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Updated ga4gh_client library in notebooks, and re-ran all of the serv…
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…ice notebooks
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@achave11-ucsc
achave11-ucsc committed Oct 12, 2016
1 parent 9b9ad95 commit 400d3a5
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Showing 7 changed files with 175 additions and 160 deletions.
12 changes: 6 additions & 6 deletions python_notebooks/1kg_allele_annotation_service.ipynb
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Expand Up @@ -20,11 +20,11 @@
"cell_type": "code",
"execution_count": 1,
"metadata": {
"collapsed": true
"collapsed": false
},
"outputs": [],
"source": [
"import ga4gh.client as client\n",
"import ga4gh_client.client as client\n",
"c = client.HttpClient(\"http://1kgenomes.ga4gh.org\")"
]
},
Expand All @@ -38,7 +38,7 @@
},
{
"cell_type": "code",
"execution_count": 4,
"execution_count": 2,
"metadata": {
"collapsed": false
},
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},
{
"cell_type": "code",
"execution_count": 10,
"execution_count": 3,
"metadata": {
"collapsed": false
},
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},
{
"cell_type": "code",
"execution_count": 12,
"execution_count": 4,
"metadata": {
"collapsed": false
},
Expand All @@ -241,7 +241,7 @@
},
{
"cell_type": "code",
"execution_count": 15,
"execution_count": 5,
"metadata": {
"collapsed": false
},
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16 changes: 8 additions & 8 deletions python_notebooks/1kg_bio_metadata_service.ipynb
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Expand Up @@ -31,13 +31,13 @@
},
{
"cell_type": "code",
"execution_count": 2,
"execution_count": 1,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"import ga4gh.client as client\n",
"import ga4gh_client.client as client\n",
"c = client.HttpClient(\"http://1kgenomes.ga4gh.org\") "
]
},
Expand All @@ -51,7 +51,7 @@
},
{
"cell_type": "code",
"execution_count": 5,
"execution_count": 2,
"metadata": {
"collapsed": false
},
Expand Down Expand Up @@ -157,7 +157,7 @@
},
{
"cell_type": "code",
"execution_count": 6,
"execution_count": 3,
"metadata": {
"collapsed": false
},
Expand Down Expand Up @@ -195,7 +195,7 @@
},
{
"cell_type": "code",
"execution_count": 7,
"execution_count": 4,
"metadata": {
"collapsed": false
},
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},
{
"cell_type": "code",
"execution_count": 10,
"execution_count": 5,
"metadata": {
"collapsed": false
},
Expand All @@ -277,8 +277,8 @@
" Desciption: GBRBritish in England and Scotlandfemale,\n",
" Individual Id: WyIxa2dlbm9tZXMiLCJpIiwiSEcwMDEwMiJd,\n",
" Disease: ,\n",
" Sample Created: 2016-07-28T14:38:49.204409,\n",
" Sample Updated: 2016-07-28T14:38:49.204413\n",
" Sample Created: 2016-10-07T10:59:00.916127,\n",
" Sample Updated: 2016-10-07T10:59:00.916130\n",
" Sample: \tHG00102\n",
" Family ID: \tHG00102\n",
" Relationship: \t\n",
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8 changes: 4 additions & 4 deletions python_notebooks/1kg_metadata_service.ipynb
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Expand Up @@ -18,13 +18,13 @@
},
{
"cell_type": "code",
"execution_count": 4,
"execution_count": 1,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"import ga4gh.client as client\n",
"import ga4gh_client.client as client\n",
"c = client.HttpClient(\"http://1kgenomes.ga4gh.org\")"
]
},
Expand All @@ -45,7 +45,7 @@
},
{
"cell_type": "code",
"execution_count": 5,
"execution_count": 2,
"metadata": {
"collapsed": false
},
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},
{
"cell_type": "code",
"execution_count": 6,
"execution_count": 3,
"metadata": {
"collapsed": false
},
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52 changes: 42 additions & 10 deletions python_notebooks/1kg_read_service.ipynb
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Expand Up @@ -18,13 +18,13 @@
},
{
"cell_type": "code",
"execution_count": 26,
"execution_count": 1,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"import ga4gh.client as client\n",
"import ga4gh_client.client as client\n",
"c = client.HttpClient(\"http://1kgenomes.ga4gh.org\")"
]
},
Expand All @@ -40,7 +40,7 @@
},
{
"cell_type": "code",
"execution_count": 27,
"execution_count": 2,
"metadata": {
"collapsed": false
},
Expand All @@ -53,7 +53,7 @@
