Skip site navigation (1)Skip section navigation (2)

FreeBSD Manual Pages

  
 
  

home | help
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 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

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 v5.32.0			  2019-12-07		   BP_UNFLATTEN_SEQ(1)

NAME | SYNOPSIS | DESCRIPTION | COMMAND LINE ARGUMENTS | TODO | FEEDBACK | AUTHOR

Want to link to this manual page? Use this URL:
<https://www.freebsd.org/cgi/man.cgi?query=bp_unflatten_seq&sektion=1&manpath=FreeBSD+12.2-RELEASE+and+Ports>

home | help