bp_unflatten_seqp - Online in the Cloud

PROGRAM:

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.

[email protected] - 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

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