwerp, Dept of Biochemistry T3.22,
RL   Universiteitsplein 1, 2610 Wilrijk, BELGIUM
XX
RN   [2]
RP   1-2016
RX   DOI; 10.1016/0006-291X(92)91286-Y.
RX   PUBMED; 1326960.
RA   Kas K., Michiels L., Merregaert J.;
RT   "Genomic structure and expression of the human fau gene: encoding the
RT   ribosomal protein S30 fused to a ubiquitin-like protein.";
RL   Biochem. Biophys. Res. Commun. 187(2):927-933(1992).
XX
DR   GDB; 191789.
DR   GDB; 191790.
DR   GDB; 354872.
DR   GDB; 4590236.
XX
FH   Key             Location/Qualifiers
FH
FT   source          1..2016
FT                   /organism="Homo sapiens"
FT                   /mol_type="genomic DNA"
FT                   /clone_lib="CML cosmid"
FT                   /clone="15.1"
FT                   /db_xref="taxon:9606"
FT   mRNA            join(408..504,774..856,951..1095,1557..1612,1787..>1912)
FT                   /gene="fau 1"
FT   exon            408..504
FT                   /number=1


  [Part of this file has been deleted for brevity]

FT                   RAKRRMQYNRRFVNVVPTFGKKKGPNANS"
FT   intron          857..950
FT                   /number=2
FT   exon            951..1095
FT                   /number=3
FT   intron          1096..1556
FT                   /number=3
FT   exon            1557..1612
FT                   /number=4
FT   intron          1613..1786
FT                   /number=4
FT   exon            1787..>1912
FT                   /number=5
FT   polyA_signal    1938..1943
XX
SQ   Sequence 2016 BP; 421 A; 562 C; 538 G; 495 T; 0 other;
     ctaccatttt ccctctcgat tctatatgta cactcgggac aagttctcct gatcgaaaac        6
0
     ggcaaaacta aggccccaag taggaatgcc ttagttttcg gggttaacaa tgattaacac       12
0
     tgagcctcac acccacgcga tgccctcagc tcctcgctca gcgctctcac caacagccgt       18
0
     agcccgcagc cccgctggac accggttctc catccccgca gcgtagcccg gaacatggta       24
0
     gctgccatct ttacctgcta cgccagcctt ctgtgcgcgc aactgtctgg tcccgccccg       30
0
     tcctgcgcga gctgctgccc aggcaggttc gccggtgcga gcgtaaaggg gcggagctag       36
0
     gactgccttg ggcggtacaa atagcaggga accgcgcggt cgctcagcag tgacgtgaca       42
0
     cgcagcccac ggtctgtact gacgcgccct cgcttcttcc tctttctcga ctccatcttc       48
0
     gcggtagctg ggaccgccgt tcaggtaaga atggggcctt ggctggatcc gaagggcttg       54
0
     tagcaggttg gctgcggggt cagaaggcgc ggggggaacc gaagaacggg gcctgctccg       60
0
     tggccctgct ccagtcccta tccgaactcc ttgggaggca ctggccttcc gcacgtgagc       66
0
     cgccgcgacc accatcccgt cgcgatcgtt tctggaccgc tttccactcc caaatctcct       72
0
     ttatcccaga gcatttcttg gcttctctta caagccgtct tttctttact cagtcgccaa       78
0
     tatgcagctc tttgtccgcg cccaggagct acacaccttc gaggtgaccg gccaggaaac       84
0
     ggtcgcccag atcaaggtaa ggctgcttgg tgcgccctgg gttccatttt cttgtgctct       90
0
     tcactctcgc ggcccgaggg aacgcttacg agccttatct ttccctgtag gctcatgtag       96
0
     cctcactgga gggcattgcc ccggaagatc aagtcgtgct cctggcaggc gcgcccctgg      102
0
     aggatgaggc cactctgggc cagtgcgggg tggaggccct gactaccctg gaagtagcag      108
0
     gccgcatgct tggaggtgag tgagagagga atgttctttg aagtaccggt aagcgtctag      114
0
     tgagtgtggg gtgcatagtc ctgacagctg agtgtcacac ctatggtaat agagtacttc      120
0
     tcactgtctt cagttcagag tgattcttcc tgtttacatc cctcatgttg aacacagacg      126
0
     tccatgggag actgagccag agtgtagttg tatttcagtc acatcacgag atcctagtct      132
0
     ggttatcagc ttccacacta aaaattaggt cagaccaggc cccaaagtgc tctataaatt      138
0
     agaagctgga agatcctgaa atgaaactta agatttcaag gtcaaatatc tgcaactttg      144
0
     ttctcattac ctattgggcg cagcttctct ttaaaggctt gaattgagaa aagaggggtt      150
0
     ctgctgggtg gcaccttctt gctcttacct gctggtgcct tcctttccca ctacaggtaa      156
0
     agtccatggt tccctggccc gtgctggaaa agtgagaggt cagactccta aggtgagtga      162
0
     gagtattagt ggtcatggtg ttaggacttt ttttcctttc acagctaaac caagtccctg      168
0
     ggctcttact cggtttgcct tctccctccc tggagatgag cctgagggaa gggatgctag      174
0
     gtgtggaaga caggaaccag ggcctgatta accttccctt ctccaggtgg ccaaacagga      180
0
     gaagaagaag aagaagacag gtcgggctaa gcggcggatg cagtacaacc ggcgctttgt      186
0
     caacgttgtg cccacctttg gcaagaagaa gggccccaat gccaactctt aagtcttttg      192
0
     taattctggc tttctctaat aaaaaagcca cttagttcag tcatcgcatt gtttcatctt      198
0
     tacttgcaag gcctcaggga gaggtgtgct tctcgg                                201
6
//

Output file format

  Output files for usage example

  File: cds.list

tembl-id:X65921[782:856]
tembl-id:X65921[951:1095]
tembl-id:X65921[1557:1612]
tembl-id:X65921[1787:1912]
tembl-id:X65921[1913:1915]

   The output list file can now be read in by a program such as union by
   specifying the list file as '@cds.list' when union prompts for input.

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
   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
   pasteseq     Insert one sequence into another
   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

   The program extract does not make list files, but creates a sequence
   from sub-regions of a single other sequence.

Author(s)

   Peter Rice (pmr © ebi.ac.uk)
   Informatics Division, European Bioinformatics Institute, Wellcome
   Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK

History

   Written (March 2002) - Peter Rice.

Target users

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

Comments

   None
