PYTHON   68
volvox_final.conf
Guest on 14th June 2022 01:23:29 AM


  1. [GENERAL]
  2. db_adaptor    = Bio::DB::SeqFeature::Store
  3. db_args       = -adaptor memory
  4.                 -dir '/var/www/gbrowse2/databases/volvox'
  5.  
  6. plugins     = Aligner RestrictionAnnotator TrackDumper
  7.  
  8. # list of tracks to turn on by default
  9. default features = ExampleFeatures
  10.  
  11. # size of the region
  12. region segment         = 10000
  13.  
  14. # examples to show in the introduction
  15. examples = ctgA
  16.  
  17. # feature to show on startup
  18. initial landmark = ctgA:5000..10000
  19.  
  20.  
  21. ########################
  22. # Default glyph settings
  23. ########################
  24.  
  25.  
  26. [TRACK DEFAULTS]
  27. glyph         = generic
  28. height        = 10
  29. bgcolor       = lightgrey
  30. fgcolor       = black
  31. font2color    = blue
  32. label density = 25
  33. bump density  = 100
  34. # where to link to when user clicks in detailed view
  35. link          = AUTO
  36.  
  37. ################## TRACK CONFIGURATION ####################
  38. # the remainder of the sections configure individual tracks
  39. ###########################################################
  40.  
  41. [ExampleFeatures]
  42. feature      = remark
  43. glyph        = generic
  44. stranded     = 1
  45. bgcolor      = orange
  46. height       = 10
  47. key          = Example Features
  48.  
  49. [NameTest]
  50. feature      = protein_coding_primary_transcript polypeptide
  51. glyph        = generic
  52. stranded     = 1
  53. bgcolor      = green
  54. height       = 10
  55. key          = Name test track
  56.  
  57. [Motifs]
  58. feature      = polypeptide_domain
  59. glyph        = span
  60. height       = 5
  61. description  = 1
  62. balloon hover = <h2>Gene $name</h2>
  63. balloon click = <h2>Gene $name</h2>
  64.        <a href='https://www.google.com/search?q=$name'>Search Google</a><br>
  65.        <a href='https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&term=$name'>Search NCBI</a><br>
  66. key          = Example motifs
  67.  
  68. [Alignments]
  69. feature      = match
  70. glyph        = segments
  71. category     = Alignments
  72. key          = Example alignments
  73.  
  74. [Genes]
  75. feature            = gene
  76. glyph              = gene
  77. bgcolor            = peachpuff
  78. label_transcripts  = 1
  79. draw_translation   = 1
  80. category           = Genes
  81. key                = Protein-coding genes
  82.  
  83. [ReadingFrame]
  84. feature            = mRNA
  85. glyph              = cds
  86. ignore_empty_phase = 1
  87. category           = Genes
  88. key                = Frame usage
  89.  
  90. [CDS]
  91. feature            = CDS:predicted mRNA:exonerate
  92. glyph              = gene
  93. bgcolor            = white
  94. category           = Genes
  95. key                = Predicted genes
  96.  
  97. [Transcript]
  98. feature            = mRNA:exonerate
  99. glyph              = so_transcript
  100. description        = 1
  101. bgcolor            = beige
  102. category           = Genes
  103. key                = Exonerate predictions
  104.  
  105. [Clones]
  106. feature      = BAC
  107. glyph        = segments
  108. bgcolor      = yellow
  109. connector    = dashed
  110. strand_arrow = 1
  111. description  = 1
  112. key          = Fingerprinted BACs
  113.  
  114. [TransChip1]
  115. feature        = microarray_oligo
  116. glyph          = wiggle_xyplot
  117. height         = 30
  118. bgcolor        = blue
  119. category       = Genes
  120. description    = 1
  121. key            = Transcriptional Profile
  122.  
  123. [DNA]
  124. glyph          = dna
  125. global feature = 1
  126. height         = 40
  127. do_gc          = 1
  128. gc_window      = auto
  129. fgcolor        = red
  130. axis_color     = blue
  131. strand         = both
  132. key            = DNA/GC Content
  133.  
  134. [Translation]
  135. glyph          = translation
  136. global feature = 1
  137. height         = 40
  138. fgcolor        = purple
  139. start_codons   = 0
  140. stop_codons    = 1
  141. translation    = 6frame
  142. key            = 6-frame translation
  143.  
  144. [EST]
  145. feature          = EST_match:est
  146. height           = 6
  147. glyph            = segments
  148. draw_target      = 1
  149. show_mismatch    = 1
  150. canonical_strand = 1
  151. label_position   = left
  152. bgcolor      = sub {
  153.                 my $feature = shift;
  154.                 my $name    = $feature->display_name;
  155.                 if ($name =~ /\.5$/) {
  156.                    return 'red';
  157.                 } else {
  158.                    return 'orange';
  159.                 }
  160.         }
  161. group_pattern     = /\.[53]$/
  162. key               = ESTs
  163.  
  164. [Traces]
  165. feature      = read
  166. glyph        = trace
  167. fgcolor      = black
  168. bgcolor      = orange
  169. strand_arrow = 1
  170. height       = 6
  171. description  = 1
  172. a_color      = green
  173. c_color      = blue
  174. g_color      = black
  175. t_color      = red
  176. trace_height = 80
  177. trace_prefix = http://localhost/gbrowse2/tutorial/data_files/
  178. key          = Traces
  179.  
  180. ########################
  181. # Plugin configuration
  182. ########################
  183.  
  184. [Aligner:plugin]
  185. alignable_tracks   = EST
  186. upcase_tracks      = CDS Motifs
  187. upcase_default     = CDS
  188.  
  189. [Motifs:overview]
  190. feature      = polypeptide_domain
  191. glyph        = span
  192. height       = 5
  193. description  = 1
  194. label        = 1
  195. key          = Motifs
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