PYTHON   66

volvox_refactored.conf

Guest on 14th June 2022 01:27:16 AM

  1. [GENERAL]
  2. databse     = basic
  3.  
  4. plugins     = Aligner RestrictionAnnotator BatchDumper TrackDumper
  5.  
  6. # list of tracks to turn on by default
  7. default features = ExampleFeatures
  8.  
  9. # size of the region
  10. region segment         = 10000
  11.  
  12. # examples to show in the introduction
  13. examples = ctgA
  14.  
  15. # feature to show on startup
  16. initial landmark = ctgA:5000..10000
  17.  
  18. ########################
  19. # Database sections
  20. ########################
  21. [basic:database]
  22. db_adaptor    = Bio::DB::SeqFeature::Store
  23. db_args       = -adaptor memory
  24.                 -dir '/var/www/gbrowse2/databases/volvox_basic'
  25.  
  26. [genes:database]
  27. db_adaptor    = Bio::DB::SeqFeature::Store
  28. db_args       = -adaptor memory
  29.                 -dir '/var/www/gbrowse2/databases/volvox_genes'
  30.  
  31. [alignments:database]
  32. db_adaptor    = Bio::DB::SeqFeature::Store
  33. db_args       = -adaptor memory
  34.                 -dir '/var/www/gbrowse2/databases/volvox_alignments'
  35.  
  36. [expression:database]
  37. db_adaptor    = Bio::DB::SeqFeature::Store
  38. db_args       = -adaptor memory
  39.                 -dir '/var/www/gbrowse2/databases/volvox_expression'
  40.  
  41. ########################
  42. # Default glyph settings
  43. ########################
  44.  
  45. [TRACK DEFAULTS]
  46. database      = basic
  47. glyph         = generic
  48. height        = 10
  49. bgcolor       = lightgrey
  50. fgcolor       = black
  51. font2color    = blue
  52. label density = 25
  53. bump density  = 100
  54. # where to link to when user clicks in detailed view
  55. link          = AUTO
  56.  
  57. ################## TRACK CONFIGURATION ####################
  58. # the remainder of the sections configure individual tracks
  59. ###########################################################
  60.  
  61. [Motifs:overview]
  62. database     = genes
  63. feature      = polypeptide_domain
  64. glyph        = span
  65. height       = 5
  66. description  = 1
  67. label        = 1
  68. key          = Motifs
  69.  
  70. [ExampleFeatures]
  71. feature      = remark
  72. glyph        = generic
  73. stranded     = 1
  74. bgcolor      = orange
  75. height       = 10
  76. key          = Example Features
  77.  
  78. [NameTest]
  79. database     = genes
  80. feature      = protein_coding_primary_transcript polypeptide
  81. glyph        = generic
  82. stranded     = 1
  83. bgcolor      = green
  84. height       = 10
  85. key          = Name test track
  86.  
  87. [Motifs]
  88. database     = genes
  89. feature      = polypeptide_domain
  90. glyph        = span
  91. height       = 5
  92. description  = 1
  93. balloon hover = <h2>Gene $name</h2>
  94. balloon click = <h2>Gene $name</h2>
  95.        <a href='http://www.google.com/search?q=$name'>Search Google</a><br>
  96.        <a href='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&term=$name'>Search NCBI</a><br>
  97. key          = Example motifs
  98.  
  99. [Alignments]
  100. database     = alignments
  101. feature      = match
  102. glyph        = segments
  103. category     = Alignments
  104. key          = Example alignments
  105.  
  106. [Genes]
  107. database           = genes
  108. feature            = gene
  109. glyph              = gene
  110. bgcolor            = peachpuff
  111. label_transcripts  = 1
  112. draw_translation   = 1
  113. category           = Genes
  114. key                = Protein-coding genes
  115.  
  116. [ReadingFrame]
  117. database           = genes
  118. feature            = mRNA
  119. glyph              = cds
  120. ignore_empty_phase = 1
  121. category           = Genes
  122. key                = Frame usage
  123.  
  124. [CDS]
  125. database           = genes
  126. feature            = CDS:predicted mRNA:exonerate
  127. glyph              = gene
  128. bgcolor            = white
  129. category           = Genes
  130. key                = Predicted genes
  131.  
  132. [Transcript]
  133. database           = genes
  134. feature            = mRNA:exonerate
  135. glyph              = so_transcript
  136. description        = 1
  137. bgcolor            = beige
  138. category           = Genes
  139. key                = Exonerate predictions
  140.  
  141. [Clones]
  142. database     = basic
  143. feature      = BAC
  144. glyph        = segments
  145. bgcolor      = yellow
  146. connector    = dashed
  147. strand_arrow = 1
  148. description  = 1
  149. key          = Fingerprinted BACs
  150.  
  151. [TransChip]
  152. database       = expression
  153. feature        = microarray_oligo
  154. glyph          = wiggle_xyplot
  155. height         = 30
  156. bgcolor        = blue
  157. category       = Quantitative Data
  158. description    = 1
  159. key            = Transcriptional Profile
  160.  
  161. [DNA]
  162. glyph          = dna
  163. global feature = 1
  164. height         = 40
  165. do_gc          = 1
  166. gc_window      = auto
  167. fgcolor        = red
  168. axis_color     = blue
  169. strand         = both
  170. key            = DNA/GC Content
  171.  
  172. [Translation]
  173. glyph          = translation
  174. global feature = 1
  175. height         = 40
  176. fgcolor        = purple
  177. start_codons   = 0
  178. stop_codons    = 1
  179. translation    = 6frame
  180. key            = 6-frame translation
  181.  
  182. [EST]
  183. database         = alignments
  184. feature          = EST_match:est
  185. height           = 6
  186. glyph            = segments
  187. draw_target      = 1
  188. show_mismatch    = 1
  189. canonical_strand = 1
  190. label_position   = left
  191. bgcolor      = sub {
  192.                 my $feature = shift;
  193.                 my $name    = $feature->display_name;
  194.                 if ($name =~ /\.5$/) {
  195.                    return 'red';
  196.                 } else {
  197.                    return 'orange';
  198.                 }
  199.         }
  200. group_pattern     = /\.[53]$/
  201. key               = ESTs
  202.  
  203. [Traces]
  204. database     = alignments
  205. feature      = read
  206. glyph        = trace
  207. fgcolor      = black
  208. bgcolor      = orange
  209. strand_arrow = 1
  210. height       = 6
  211. description  = 1
  212. a_color      = green
  213. c_color      = blue
  214. g_color      = black
  215. t_color      = red
  216. trace_height = 80
  217. trace_prefix = http://localhost/gbrowse2/tutorial/data_files/
  218. key          = Traces
  219.  
  220. ########################
  221. # Plugin configuration
  222. ########################
  223.  
  224. [Aligner:plugin]
  225. alignable_tracks   = EST
  226. upcase_tracks      = CDS Motifs
  227. upcase_default     = CDS

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