[Bio] / FigKernelScripts / svr_tree_to_html.pl Repository:
ViewVC logotype

Diff of /FigKernelScripts/svr_tree_to_html.pl

Parent Directory Parent Directory | Revision Log Revision Log | View Patch Patch

revision 1.7, Tue Feb 1 03:57:00 2011 UTC revision 1.9, Wed Feb 16 23:16:01 2011 UTC
# Line 41  Line 41 
41                              or groups specified in a file     # table: [id group]                              or groups specified in a file     # table: [id group]
42         -d   desc_file     - add description to each tip       # table: [id description]         -d   desc_file     - add description to each tip       # table: [id description]
43         -f   focus_list    - highlight a list of tips          # table: [id]         -f   focus_list    - highlight a list of tips          # table: [id]
44           -k   keep_list     - keep only the taxa listed         # table: [id]
45         -l   link_file     - add URL to each tip               # table: [id URL]         -l   link_file     - add URL to each tip               # table: [id URL]
46         -lt  link_w_text   - add additional linked text        # table: [id text URL]         -lt  link_w_text   - add additional linked text        # table: [id text URL]
47         -m   popup_file    - add simple mouseover to each tip  # table: [id popup]         -m   popup_file    - add simple mouseover to each tip  # table: [id popup]
# Line 56  Line 57 
57         -anno              - use the annotator's SEED for URLs         -anno              - use the annotator's SEED for URLs
58         -gray n            - gray out name from the n-th word  # default: 2         -gray n            - gray out name from the n-th word  # default: 2
59         -pseed             - use PSEED         -pseed             - use PSEED
60           -ppseed            - use PUBLIC_SEED
61         -raw               - do not color or collapse tree,         -raw               - do not color or collapse tree,
62                              may be superseded by -c and -p                              may be superseded by -c and -p
63    
# Line 104  Line 106 
106    
107  A file with space-delimited IDs for sequences to be highlighted.  A file with space-delimited IDs for sequences to be highlighted.
108    
109    =item -k keep_list
110    
111    Keep only the taxa listed (one per line) in the file keep.
112    
113  =item -l link_file  =item -l link_file
114    
115  A two-column table [ id, url ] for inserting URL for tree tips.  A two-column table [ id, url ] for inserting URL for tree tips.
# Line 162  Line 168 
168  retrieved from the PSEED server. Setting the environment variable  retrieved from the PSEED server. Setting the environment variable
169  SAS_SERVER to 'PSEED' has the same effect.  SAS_SERVER to 'PSEED' has the same effect.
170    
171    =item -ppseed
172    
173    With the -ppseed option, the taxonomy and function information is
174    retrieved from the PUBLIC_SEED server. Setting the environment variable
175    SAS_SERVER to 'PUBLIC_SEED' has the same effect.
176    
177  =item -raw  =item -raw
178    
179  Do not color or collapse the tree. This option maybe superseded if -c  Do not color or collapse the tree. This option maybe superseded if -c
# Line 197  Line 209 
209                              or groups specified in a file     # file: [id group]                              or groups specified in a file     # file: [id group]
210         -d   desc_file     - add description to each tip       # file: [id description]         -d   desc_file     - add description to each tip       # file: [id description]
211         -f   focus_list    - highlight a list of tips          # file: [id]         -f   focus_list    - highlight a list of tips          # file: [id]
212           -k   keep_list     - keep only the taxa listed         # table: [id]
213         -l   link_file     - add URL to each tip               # file: [id URL]         -l   link_file     - add URL to each tip               # file: [id URL]
214         -lt  link_w_text   - add additional linked text        # file: [id text URL]         -lt  link_w_text   - add additional linked text        # file: [id text URL]
215         -m   popup_file    - add simple mouseover to each tip  # file: [id popup]         -m   popup_file    - add simple mouseover to each tip  # file: [id popup]
# Line 211  Line 224 
224         -anno              - use the annotator's SEED for URLs         -anno              - use the annotator's SEED for URLs
225         -gray n            - gray out name from the n-th word  # default: 2         -gray n            - gray out name from the n-th word  # default: 2
