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update igv
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@jrobinso
jrobinso committed Jan 18, 2019
1 parent b99bc28 commit f1dbf55
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Showing 6 changed files with 59 additions and 49,198 deletions.
163 changes: 12 additions & 151 deletions examples/BamFiles.ipynb
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17 changes: 5 additions & 12 deletions examples/EmbeddedFeatures.ipynb
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Expand Up @@ -110,32 +110,25 @@
"source": [
"b.display_svg()"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3",
"display_name": "Python 2",
"language": "python",
"name": "python3"
"name": "python2"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
"version": 2
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.7.1"
"pygments_lexer": "ipython2",
"version": "2.7.15"
}
},
"nbformat": 4,
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17 changes: 12 additions & 5 deletions examples/Embeded-DataURI.ipynb
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Expand Up @@ -60,25 +60,32 @@
"source": [
"b.search(\"CIC--DUX4:10,796-10,844\")"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3",
"display_name": "Python 2",
"language": "python",
"name": "python3"
"name": "python2"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
"version": 2
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.7.1"
"pygments_lexer": "ipython2",
"version": "2.7.15"
}
},
"nbformat": 4,
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145 changes: 10 additions & 135 deletions examples/Events.ipynb
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Expand Up @@ -2,7 +2,7 @@
"cells": [
{
"cell_type": "code",
"execution_count": 2,
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -11,7 +11,7 @@
},
{
"cell_type": "code",
"execution_count": 3,
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -33,42 +33,18 @@
},
{
"cell_type": "code",
"execution_count": 4,
"execution_count": null,
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"<div id=\"igv_2814557\"></div>"
],
"text/plain": [
"<IPython.core.display.HTML object>"
]
},
"metadata": {},
"output_type": "display_data"
}
],
"outputs": [],
"source": [
"b.show()"
]
},
{
"cell_type": "code",
"execution_count": 5,
"execution_count": null,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"'OK'"
]
},
"execution_count": 5,
"metadata": {},
"output_type": "execute_result"
}
],
"outputs": [],
"source": [
"def locuschange(data):\n",
" b.locus = data\n",
Expand All @@ -77,122 +53,21 @@
},
{
"cell_type": "code",
"execution_count": 6,
"execution_count": null,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"'OK'"
]
},
"execution_count": 6,
"metadata": {},
"output_type": "execute_result"
}
],
"outputs": [],
"source": [
"b.zoom_in()"
]
},
{
"cell_type": "code",
"execution_count": 7,
"execution_count": null,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"{u'chr': u'chr20',\n",
" u'end': u'1,234,839',\n",
" u'label': u'chr20:1,234,160-1,234,839',\n",
" u'start': u'1,234,160'}"
]
},
"execution_count": 7,
"metadata": {},
"output_type": "execute_result"
}
],
"outputs": [],
"source": [
"b.locus"
]
},
{
"cell_type": "code",
"execution_count": 8,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Help on class Browser in module igv.browser:\n",
"\n",
"class Browser\n",
" | Methods defined here:\n",
" | \n",
" | __init__(self, config)\n",
" | Initialize an igv Browser object.\n",
" | \n",
" | :param: config - A dictionary specifying the browser configuration. This will be converted to JSON and passed\n",
" | to igv.js \"igv.createBrowser(config)\" as described in the igv.js documentation. See\n",
" | https://github.com/igvteam/igv.js/wiki/Browser-Configuration-2.0 for configuration options.\n",
" | :type dict\n",
" | \n",
" | display_svg(self)\n",
" | Display the current SVG image. You must call get_svg() before calling this method.\n",
" | \n",
" | get_svg(self)\n",
" | Fetch the current IGV view as an SVG image. To display the message call display_svg()\n",
" | \n",
" | load_track(self, track)\n",
" | Load a track. Corresponds to the igv.js Browser function loadTrack (see https://github.com/igvteam/igv.js/wiki/Browser-Control-2.0#loadtrack).\n",
" | \n",
" | :param track: A dictionary specifying track options. See https://github.com/igvteam/igv.js/wiki/Tracks-2.0.\n",
" | :type dict\n",
" | \n",
" | on(self, eventName, cb)\n",
" | Subscribe to an igv.js event.\n",
" | \n",
" | :param Name of the event. Currently only \"locuschange\" is supported.\n",
" | :type str\n",
" | :param cb - callback function taking a single argument. For the locuschange event this argument will contain\n",
" | a dictionary of the form {chr, start, end}\n",
" | :type function\n",
" | \n",
" | remove(self)\n",
" | Remove the igv.js Browser instance from the front end. The server Browser object should be disposed of after calling\n",
" | this method.\n",
" | \n",
" | search(self, locus)\n",
" | Go to the specified locus.\n",
" | \n",
" | :param locus: Chromosome location of the form \"chromsosome:start-end\", or for supported genomes (hg38, hg19, and mm10) a gene name.\n",
" | :type str\n",
" | \n",
" | show(self)\n",
" | Create an igv.js \"Browser\" instance on the front end.\n",
" | \n",
" | zoom_in(self)\n",
" | Zoom in by a factor of 2\n",
" | \n",
" | zoom_out(self)\n",
" | Zoom out by a factor of 2\n",
"\n"
]
}
],
"source": [
"help(igv.Browser)"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
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31 changes: 9 additions & 22 deletions examples/RemoteFiles.ipynb
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Expand Up @@ -2,7 +2,7 @@
"cells": [
{
"cell_type": "code",
"execution_count": 1,
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -11,7 +11,7 @@
},
{
"cell_type": "code",
"execution_count": 2,
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -20,22 +20,9 @@
},
{
"cell_type": "code",
"execution_count": 3,
"execution_count": null,
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"<div id=\"igv_3965189\" class=\"igv-js\"></div>"
],
"text/plain": [
"<IPython.core.display.HTML object>"
]
},
"metadata": {},
"output_type": "execute_result"
}
],
"outputs": [],
"source": [
"b.show()"
]
Expand Down Expand Up @@ -91,21 +78,21 @@
],
"metadata": {
"kernelspec": {
"display_name": "Python 3",
"display_name": "Python 2",
"language": "python",
"name": "python3"
"name": "python2"
},
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"codemirror_mode": {
"name": "ipython",
"version": 3
"version": 2
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.7.1"
"pygments_lexer": "ipython2",
"version": "2.7.15"
}
},
"nbformat": 4,
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48,884 changes: 11 additions & 48,873 deletions igv/static/igvjs/igv.js
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