EMBOSS: yank

| yank

## Function

Add a sequence reference (a full USA) to a list file

## Description

yank adds the full Uniform Sequence Address (USA) of a specified sequence, or a region (subsequence) of a sequence, to a list file. The file is appended to by default but (optionally) is overwritten.A list file contains one or more sequence references (USAs). For example, a database entry, the name of a file containing sequences, or even the names of another list file. In addition to the name of the sequence, it can write 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.

## 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
    Add a sequence reference (a 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 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

Standard (Mandatory) qualifiers | Allowed values | Default
--- | --- | ---
[-sequence] (Parameter 1) | (Gapped) sequence filename and optional format, or reference (input USA) | Readable sequence | Required
[-outfile] (Parameter 2) | List of USAs output file | Output file | <*>.yank
Additional (Optional) qualifiers | Allowed values | Default
(none)
Advanced (Unprompted) qualifiers | Allowed values | Default
-newfile | Overwrite existing output file | Boolean value Yes/No | No

## 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        60
         ggcaaaacta aggccccaag taggaatgcc ttagttttcg gggttaacaa tgattaacac       120
         tgagcctcac acccacgcga tgccctcagc tcctcgctca gcgctctcac caacagccgt       180
         agcccgcagc cccgctggac accggttctc catccccgca gcgtagcccg gaacatggta       240
         gctgccatct ttacctgcta cgccagcctt ctgtgcgcgc aactgtctgg tcccgccccg       300
         tcctgcgcga gctgctgccc aggcaggttc gccggtgcga gcgtaaaggg gcggagctag       360
         gactgccttg ggcggtacaa atagcaggga accgcgcggt cgctcagcag tgacgtgaca       420
         cgcagcccac ggtctgtact gacgcgccct cgcttcttcc tctttctcga ctccatcttc       480
         gcggtagctg ggaccgccgt tcaggtaaga atggggcctt ggctggatcc gaagggcttg       540
         tagcaggttg gctgcggggt cagaaggcgc ggggggaacc gaagaacggg gcctgctccg       600
         tggccctgct ccagtcccta tccgaactcc ttgggaggca ctggccttcc gcacgtgagc       660
         cgccgcgacc accatcccgt cgcgatcgtt tctggaccgc tttccactcc caaatctcct       720
         ttatcccaga gcatttcttg gcttctctta caagccgtct tttctttact cagtcgccaa       780
         tatgcagctc tttgtccgcg cccaggagct acacaccttc gaggtgaccg gccaggaaac       840
         ggtcgcccag atcaaggtaa ggctgcttgg tgcgccctgg gttccatttt cttgtgctct       900
         tcactctcgc ggcccgaggg aacgcttacg agccttatct ttccctgtag gctcatgtag       960
         cctcactgga gggcattgcc ccggaagatc aagtcgtgct cctggcaggc gcgcccctgg      1020
         aggatgaggc cactctgggc cagtgcgggg tggaggccct gactaccctg gaagtagcag      1080
         gccgcatgct tggaggtgag tgagagagga atgttctttg aagtaccggt aagcgtctag      1140
         tgagtgtggg gtgcatagtc ctgacagctg agtgtcacac ctatggtaat agagtacttc      1200
         tcactgtctt cagttcagag tgattcttcc tgtttacatc cctcatgttg aacacagacg      1260
         tccatgggag actgagccag agtgtagttg tatttcagtc acatcacgag atcctagtct      1320
         ggttatcagc ttccacacta aaaattaggt cagaccaggc cccaaagtgc tctataaatt      1380
         agaagctgga agatcctgaa atgaaactta agatttcaag gtcaaatatc tgcaactttg      1440
         ttctcattac ctattgggcg cagcttctct ttaaaggctt gaattgagaa aagaggggtt      1500
         ctgctgggtg gcaccttctt gctcttacct gctggtgcct tcctttccca ctacaggtaa      1560
         agtccatggt tccctggccc gtgctggaaa agtgagaggt cagactccta aggtgagtga      1620
         gagtattagt ggtcatggtg ttaggacttt ttttcctttc acagctaaac caagtccctg      1680
         ggctcttact cggtttgcct tctccctccc tggagatgag cctgagggaa gggatgctag      1740
         gtgtggaaga caggaaccag ggcctgatta accttccctt ctccaggtgg ccaaacagga      1800
         gaagaagaag aagaagacag gtcgggctaa gcggcggatg cagtacaacc ggcgctttgt      1860
         caacgttgtg cccacctttg gcaagaagaa gggccccaat gccaactctt aagtcttttg      1920
         taattctggc tttctctaat aaaaaagcca cttagttcag tcatcgcatt gtttcatctt      1980
         tacttgcaag gcctcaggga gaggtgtgct tctcgg                                2016
    //

## 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

There are many ways of specifying input and output sequences for EMBOSS programs, including wildcarded sequence file names, wildcarded database entry names and list files. List files (files of file names) are the most flexible. Instead of containing the sequences themselves, a list file contains one or more sequence references (USAs). For example, a database entry, the name of a file containing sequences, or even the names of another list file. For example, here's a valid list file:

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

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.

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.

## References

None.

## Warnings

None.

## 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
cutseq | Removes a section from a sequence
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)

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