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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)

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