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PROGRAM:

NAME


bp_flanks - finding flanking sequences for a variant in a sequence position

SYNOPSIS


bp_flanks --position POS [-p POS ...] [--flanklen INT]
accession | filename

DESCRIPTION


This script allows you to extract a subsequence around a region of interest from an
existing sequence. The output if fasta formatted sequence entry where the header line
contains additional information about the location.

OPTIONS


The script takes one unnamed argument which be either a file name in the local file system
or a nucleotide sequence accession number.

-p Position uses simple nucleotide sequence feature table
--position notation to define the region of interest, typically a
SNP or microsatellite repeat around which the flanks are
defined.

There can be more than one position option or you can
give a comma separated list to one position option.

The format of a position is:

[id:] int | range | in-between [-]

The optional id is the name you want to call the new
sequence. If it not given in joins running number to the
entry name with an underscore.

The position is either a point (e.g. 234), a range (e.g
250..300) or insertion point between nucleotides
(e.g. 234^235)

If the position is not completely within the source
sequence the output sequence will be truncated and it
will print a warning.

The optional hyphen [-] at the end of the position
indicates that that you want the retrieved sequence to be
in the opposite strand.

-f Defaults to 100. This is the length of the nucleotides
--flanklen sequence retrieved on both sides of the given position.

If the source file does not contain

OUTPUT FORMAT


The output is a fasta formatted entry where the description file contains tag=value pairs
for information about where in the original sequence the subsequence was taken.

The ID of the fasta entry is the name given at the command line joined by hyphen to the
filename or accesion of the source sequence. If no id is given a series of consequtive
integers is used.

The tag=value pairs are:

oripos=int
position in the source file

strand=1|-1
strand of the sequence compared to the source sequence

allelepos=int
position of the region of interest in the current entry. The tag is the same as used
by dbSNP@NCBI

The sequence highlights the allele variant position by showing it in upper case and rest
of the sequence in lower case characters.

EXAMPLE


% bp_flanks ~/seq/ar.embl

>1_/HOME/HEIKKI/SEQ/AR.EMBL oripos=100 strand=1 allelepos=100
taataactcagttcttatttgcacctacttcagtggacactgaatttggaaggtggagga
ttttgtttttttcttttaagatctgggcatcttttgaatCtacccttcaagtattaagag
acagactgtgagcctagcagggcagatcttgtccaccgtgtgtcttcttctgcacgagac
tttgaggctgtcagagcgct

TODO


The input files are assumed to be in EMBL format and the sequences are retrieved only from
the EMB database. Make this more generic and use the registry.

head1 FEEDBACK

Mailing Lists
User feedback is an integral part of the evolution of this and other Bioperl modules. Send
your comments and suggestions preferably to the Bioperl mailing lists Your participation
is much appreciated.

bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists

Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their
resolution. Bug reports can be submitted via the web:

https://github.com/bioperl/bioperl-live/issues

AUTHOR - Heikki Lehvaslaiho


Email: <heikki-at-bioperl-dot-org>

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