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extractalign
Function
Extract regions from a sequence alignment
Description
extractalign allows you to specify one or more regions of a sequence
alignment to extract sub-sequences from to build up a resulting
sub-sequence alignment. extractakign reads in a sequence alignment and
a set of regions of that alignment as specified by pairs of start and
end positions (either on the command-line or contained in a file)
using gapped alignment positions as the coordinates, and writes out
the specified regions of the input sequence in the order in which they
have been specified. Thus, if the sequence "AAAGGGTTT" has been input
and the regions: "7-9, 3-4" have been specified, then the output
sequence will be: "TTTAG".
Usage
Here is a sample session with extractalign
Extract the region from position 10 to 20:
% extractalign dna.msf result.seq -regions '11-30'
Extract regions from a sequence alignment
Go to the input files for this example
Go to the output files for this example
Command line arguments
Standard (Mandatory) qualifiers:
[-sequence] seqset (Aligned) sequence set filename and optional
format, or reference (input USA)
-regions range [Whole sequence] Regions to extract.
A set of regions is specified by a set of
pairs of positions.
The positions are integers.
They are separated by any non-digit,
non-alpha character.
Examples of region specifications are:
24-45, 56-78
1:45, 67=99;765..888
1,5,8,10,23,45,57,99
[-outseq] seqoutall [.] Sequence set(s)
filename and optional format (output USA)
Additional (Optional) qualifiers: (none)
Advanced (Unprompted) qualifiers: (none)
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
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
extractalign reads a normal sequence USA.
Input files for usage example
File: dna.msf
!!NA_MULTIPLE_ALIGNMENT
dna.msf MSF: 120 Type: N January 01, 1776 12:00 Check: 3196 ..
Name: MSFM1 Len: 120 Check: 8587 Weight: 1.00
Name: MSFM2 Len: 120 Check: 6178 Weight: 1.00
Name: MSFM3 Len: 120 Check: 8431 Weight: 1.00
//
MSFM1 ACGTACGTAC GTACGTACGT ACGTACGTAC GTACGTACGT ACGTACGTAC
MSFM2 ACGTACGTAC GTACGTACGT ....ACGTAC GTACGTACGT ACGTACGTAC
MSFM3 ACGTACGTAC GTACGTACGT ACGTACGTAC GTACGTACGT CGTACGTACG
MSFM1 GTACGTACGT ACGTACGTAC GTACGTACGT ACGTACGTAC GTACGTACGT
MSFM2 GTACGTACGT ACGTACGTAC GTACGTACGT ACGTACGTAC GTACGTACGT
MSFM3 TACGTACGTA CGTACGTACG TACGTACGTA ACGTACGTAC GTACGTACGT
MSFM1 ACGTACGTAC GTACGTACGT
MSFM2 ACGTACGTTG CAACGTACGT
MSFM3 ACGTACGTAC GTACGTACGT
You can specifiy a file of ranges to extract by giving the '-regions'
qualifier the value '@' followed by the name of the file containing
the ranges. (eg: '-regions @myfile').
The format of the range file is:
* Comment lines start with '#' in the first column.
* Comment lines and blank lines are ignored.
* The line may start with white-space.
* There are two positive (integer) numbers per line separated by one
or more space or TAB characters.
* The second number must be greater or equal to the first number.
* There can be optional text after the two numbers to annotate the
line.
* White-space before or after the text is removed.
An example range file is:
# this is my set of ranges
12 23
4 5 this is like 12-23, but smaller
67 10348 interesting region
Output file format
The output is a normal sequence file.
Output files for usage example
File: result.seq
>MSFM1
GTACGTACGTACGTACGTAC
>MSFM2
GTACGTACGT----ACGTAC
>MSFM3
GTACGTACGTACGTACGTAC
If the option '-separate' is used then each specified region is
written to the output file as a separate sequence. The name of the
sequence is created from the name of the original sequence with the
start and end positions of the range appended with underscore
characters between them,
For example: "XYZ region 2 to 34" is written as: "XYZ_2_34"
Data files
None.
Notes
None.
References
None.
Warnings
None.
Diagnostic Error Messages
Several warning messages about malformed region specifications:
* Non-digit found in region ...
* Unpaired start of a region found in ...
* Non-digit found in region ...
* The start of a pair of region positions must be smaller than the
end in ...
Exit status
It exits with status 0, unless a region is badly constructed.
Known bugs
None noted.
Comments
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
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
yank Reads a sequence range, appends the full USA to a list file
Author(s)
Peter Rice (pmr ebi.ac.uk)
Informatics Division, European Bioinformatics Institute, Wellcome
Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
History
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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