Appdoc:Extractalign

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Contents

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.

extractalign 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

Qualifier Type Description Allowed values Default
Standard (Mandatory) qualifiers
[-sequence]
(Parameter 1) 		seqset (Aligned) sequence set filename and optional format, or reference (input USA) Readable set of sequences Required
-regions range 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, 56-781:45, 67=99;765..8881,5,8,10,23,45,57,99 Sequence range Whole sequence
[-outseq]
(Parameter 2) 		seqoutall Sequence set(s) filename and optional format (output USA) Writeable sequence(s) <*>.format
Additional (Optional) qualifiers
(none)
Advanced (Unprompted) qualifiers
(none)
Associated qualifiers
"-sequence" associated seqset qualifiers
-sbegin1
-sbegin_sequence 		integer Start of each sequence to be used Any integer value 0
-send1
-send_sequence 		integer End of each 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 N
-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  
"-outseq" associated seqoutall qualifiers
-osformat2
-osformat_outseq 		string Output seq format Any string  
-osextension2
-osextension_outseq 		string File name extension Any string  
-osname2
-osname_outseq 		string Base file name Any string  
-osdirectory2
-osdirectory_outseq 		string Output directory Any string  
-osdbname2
-osdbname_outseq 		string Database name to add Any string  
-ossingle2
-ossingle_outseq 		boolean Separate file for each entry Boolean value Yes/No N
-oufo2
-oufo_outseq 		string UFO features Any string  
-offormat2
-offormat_outseq 		string Features format Any string  
-ofname2
-ofname_outseq 		string Features file name Any string  
-ofdirectory2
-ofdirectory_outseq 		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. 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

Input file format

extractalign reads a normal sequence USA.


Input 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 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

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
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
nthseqset Reads and writes (returns) one set of sequences from many
pasteseq Insert one sequence into another
revseq Reverse and complement a nucleotide sequence
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)
yank Add a sequence reference (a full USA) to a list file

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

Target users

This program is intended to be used by everyone and everything, from naive users to embedded scripts.

Comments

None

Retrieved from "http://emboss.open-bio.org/wiki/Appdoc:Extractalign"
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