NAME

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

SYNOPSIS

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

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

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

         bp_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 doesn't 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://github.com/bioperl/bioperl-live/issues

AUTHOR

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