bp_unflatten_seq - unflatten a genbank or genbank-style feature file into a
nested SeqFeature hierarchy
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
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
- -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
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
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.
[email protected] - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
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
Chris Mungall E<lt>cjm-at-bioperl.orgE<gt>