Langue: en

Autres versions - même langue

Version: 2008-11-10 (debian - 07/07/09)

Section: 3 (Bibliothèques de fonctions)






       Bioperl class for:
         gff2ps  Produces PostScript graphical output from GFF-files (Josep Francesc ABRIL FERRANDO, Roderic GUIGO SERRA)
         (see also:
          for available values):
                 gff2ps (String)
                 outfile (OutFile)
                 gff_file (InFile)
                         GFF file
                 page_size (String)
                         Modify page size (-D)
                 orientation (Switch)
                         Switches page orientation to Portrait (default is Landscape) (-p)
                 split (Integer)
                         Sets how many pages are needed to split your output (-P)
                 zoom_first (Integer)
                         Zoom first nucleotide (default is sequence origin) (-S)
                 zoom_last (Integer)
                         Zoom last nucleotide (default is sequence length) (-E)
                 blocks (Integer)
                         Sets blocks per page (-B)
                 nuc_per_line (Integer)
                         Sets nucleotides per line (default is the largest sequence position from input gff-files) (-N)
                 blocks_from_left_to_right (Switch)
                         Blocks from left to right and from top to bottom (default is top to bottom first) (-b)
                 no_headers (Switch)
                         Switch off Header (Title area) (-L)
                 set_title (String)
                         Defining title (default is input gff filename) (-T)
                 no_page_nb (Switch)
                         Does not show page numbering (-l)
                 no_date (Switch)
                         Does not show date (-O)
                 no_time (Switch)
                         Does not show time (-o)
                 no_copyright (Switch)
                         Switch off CopyRight line on plot (-a)
                 fg_color_name (String)
                         Sets color for FOREGROUND (-G)
                 bg_color_name (String)
                         Sets color for BACKGROUND (-G)
                 f0_color_name (String)
                         Sets color for frame 0 (-0)
                 f1_color_name (String)
                         Sets color for frame 1 (-1)
                 f2_color_name (String)
                         Sets color for frame 2 (-2)
                 f_color_name (String)
                         Sets color for frame . (-3)
                 major_tickmarks (Integer)
                         Number of major tickmarks per line (-M)
                 major_tickmarks_scale (Integer)
                         Major tickmarks scale in nucleotides (-K)
                 minor_tickmarks (Integer)
                         Number of minor tickmarks between major tickmarks (-m)
                 minor_tickmarks_scale (Integer)
                         Minor tickmarks scale in nucleotides (-k)
                 no_forward_strand (Switch)
                         Switch off displaying forward-strand(Watson) elements (-w)
                 no_reverse_strand (Switch)
                         Switch off displaying reverse-strand(Crick) elements (-c)
                 no_strand_independent (Switch)
                         Switch off displaying strand-independent elements (-i)
                 no_label (Switch)
                         Switch off labels for element positions (-n)
                 default_custom_file (Switch)
                         Create a new default customfile (.gff2psrc) (-D)
                 user_custom_file (InFile)
                         Your custom rc file (.gff2psrc)


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.                  - General discussion  - 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 the web:


Catherine Letondal ( Copyright (C) 2003 Institut Pasteur & Catherine Letondal. All Rights Reserved.

This module is free software; you can redistribute it and/or modify it under the same terms as Perl itself.


This software is provided ``as is'' without warranty of any kind.



  Title   : new()
  Usage   : my $gff2ps = Bio::Tools::Run::PiseApplication::gff2ps->new($location, $email, @params);
  Function: Creates a Bio::Tools::Run::PiseApplication::gff2ps object.
            This method should not be used directly, but rather by 
            a Bio::Tools::Run::AnalysisFactory::Pise instance.
            my $factory = Bio::Tools::Run::AnalysisFactory::Pise->new();
            my $gff2ps = $factory->program('gff2ps');
  Example : -
  Returns : An instance of Bio::Tools::Run::PiseApplication::gff2ps.