Skip to content

Commit f9d68de

Browse files
committed
Update motif spacing notebook
1 parent 816ba22 commit f9d68de

File tree

1 file changed

+202
-1
lines changed

1 file changed

+202
-1
lines changed

src/in_silico_mutagenesis_bpnet_motif_spacing.ipynb

Lines changed: 202 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1287,7 +1287,7 @@
12871287
},
12881288
{
12891289
"cell_type": "code",
1290-
"execution_count": null,
1290+
"execution_count": 75,
12911291
"metadata": {},
12921292
"outputs": [
12931293
{
@@ -1382,6 +1382,207 @@
13821382
"NotebookApp.rate_limit_window=3.0 (secs)\n",
13831383
"\n"
13841384
]
1385+
},
1386+
{
1387+
"name": "stdout",
1388+
"output_type": "stream",
1389+
"text": [
1390+
"Reduced number of instruments down from 12000000 to 99394 (0.83 %)\n",
1391+
"(2000, 3, 1000)\n",
1392+
"/home/ubuntu/dev/an1lam/deepmr/dat/res-bpnet-2022-07-04-21-30-22/Sox2_Oct4_effect_sizes_v2.csv\n",
1393+
"Sox2_Nanog_distance\n"
1394+
]
1395+
},
1396+
{
1397+
"data": {
1398+
"application/vnd.jupyter.widget-view+json": {
1399+
"model_id": "452d17b7d3a3429fa41cc0812e3c064b",
1400+
"version_major": 2,
1401+
"version_minor": 0
1402+
},
1403+
"text/plain": [
1404+
" 0%| | 0/2000 [00:00<?, ?it/s]"
1405+
]
1406+
},
1407+
"metadata": {},
1408+
"output_type": "display_data"
1409+
},
1410+
{
1411+
"name": "stdout",
1412+
"output_type": "stream",
1413+
"text": [
1414+
"Reduced number of instruments down from 12000000 to 99394 (0.83 %)\n",
1415+
"(2000, 3, 1000)\n",
1416+
"/home/ubuntu/dev/an1lam/deepmr/dat/res-bpnet-2022-07-04-21-30-22/Sox2_Nanog_effect_sizes_v2.csv\n",
1417+
"Sox2_Klf4_distance\n"
1418+
]
1419+
},
1420+
{
1421+
"data": {
1422+
"application/vnd.jupyter.widget-view+json": {
1423+
"model_id": "146afa65f9af489b88dd10c7c30d7e61",
1424+
"version_major": 2,
1425+
"version_minor": 0
1426+
},
1427+
"text/plain": [
1428+
" 0%| | 0/2000 [00:00<?, ?it/s]"
1429+
]
1430+
},
1431+
"metadata": {},
1432+
"output_type": "display_data"
1433+
},
1434+
{
1435+
"name": "stdout",
1436+
"output_type": "stream",
1437+
"text": [
1438+
"Reduced number of instruments down from 12000000 to 99394 (0.83 %)\n",
1439+
"(2000, 3, 1000)\n",
1440+
"/home/ubuntu/dev/an1lam/deepmr/dat/res-bpnet-2022-07-04-21-30-22/Sox2_Klf4_effect_sizes_v2.csv\n",
1441+
"Nanog_Oct4_distance\n"
1442+
]
1443+
},
1444+
{
1445+
"data": {
1446+
"application/vnd.jupyter.widget-view+json": {
1447+
"model_id": "b712815c8e2c4c0ab2c977de9fd9b8f6",
1448+
"version_major": 2,
1449+
"version_minor": 0
1450+
},
1451+
"text/plain": [
1452+
" 0%| | 0/2000 [00:00<?, ?it/s]"
1453+
]
1454+
},
1455+
"metadata": {},
1456+
"output_type": "display_data"
1457+
},
1458+
{
1459+
"name": "stdout",
1460+
"output_type": "stream",
1461+
"text": [
1462+
"Reduced number of instruments down from 12000000 to 124161 (1.03 %)\n",
1463+
"(2000, 3, 1000)\n",
1464+
"/home/ubuntu/dev/an1lam/deepmr/dat/res-bpnet-2022-07-04-21-30-22/Nanog_Oct4_effect_sizes_v2.csv\n",
1465+
"Nanog_Sox2_distance\n"
1466+
]
1467+
},
1468+
{
1469+
"data": {
1470+
"application/vnd.jupyter.widget-view+json": {
1471+
"model_id": "b41575fe4f8d4b3190b3a4c6d587ae7e",
1472+
"version_major": 2,
1473+
"version_minor": 0
1474+
},
1475+
"text/plain": [
