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union
Function
Reads sequence fragments and builds one sequence
Description
union reads in several sequences, concatenates them and writes them
out as a single sequence.
It is most useful when the input sequences are specified in a List
file. The List file (file of sequence names) can be any set of
sequences in files or database entries specified in the normal EMBOSS
USA (which can include the spcification of sub-regions of the
sequence, eg. 'em:hsfau[20,55]'). Specifying several such subregions
in a sequence or sequences allows you to enter disjoint sequences to
be joined.
Usage
Here is a sample session with union
The file 'cds.list' contains a list of the regions making up the
coding sequence of 'embl:x65923':
% union
Reads sequence fragments and builds one sequence
Input (gapped) sequence(s): @cds.list
output sequence [x65921.fasta]:
Go to the input files for this example
Go to the output files for this example
Command line arguments
Standard (Mandatory) qualifiers:
[-sequence] seqall (Gapped) sequence(s) filename and optional
format, or reference (input USA)
[-outseq] seqout [.] Sequence filename and
optional format (output USA)
Additional (Optional) qualifiers:
-overlapfile outfile [*.union] Sequence overlaps output file
(optional)
Advanced (Unprompted) qualifiers:
-feature boolean [N] Use feature information
-source boolean [N] Create source features
-findoverlap boolean [N] Look for overlaps when joining
Associated qualifiers:
"-sequence" associated qualifiers
-sbegin1 integer Start of each sequence to be used
-send1 integer End of each 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
"-outseq" associated qualifiers
-osformat2 string Output seq format
-osextension2 string File name extension
-osname2 string Base file name
-osdirectory2 string Output directory
-osdbname2 string Database name to add
-ossingle2 boolean Separate file for each entry
-oufo2 string UFO features
-offormat2 string Features format
-ofname2 string Features file name
-ofdirectory2 string Output directory
"-overlapfile" associated qualifiers
-odirectory 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
The input can be any set of sequences in a file of multiple sequence
entries or in a List file. The sequences are concatenated in the order
in which they appear in the file.
Input 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]
You may find the program yank useful for creating List files.
Output file format
Output files for usage example
File: x65921.fasta
>X65921 X65921.1 H.sapiens fau 1 gene
atgcagctctttgtccgcgcccaggagctacacaccttcgaggtgaccggccaggaaacg
gtcgcccagatcaaggctcatgtagcctcactggagggcattgccccggaagatcaagtc
gtgctcctggcaggcgcgcccctggaggatgaggccactctgggccagtgcggggtggag
gccctgactaccctggaagtagcaggccgcatgcttggaggtaaagtccatggttccctg
gcccgtgctggaaaagtgagaggtcagactcctaaggtggccaaacaggagaagaagaag
aagaagacaggtcgggctaagcggcggatgcagtacaaccggcgctttgtcaacgttgtg
cccacctttggcaagaagaagggccccaatgccaactcttaa
The result is a normal sequence file containing a single sequence
resulting from the concatenation of the input sequences.
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
vectorstrip Strips out DNA between a pair of vector sequences
yank Reads a sequence range, appends the full USA to a list file
You may find the program yank useful for creating List files.
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
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