bp_unflatten_seq.pl man page on Pidora

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BP_UNFLATTEN_SEQ(1)   User Contributed Perl Documentation  BP_UNFLATTEN_SEQ(1)

NAME
       unflatten_seq - unflatten a genbank or genbank-style feature file into
       a nested SeqFeature hierarchy

SYNOPSIS
	 unflatten_seq.PLS -e 3 -gff ~/cvs/bioperl-live/t/data/AE003644_Adh-genomic.gb

	 unflatten_seq.PLS --detail ~/cvs/bioperl-live/t/data/AE003644_Adh-genomic.gb

	 unflatten_seq.PLS -i foo.embl --from embl --to chadoxml -o out.chado.xml

	 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:

	 http://bugzilla.open-bio.org/

AUTHOR
	Chris Mungall E<lt>cjm-at-bioperl.orgE<gt>

perl v5.14.1			  2011-07-22		   BP_UNFLATTEN_SEQ(1)
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