1476+
" 0%| | 0/2000 [00:00<?, ?it/s]"
1477+
]
1478+
},
1479+
"metadata": {},
1480+
"output_type": "display_data"
1481+
},
1482+
{
1483+
"name": "stdout",
1484+
"output_type": "stream",
1485+
"text": [
1486+
"Reduced number of instruments down from 12000000 to 124161 (1.03 %)\n",
1487+
"(2000, 3, 1000)\n",
1488+
"/home/ubuntu/dev/an1lam/deepmr/dat/res-bpnet-2022-07-04-21-30-22/Nanog_Sox2_effect_sizes_v2.csv\n",
1489+
"Nanog_Klf4_distance\n"
1490+
]
1491+
},
1492+
{
1493+
"data": {
1494+
"application/vnd.jupyter.widget-view+json": {
1495+
"model_id": "315c6e28ef314a47ab8f9ed8c7e32f0b",
1496+
"version_major": 2,
1497+
"version_minor": 0
1498+
},
1499+
"text/plain": [
1500+
" 0%| | 0/2000 [00:00<?, ?it/s]"
1501+
]
1502+
},
1503+
"metadata": {},
1504+
"output_type": "display_data"
1505+
},
1506+
{
1507+
"name": "stdout",
1508+
"output_type": "stream",
1509+
"text": [
1510+
"Reduced number of instruments down from 12000000 to 124161 (1.03 %)\n",
1511+
"(2000, 3, 1000)\n",
1512+
"/home/ubuntu/dev/an1lam/deepmr/dat/res-bpnet-2022-07-04-21-30-22/Nanog_Klf4_effect_sizes_v2.csv\n",
1513+
"Klf4_Oct4_distance\n"
1514+
]
1515+
},
1516+
{
1517+
"data": {
1518+
"application/vnd.jupyter.widget-view+json": {
1519+
"model_id": "a43781d4a9204aab8238ac1d75bca09c",
1520+
"version_major": 2,
1521+
"version_minor": 0
1522+
},
1523+
"text/plain": [
1524+
" 0%| | 0/2000 [00:00<?, ?it/s]"
1525+
]
1526+
},
1527+
"metadata": {},
1528+
"output_type": "display_data"
1529+
},
1530+
{
1531+
"name": "stdout",
1532+
"output_type": "stream",
1533+
"text": [
1534+
"Reduced number of instruments down from 12000000 to 115001 (0.96 %)\n",
1535+
"(2000, 3, 1000)\n",
1536+
"/home/ubuntu/dev/an1lam/deepmr/dat/res-bpnet-2022-07-04-21-30-22/Klf4_Oct4_effect_sizes_v2.csv\n",
1537+
"Klf4_Sox2_distance\n"
1538+
]
1539+
},
1540+
{
1541+
"data": {
1542+
"application/vnd.jupyter.widget-view+json": {
1543+
"model_id": "52dbba2f45094ac8bc6d3afa02077500",
1544+
"version_major": 2,
1545+
"version_minor": 0
1546+
},
1547+
"text/plain": [
1548+
" 0%| | 0/2000 [00:00<?, ?it/s]"
1549+
]
1550+
},
1551+
"metadata": {},
1552+
"output_type": "display_data"
1553+
},
1554+
{
1555+
"name": "stdout",
1556+
"output_type": "stream",
1557+
"text": [
1558+
"Reduced number of instruments down from 12000000 to 115001 (0.96 %)\n",
1559+
"(2000, 3, 1000)\n",
1560+
"/home/ubuntu/dev/an1lam/deepmr/dat/res-bpnet-2022-07-04-21-30-22/Klf4_Sox2_effect_sizes_v2.csv\n",
1561+
"Klf4_Nanog_distance\n"
1562+
]
1563+
},
1564+
{
1565+
"data": {
1566+
"application/vnd.jupyter.widget-view+json": {
1567+
"model_id": "b1b26cfadf9b43a6b30b6275d5469ba7",
1568+
"version_major": 2,
1569+
"version_minor": 0
1570+
},
1571+
"text/plain": [
1572+
" 0%| | 0/2000 [00:00<?, ?it/s]"
1573+
]
1574+
},
1575+
"metadata": {},
1576+
"output_type": "display_data"
1577+
},
1578+
{
1579+
"name": "stdout",
1580+
"output_type": "stream",
1581+
"text": [
1582+
"Reduced number of instruments down from 12000000 to 115001 (0.96 %)\n",
1583+
"(2000, 3, 1000)\n",
1584+
"/home/ubuntu/dev/an1lam/deepmr/dat/res-bpnet-2022-07-04-21-30-22/Klf4_Nanog_effect_sizes_v2.csv\n"
1585+
]
13851586
}
13861587
],
13871588
"source": [

0 commit comments

Comments
 (0)