BP_UNFLATTEN_SEQ(1p)					User Contributed Perl Documentation				      BP_UNFLATTEN_SEQ(1p)

NAME

       unflatten_seq - unflatten a genbank or genbank-style feature file into a nested SeqFeature hierarchy

SYNOPSIS

	 unflatten_seq.PLS -e 3 -gff ~/cvs/bioperl-live/t/data/AE003644_Adh-genomic.gb

	 unflatten_seq.PLS --detail ~/cvs/bioperl-live/t/data/AE003644_Adh-genomic.gb

	 unflatten_seq.PLS -i foo.embl --from embl --to chadoxml -o out.chado.xml

	 unflatten_seq.PLS --notypemap --detail --to asciitree -ethresh 2 AE003644_Adh-genomic.gb

DESCRIPTION

       This script will unflatten a genbank or genbank-style file of SeqFeatures into a nested hierarchy.

       See Bio::SeqFeature::Tools::Unflattener

       In a GenBank/EMBL representation, features are 'flat' - for example, there is no link between an mRNA and a CDS, other than implicit links
       (eg via tags or via splice site coordinates) which may be hard to code for.

       This is most easily illustrated with the default output format, asciitree

       An unflattened genbank feature set may look like this (AB077698)

	 Seq: AB077698
	   databank_entry				    1..2701[+]
	   gene
	     mRNA
	       CDS hCHCR-G				    80..1144[+]
	       exon					    80..1144[+]
	     five_prime_UTR				    1..79[+]
	     located_sequence_feature			    137..196[+]
	     located_sequence_feature			    239..292[+]
	     located_sequence_feature			    617..676[+]
	     located_sequence_feature			    725..778[+]
	     three_prime_UTR				    1145..2659[+]
	     polyA_site 				    1606..1606[+]
	     polyA_site 				    2660..2660[+]

       Or like this (portion of AE003734)

	 gene
	   mRNA CG3320-RA
	     CDS CG3320-PA				  53126..54971[-]
	     exon					  52204..53323[-]
	     exon					  53404..53631[-]
	     exon					  53688..53735[-]
	     exon					  53798..53918[-]
	     exon					  54949..55287[-]
	   mRNA CG3320-RB
	     CDS CG3320-PB				  53383..54971[-]
	     exon					  52204..53631[-]
	     exon					  53688..53735[-]
	     exon					  53798..53918[-]
	     exon					  54949..55287[-]

       The unflattening will also 'normalize' the containment hierarchy (in the sense of standardising it - e.g. making sure there is always a
       transcript record, even if genbank just specifies CDS and gene)

       By default, the GenBank types will be mapped to SO types

       See Bio::SeqFeature::Tools::TypeMapper

COMMAND LINE ARGUMENTS

       -i|input FILE
	   input file (can also be specified as last argument)

       -from FORMAT
	   input format (defaults to genbank)

	   probably doesnt make so much sense to use this for non-flat formats; ie other than embl/genbank

       -to FORMAT
	   output format (defaults to asciitree)

	   should really be a format that is nested SeqFeature aware; I think this is only asciitree, chadoxml and gff3

       -gff
	   with export to GFF3 format (pre-3 GFFs make no sense with unflattened sequences, as they have no set way of representing feature
	   graphs)

       -o|output FILE
	   outfile defaults to STDOUT

       -detail
	   show extra detail on features (asciitree mode only)

       -e|ethresh INT
	   sets the error threshold on unflattening

	   by default this script will throw a wobbly if it encounters weird stuff in the genbank file - raise the error threshold to signal these
	   to be ignored (and reported on STDERR)

       -nomagic
	   suppress use_magic in unflattening (see Bio::SeqFeature::Tools::Unflattener

       -notypemap
	   suppress type mapping (see Bio::SeqFeature::Tools::TypeMapper

TODO

       Bio::SeqFeature::Tools::Unflattener allows fine-grained control over the unflattening process - need to add more options to allow this
       control at the command line

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 list.  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 of the bugs and their resolution. Bug reports can be submitted via
       email or the web:

	 https://redmine.open-bio.org/projects/bioperl/

AUTHOR

	Chris Mungall E<lt>cjm-at-bioperl.orgE<gt>

perl v5.14.2							    2012-03-02						      BP_UNFLATTEN_SEQ(1p)