"id: WyIxa2dlbm9tZXMiLCJyZ3MiLCJIRzAzMjcwIl0\n",
"dataset_id: WyIxa2dlbm9tZXMiXQ\n",
"Aligned Read Count: 177645990\n",
"Unaligned Read Count: 3353212\n",
"Unaligned Read Count: 746202\n",
"\n",
" Read group:\n",
" id: WyIxa2dlbm9tZXMiLCJyZ3MiLCJIRzAzMjcwIiwiRVJSMTgxMzI5Il0\n",
Expand Down Expand Up @@ -83,7 +83,7 @@
"id: WyIxa2dlbm9tZXMiLCJyZ3MiLCJIRzAzMjcxIl0\n",
"dataset_id: WyIxa2dlbm9tZXMiXQ\n",
"Aligned Read Count: 201280730\n",
"Unaligned Read Count: 3353212\n",
"Unaligned Read Count: 944735\n",
"\n",
" Read group:\n",
" id: WyIxa2dlbm9tZXMiLCJyZ3MiLCJIRzAzMjcxIiwiRVJSMTgxMzI4Il0\n",
Expand All @@ -108,6 +108,36 @@
" Name: ERR184343\n",
" Description: SRP015238\n",
" Biosample Id: WyIxa2dlbm9tZXMiLCJiIiwiSEcwMzI3MSJd\n",
"\n",
"Read Group Set: NA19675\n",
"id: WyIxa2dlbm9tZXMiLCJyZ3MiLCJOQTE5Njc1Il0\n",
"dataset_id: WyIxa2dlbm9tZXMiXQ\n",
"Aligned Read Count: 251846416\n",
"Unaligned Read Count: 3935762\n",
"\n",
" Read group:\n",
" id: WyIxa2dlbm9tZXMiLCJyZ3MiLCJOQTE5Njc1IiwiU1JSMDU4OTM3Il0\n",
" Name: SRR058937\n",
" Description: SRP000803\n",
" Biosample Id: WyIxa2dlbm9tZXMiLCJiIiwiTkExOTY3NSJd\n",
"\n",
" Read group:\n",
" id: WyIxa2dlbm9tZXMiLCJyZ3MiLCJOQTE5Njc1IiwiU1JSMDU4OTM4Il0\n",
" Name: SRR058938\n",
" Description: SRP000803\n",
" Biosample Id: WyIxa2dlbm9tZXMiLCJiIiwiTkExOTY3NSJd\n",
"\n",
" Read group:\n",
" id: WyIxa2dlbm9tZXMiLCJyZ3MiLCJOQTE5Njc1IiwiU1JSMDU4OTM5Il0\n",
" Name: SRR058939\n",
" Description: SRP000803\n",
" Biosample Id: WyIxa2dlbm9tZXMiLCJiIiwiTkExOTY3NSJd\n",
"\n",
" Read group:\n",
" id: WyIxa2dlbm9tZXMiLCJyZ3MiLCJOQTE5Njc1IiwiU1JSMDU4OTY0Il0\n",
" Name: SRR058964\n",
" Description: SRP000803\n",
" Biosample Id: WyIxa2dlbm9tZXMiLCJiIiwiTkExOTY3NSJd\n",
"\n"
]
}
Expand All @@ -116,18 +146,20 @@
"counter = 0\n",
"for read_group_set in c.search_read_group_sets(dataset_id=\"WyIxa2dlbm9tZXMiXQ\"):\n",
" counter += 1\n",
" if counter < 3:\n",
" if counter < 4:\n",
" print \"Read Group Set: {}\".format(read_group_set.name)\n",
" print \"id: {}\".format(read_group_set.id)\n",
" print \"dataset_id: {}\".format(read_group_set.dataset_id)\n",
" print \"Aligned Read Count: {}\".format(read_group_set.stats.aligned_read_count)\n",
" print \"Unaligned Read Count: {}\\n\".format(read_groups.stats.unaligned_read_count)\n",
" print \"Unaligned Read Count: {}\\n\".format(read_group_set.stats.unaligned_read_count)\n",
" for read_group in read_group_set.read_groups:\n",
" print \" Read group:\"\n",
" print \" id: {}\".format(read_group.id)\n",
" print \" Name: {}\".format(read_group.name)\n",
" print \" Description: {}\".format(read_group.description)\n",
" print \" Biosample Id: {}\\n\".format(read_group.bio_sample_id)"
" print \" Biosample Id: {}\\n\".format(read_group.bio_sample_id)\n",
" else:\n",
" break"
]
},
{
Expand All @@ -147,7 +179,7 @@
},
{
"cell_type": "code",
"execution_count": 28,
"execution_count": 3,
"metadata": {
"collapsed": false
},
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},
{
"cell_type": "code",
"execution_count": 30,
"execution_count": 4,
"metadata": {
"collapsed": false
},
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14 changes: 7 additions & 7 deletions python_notebooks/1kg_reference_service.ipynb
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Expand Up @@ -18,13 +18,13 @@
},
{
"cell_type": "code",
"execution_count": 13,
"execution_count": 1,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"import ga4gh.client as client\n",
"import ga4gh_client.client as client\n",
"c = client.HttpClient(\"http://1kgenomes.ga4gh.org\")"
]
},
Expand All @@ -42,7 +42,7 @@
},
{
"cell_type": "code",
"execution_count": 14,
"execution_count": 2,
"metadata": {
"collapsed": false
},
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},
{
"cell_type": "code",
"execution_count": 15,
"execution_count": 3,
"metadata": {
"collapsed": false
},
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},
{
"cell_type": "code",
"execution_count": 16,
"execution_count": 4,
"metadata": {
"collapsed": false
},
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},
{
"cell_type": "code",
"execution_count": 10,
"execution_count": 5,
"metadata": {
"collapsed": false
},
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},
{
"cell_type": "code",
"execution_count": 17,
"execution_count": 6,
"metadata": {
"collapsed": false
},
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