226         -pseed             - use PSEED         -pseed             - use PSEED
227           -ppseed            - use PUBLIC_SEED
228         -raw               - do not color or collapse the tree,         -raw               - do not color or collapse the tree,
229                              may be superseded by -c and -p                              may be superseded by -c and -p
230    
231  End_of_Usage  End_of_Usage
232    
233  my ($help, $url, $alias_file, $focus_file, $branch, $collapse_by, $show_file,  my ($help, $url, $alias_file, $focus_file, $branch, $collapse_by, $show_file,
234      $desc_file, $link_file, $text_link, $popup_file, $id_file, $title,      $desc_file, $keep_file, $link_file, $text_link, $popup_file, $id_file, $title,
235      $min_dx, $dy, $ncolor, $color_by, $anno, $gray, $pseed, $raw);      $min_dx, $dy, $ncolor, $color_by, $anno, $gray, $pseed, $ppseed, $raw);
236    
237  GetOptions("h|help"         => \$help,  GetOptions("h|help"         => \$help,
238             "a|alias=s"      => \$alias_file,             "a|alias=s"      => \$alias_file,
# Line 227  Line 241 
241             "d|desc=s"       => \$desc_file,             "d|desc=s"       => \$desc_file,
242             "f|focus=s"      => \$focus_file,             "f|focus=s"      => \$focus_file,
243             "i|id=s"         => \$id_file,             "i|id=s"         => \$id_file,
244               "k|keep=s"       => \$keep_file,
245             "l|link=s"       => \$link_file,             "l|link=s"       => \$link_file,
246             "lt=s"           => \$text_link,             "lt=s"           => \$text_link,
247             "m|popup=s"      => \$popup_file,             "m|popup=s"      => \$popup_file,
# Line 239  Line 254 
254             "anno"           => \$anno,             "anno"           => \$anno,
255             "g|gray=i"       => \$gray,             "g|gray=i"       => \$gray,
256             "pseed"          => \$pseed,             "pseed"          => \$pseed,
257               "ppseed"         => \$ppseed,
258             "raw"            => \$raw);             "raw"            => \$raw);
259    
260  $help and die $usage;  $help and die $usage;
# Line 253  Line 269 
269  $opts->{color_by}      = ffxtree::read_hash($color_by)     if $color_by      && -s $color_by;  $opts->{color_by}      = ffxtree::read_hash($color_by)     if $color_by      && -s $color_by;
270  $opts->{collapse_by}   = ffxtree::read_hash($collapse_by)  if $collapse_by   && -s $collapse_by;  $opts->{collapse_by}   = ffxtree::read_hash($collapse_by)  if $collapse_by   && -s $collapse_by;
271  $opts->{collapse_show} = ffxtree::read_set($show_file)     if $show_file     && -s $show_file;  $opts->{collapse_show} = ffxtree::read_set($show_file)     if $show_file     && -s $show_file;
272    $opts->{keep}          = ffxtree::read_set($keep_file)     if $keep_file     && -s $keep_file;
273  $opts->{desc}          = ffxtree::read_hash($desc_file)    if $desc_file     && -s $desc_file;  $opts->{desc}          = ffxtree::read_hash($desc_file)    if $desc_file     && -s $desc_file;
274  $opts->{popup}         = ffxtree::read_hash($popup_file)   if $popup_file    && -s $popup_file;  $opts->{popup}         = ffxtree::read_hash($popup_file)   if $popup_file    && -s $popup_file;
275  $opts->{link}          = ffxtree::read_hash($link_file)    if $link_file     && -s $link_file;  $opts->{link}          = ffxtree::read_hash($link_file)    if $link_file     && -s $link_file;
# Line 270  Line 287 
287  $opts->{collapse_by}   ||= $raw ? 'none' : 'genus';  $opts->{collapse_by}   ||= $raw ? 'none' : 'genus';
288  $opts->{collapse_show} ||= $raw ? 'none' : 'woese';  $opts->{collapse_show} ||= $raw ? 'none' : 'woese';
289    
290  $opts->{color_by}      = 0 if $opts->{color_by}    =~ /none/i;  $opts->{color_by}      = 0 if $opts->{color_by}    =~ /^none$/i;
291  $opts->{collapse_by}   = 0 if $opts->{collapse_by} =~ /none/i;  $opts->{collapse_by}   = 0 if $opts->{collapse_by} =~ /^none$/i;
292  $opts->{collapse_show} = 0 if $show_file           =~ /(none|0)/i;  $opts->{collapse_show} = 0 if $show_file           =~ /^none$/i;
293    
294  my $envParm = $ENV{SAS_SERVER};  my $envParm = $ENV{SAS_SERVER};
295    
296  $ENV{SAS_SERVER} = 'PSEED' if $pseed;  $ENV{SAS_SERVER} = 'PSEED' if $pseed;
297    $ENV{SAS_SERVER} = 'PUBLIC_SEED' if $ppseed;
298    
299  my $html = ffxtree::tree_to_html($opts);  my $html = ffxtree::tree_to_html($opts);
300    
301  $ENV{SAS_SERVER} = $envParm if $pseed;  $ENV{SAS_SERVER} = $envParm if $pseed || $ppseed;
302    
303  print $html;  print $html;

Legend:
Removed from v.1.7  
changed lines
  Added in v.1.9

MCS Webmaster
ViewVC Help
Powered by ViewVC 1.0.3