BP_UNFLATTEN_SEQ(1) User Contributed Perl Documentation BP_UNFLATTEN_SEQ(1)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 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://github.com/bioperl/bioperl-live/issues
AUTHOR
Chris Mungall E<lt>cjm-at-bioperl.orgE<gt>
perl v5.20.2 2015-09-15 BP_UNFLATTEN_SEQ(1)