From 05849a37242695d0d3dfb52059c4d0230842cda8 Mon Sep 17 00:00:00 2001 From: Eric Weitz Date: Thu, 8 Apr 2021 18:00:23 -0400 Subject: [PATCH] Scaffold support for custom organism --- data/bands/native/custom.json | 53 +++++++++++++++++++++++++++ examples/vanilla/custom-organism.html | 41 +++++++++++++++++++++ 2 files changed, 94 insertions(+) create mode 100644 data/bands/native/custom.json create mode 100644 examples/vanilla/custom-organism.html diff --git a/data/bands/native/custom.json b/data/bands/native/custom.json new file mode 100644 index 00000000..d829d1ae --- /dev/null +++ b/data/bands/native/custom.json @@ -0,0 +1,53 @@ +{"chrBands": ["1 p p1 1 15617197 1 15617197 gpos50", + "1 p p1 15617197 17000000 15617197 17000000 acen", + "1 q q1 17000000 18051616 17000000 18051616 acen", + "1 q q1 18051616 43270923 18051616 43270923 gpos50", + "2 p p2 1 12620885 1 12620885 gpos50", + "2 p p2 12620885 14000000 12620885 14000000 acen", + "2 q q2 14000000 15480028 14000000 15480028 acen", + "2 q q2 15480028 35937250 15480028 35937250 gpos50", + "3 p q3 1 17882716 1 17882716 gpos50", + "3 p q3 17882716 19000000 17882716 19000000 acen", + "3 q p3 19000000 20185397 19000000 20185397 acen", + "3 q p3 20185397 36413819 20185397 36413819 gpos50", + "4 p p4 1 8234513 1 8234513 gpos50", + "4 p p4 8234513 9000000 8234513 9000000 acen", + "4 q q4 9000000 10055794 9000000 10055794 acen", + "4 q q4 10055794 35502694 10055794 35502694 gpos50", + "5 p p5 1 11393044 1 11393044 gpos50", + "5 p p5 11393044 12000000 11393044 12000000 acen", + "5 q q5 12000000 13487138 12000000 13487138 acen", + "5 q q5 13487138 29958434 13487138 29958434 gpos50", + "6 p p6 1 13200682 1 13200682 gpos50", + "6 p p6 13200682 15000000 13200682 15000000 acen", + "6 q q6 15000000 17559239 15000000 17559239 acen", + "6 q q6 17559239 31248787 17559239 31248787 gpos50", + "7 p p7 1 9103739 1 9103739 gpos50", + "7 p p7 9103739 11000000 9103739 11000000 acen", + "7 q q7 11000000 12716723 11000000 12716723 acen", + "7 q q7 12716723 29697621 12716723 29697621 gpos50", + "8 p p8 1 11983657 1 11983657 gpos50", + "8 p p8 11983657 13000000 11983657 13000000 acen", + "8 q q8 13000000 14416278 13000000 14416278 acen", + "8 q q8 14416278 28443022 14416278 28443022 gpos50", + "9 p p9 1 1211963 1 1211963 gpos50", + "9 p p9 1211963 2000000 1211963 2000000 acen", + "9 q q9 2000000 3929561 2000000 3929561 acen", + "9 q q9 3929561 23012720 3929561 23012720 gpos50", + "10 p p10 1 7639733 1 7639733 gpos50", + "10 p p10 7639733 8000000 7639733 8000000 acen", + "10 q q10 8000000 8625675 8000000 8625675 acen", + "10 q q10 8625675 23207287 8625675 23207287 gpos50", + "11 p p11 1 11341762 1 11341762 gpos50", + "11 p p11 11341762 12000000 11341762 12000000 acen", + "11 q q11 12000000 13043189 12000000 13043189 acen", + "11 q q11 13043189 29021106 13043189 29021106 gpos50", + "12 p p12 1 11058522 1 11058522 gpos50", + "12 p p12 11058522 11600000 11058522 11600000 acen", + "12 q q12 11600000 12239912 11600000 12239912 acen", + "12 q q12 12239912 27531856 12239912 27531856 gpos50", + "13 p p13 1 9058522 1 9058522 gpos50", + "13 p p13 9058522 11600000 11058522 11600000 acen", + "13 q q13 11600000 12239912 11600000 12239912 acen", + "13 q q13 12239912 27531856 12239912 27531856 gpos50"] +} diff --git a/examples/vanilla/custom-organism.html b/examples/vanilla/custom-organism.html new file mode 100644 index 00000000..4d6ffbe5 --- /dev/null +++ b/examples/vanilla/custom-organism.html @@ -0,0 +1,41 @@ + + + + Custom organism | Ideogram + + + + + +

Custom organism | Ideogram

+ Overview | + Previous | + Next | + Source +

+ A custom genome is depicted below. The grey and black bands in each chromosome + represent + heterochromatin. + The pink region is the area around the + centromere, and the blue represents variable regions. +

+

+ This ideogram shows most chromosomes in a + haploid state for + simplicity. For more accurate, diploid representation of custom genomes, + see Ploidy, basic and + Multiple, trio. +

+ + +