BP_UNFLATTEN_SEQ(1p) | User Contributed Perl Documentation | BP_UNFLATTEN_SEQ(1p) |
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
probably doesn't make so much sense to use this for non-flat formats; ie other than embl/genbank
should really be a format that is nested SeqFeature aware; I think this is only asciitree, chadoxml and gff3
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)
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
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Chris Mungall E<lt>cjm-at-bioperl.orgE<gt>
2020-10-28 | perl v5.30.3 |