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EMBOSS: yank
yank

 

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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 

Add a sequence reference (a full USA) to a list file
Version: EMBOSS:6.4.0.0

   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 and exit. 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
   -version            boolean    Report version number and exit

Qualifier Type Description Allowed values Default
Standard (Mandatory) qualifiers
[-sequence]
(Parameter 1)		 sequence (Gapped) sequence filename and optional format, or reference (input USA) Readable sequence Required
[-outfile]
(Parameter 2)		 outfile List of USAs output file Output file <*>.yank
Additional (Optional) qualifiers
(none)
Advanced (Unprompted) qualifiers
-newfile boolean Overwrite existing output file Boolean value Yes/No No
Associated qualifiers
"-sequence" associated sequence qualifiers
-sbegin1
-sbegin_sequence		 integer Start of the sequence to be used Any integer value 0
-send1
-send_sequence		 integer End of the sequence to be used Any integer value 0
-sreverse1
-sreverse_sequence		 boolean Reverse (if DNA) Boolean value Yes/No N
-sask1
-sask_sequence		 boolean Ask for begin/end/reverse Boolean value Yes/No Y
-snucleotide1
-snucleotide_sequence		 boolean Sequence is nucleotide Boolean value Yes/No N
-sprotein1
-sprotein_sequence		 boolean Sequence is protein Boolean value Yes/No N
-slower1
-slower_sequence		 boolean Make lower case Boolean value Yes/No N
-supper1
-supper_sequence		 boolean Make upper case Boolean value Yes/No N
-sformat1
-sformat_sequence		 string Input sequence format Any string  
-sdbname1
-sdbname_sequence		 string Database name Any string  
-sid1
-sid_sequence		 string Entryname Any string  
-ufo1
-ufo_sequence		 string UFO features Any string  
-fformat1
-fformat_sequence		 string Features format Any string  
-fopenfile1
-fopenfile_sequence		 string Features file name Any string  
"-outfile" associated outfile qualifiers
-odirectory2
-odirectory_outfile		 string Output directory Any string  
General qualifiers
-auto boolean Turn off prompts Boolean value Yes/No N
-stdout boolean Write first file to standard output Boolean value Yes/No N
-filter boolean Read first file from standard input, write first file to standard output Boolean value Yes/No N
-options boolean Prompt for standard and additional values Boolean value Yes/No N
-debug boolean Write debug output to program.dbg Boolean value Yes/No N
-verbose boolean Report some/full command line options Boolean value Yes/No Y
-help boolean Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose Boolean value Yes/No N
-warning boolean Report warnings Boolean value Yes/No Y
-error boolean Report errors Boolean value Yes/No Y
-fatal boolean Report fatal errors Boolean value Yes/No Y
-die boolean Report dying program messages Boolean value Yes/No Y
-version boolean Report version number and exit Boolean value Yes/No N

Input file format

yank reads a single nucleotide or protein sequence.

The input is a standard EMBOSS sequence query (also known as a 'USA').

Major sequence database sources defined as standard in EMBOSS installations include srs:embl, srs:uniprot and ensembl

Data can also be read from sequence output in any supported format written by an EMBOSS or third-party application.

The input format can be specified by using the command-line qualifier -sformat xxx, where 'xxx' is replaced by the name of the required format. The available format names are: gff (gff3), gff2, embl (em), genbank (gb, refseq), ddbj, refseqp, pir (nbrf), swissprot (swiss, sw), dasgff and debug.

See: http://emboss.sf.net/docs/themes/SequenceFormats.html for further information on sequence formats.

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
feattext Return a feature table original text
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 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
nthseqset Reads and writes (returns) one set of sequences from many
pasteseq Insert one sequence into another
revseq Reverse and complement a nucleotide sequence
seqcount Reads and counts sequences
seqret Reads and writes (returns) sequences
seqretsetall Reads and writes (returns) many sets of 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
splitsource Split sequence(s) into original source sequences
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
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK

Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.

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