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:6.6.0.0
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
-scircular1 boolean Sequence is circular
-squick1 boolean Read id and sequence only
-sformat1 string Input sequence format
-iquery1 string Input query fields or ID list
-ioffset1 integer Input start position offset
-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
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 INSDC.
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 Ensembl-Gn; ENSG00000149806; Homo_sapiens.
DR Ensembl-Tr; ENST00000279259; Homo_sapiens.
DR Ensembl-Tr; ENST00000434372; Homo_sapiens.
DR Ensembl-Tr; ENST00000525297; Homo_sapiens.
DR Ensembl-Tr; ENST00000526555; Homo_sapiens.
DR Ensembl-Tr; ENST00000527548; Homo_sapiens.
DR Ensembl-Tr; ENST00000529259; Homo_sapiens.
DR Ensembl-Tr; ENST00000529639; Homo_sapiens.
DR Ensembl-Tr; ENST00000531743; Homo_sapiens.
DR GDB; 191789.
DR GDB; 191790.
DR GDB; 354872.
DR GDB; 4590236.
XX
FH Key Location/Qualifiers
FH
FT source 1..2016
[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 i
n from the current directory.
* sw:opsd_xenla - this is a reference to a specific sequence in the SwissPro
t database
* sw:opsd_c* - this represents all the sequences in SwissProt whose identifi
ers 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 Read and write alignments
aligncopypair Read and write pairs from alignments
biosed Replace or delete sequence sections
codcopy Copy and reformat a codon usage table
cutseq Remove a section from a sequence
degapseq Remove non-alphabetic (e.g. gap) characters from sequences
descseq Alter the name or description of a sequence
entret Retrieve 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 Read and write a feature table
featmerge Merge two overlapping feature tables
featreport Read and write 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 Mask all ambiguity characters in nucleotide sequences with
N
maskambigprot Mask 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 Read and write (return) one set of sequences from many
pasteseq Insert one sequence into another
revseq Reverse and complement a nucleotide sequence
seqcount Read and count sequences
seqret Read and write (return) sequences
seqretsetall Read and write (return) many sets of sequences
seqretsplit Read sequences and write them to individual files
sizeseq Sort sequences by size
skipredundant Remove redundant sequences from an input set
skipseq Read and write (return) 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 Remove 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 (c) 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