Produces PostScript graphical output from GFF-files Josep Francesc ABRIL FERRANDO, Roderic GUIGO SERRA http://genome.imim.es/software/gfftools/GFF2PS.html gff2ps gff2ps perl "gff2ps" 0 outfile perl "; ln -s gff2ps.out gff2ps.ps" "gff2ps.ps" 1000 rcfile gff2ps.ps psfile perl $default_custom_file .gff2psrc gff_file GFF file perl " $value" 100 output_options Output Options 1 page_size Modify page size (-D) a4 perl (defined $value and $value ne $vdef)? " -s $value" : "" 1 orientation Switches page orientation to Portrait (default is Landscape) (-p) perl ($value)? " -p" : "" 1 split Sets how many pages are needed to split your output (-P) 1 perl ($value and $value != $vdef)? " -P $value" : "" 1 zoom_first Zoom first nucleotide (default is sequence origin) (-S) perl ($value)? " -S $value" : "" 1 zoom_last Zoom last nucleotide (default is sequence length) (-E) perl ($value)? " -E $value" : "" 1 blocks Sets blocks per page (-B) 1 perl ($value and $value != $vdef)? " -B $value" : "" 1 nuc_per_line Sets nucleotides per line (default is the largest sequence position from input gff-files) (-N) perl ($value)? " -N $value" : "" 1 blocks_from_left_to_right Blocks from left to right and from top to bottom (default is top to bottom first) (-b) perl ($value)? " -b" : "" 1 no_headers Switch off Header (Title area) (-L) perl ($value)? " -L" : "" 1 set_title Defining title (default is input gff filename) (-T) perl ($value)? " -T $value" : "" 1 no_page_nb Does not show page numbering (-l) perl ($value)? " -l" : "" 1 no_date Does not show date (-O) perl ($value)? " -O" : "" 1 no_time Does not show time (-o) perl ($value)? " -o" : "" 1 no_copyright Switch off CopyRight line on plot (-a) perl ($value)? " -a" : "" 1 color_options Color Options 3 fg_color_name Sets color for FOREGROUND (-G) black perl ($value and $value ne $vdef)? " -G $value" : "" bg_color_name Sets color for BACKGROUND (-G) white perl ($value and $value ne $vdef)? " -g $value" : "" f0_color_name Sets color for frame 0 (-0) blue perl ($value and $value ne $vdef)? " -0 $value" : "" f1_color_name Sets color for frame 1 (-1) red perl ($value and $value ne $vdef)? " -1 $value" : "" f2_color_name Sets color for frame 2 (-2) green perl ($value and $value ne $vdef)? " -2 $value" : "" f_color_name Sets color for frame . (-3) orange perl ($value and $value ne $vdef)? " -3 $value" : "" tickmark_options Tickmark Options 2 major_tickmarks Number of major tickmarks per line (-M) 10 perl ($value and $value != $vdef)? " -M $value" : "" major_tickmarks_scale Major tickmarks scale in nucleotides (-K) perl ($value)? " -K $value" : "" Default is nucleotide length for lines divided by major tickmarks number (see option -T). minor_tickmarks Number of minor tickmarks between major tickmarks (-m) 10 perl ($value and $value != $vdef)? " -m $value" : "" minor_tickmarks_scale Minor tickmarks scale in nucleotides (-k) perl ($value)? " -k $value" : "" Default is major tickmarks size divided by minor tickmarks number (see option -t). element_options Display elements Options 4 no_forward_strand Switch off displaying forward-strand(Watson) elements (-w) perl ($value)? " -w" : "" no_reverse_strand Switch off displaying reverse-strand(Crick) elements (-c) perl ($value)? " -c" : "" no_strand_independent Switch off displaying strand-independent elements (-i) perl ($value)? " -i" : "" no_label Switch off labels for element positions (-n) perl ($value)? " -n" : "" other_options Other Options 1 default_custom_file Create a new default customfile (.gff2psrc) (-D) perl (defined $value)? " -D .gff2psrc" : "" 5 user_custom_file Your custom rc file (.gff2psrc) perl ($value)? " -C $value" : "" 1