diff --git a/mrdna/readers/segmentmodel_from_cadnano.py b/mrdna/readers/segmentmodel_from_cadnano.py
index ee83a3d9e7540ba33d8dca8f630fa8ae9c357f13..1d4f7cdf2c3bf1f5b795e96d4c3c0b192186d3d2 100644
--- a/mrdna/readers/segmentmodel_from_cadnano.py
+++ b/mrdna/readers/segmentmodel_from_cadnano.py
@@ -190,6 +190,7 @@ def mrdna_model_from_cadnano(json_file,seq=None,**model_parameters):
r=np.array(list(nt_prop['r']))
bp=np.array(list(nt_prop['bp']))
three_prime=np.array((list(nt_prop["threeprime"])))
+ stack=np.array((list(nt_prop["stack"])))
orientation=np.array(list(nt_prop["orientation"]))
- model = model_from_basepair_stack_3prime( r, bp, stack, three_prime, seq, orientation, **model_parameters )
+ model = model_from_basepair_stack_3prime( r, bp, stack, three_prime, seq, orientation=None, **model_parameters )
return model
diff --git a/mrdna/readers/test.ipynb b/mrdna/readers/test.ipynb
index 4a0fa1368bb6d1a5ec43f981c106028798f2b908..207998d94578efcb8916ef58fcb29016ab1e6bd4 100644
--- a/mrdna/readers/test.ipynb
+++ b/mrdna/readers/test.ipynb
@@ -3,7 +3,7 @@
{
"cell_type": "code",
"execution_count": 9,
- "id": "d3431aaa",
+ "id": "03eb8540",
"metadata": {
"scrolled": true
},
@@ -21,7 +21,7 @@
{
"cell_type": "code",
"execution_count": 2,
- "id": "1b3781b0",
+ "id": "cb40f6b8",
"metadata": {},
"outputs": [],
"source": [
@@ -31,7 +31,7 @@
{
"cell_type": "code",
"execution_count": 1,
- "id": "d599c577",
+ "id": "ea7e8da0",
"metadata": {},
"outputs": [
{
@@ -56,7 +56,7 @@
{
"cell_type": "code",
"execution_count": 6,
- "id": "7a326c43",
+ "id": "4fc535bb",
"metadata": {},
"outputs": [],
"source": [
@@ -153,7 +153,7 @@
{
"cell_type": "code",
"execution_count": 7,
- "id": "19281ee2",
+ "id": "f83dff7d",
"metadata": {},
"outputs": [],
"source": [
@@ -225,7 +225,7 @@
{
"cell_type": "code",
"execution_count": 11,
- "id": "77a45909",
+ "id": "1d900942",
"metadata": {},
"outputs": [
{
@@ -263,53 +263,50 @@
},
{
"cell_type": "code",
- "execution_count": 20,
- "id": "60d832bf",
+ "execution_count": 23,
+ "id": "04c497ae",
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "nt_prop.to_csv(\"test.csv\")"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "f2116b88",
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "import mrdna\n",
+ "from mrdna.readers import read_list"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 29,
+ "id": "4c954133",
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
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- " [ 0.22252093, -0.97492791, 0. ],\n",
- " [ 0. , 0. , 1. ]]])"
+ "(415,)"
]
},
- "execution_count": 20,
+ "execution_count": 29,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
- "np.array(list(nt_prop['orientation']))"
+ "np.array(list(nt_prop['bp'])).shape"
]
},
{
"cell_type": "code",
"execution_count": 560,
- "id": "cd1d0730",
+ "id": "5ee54071",
"metadata": {},
"outputs": [
{
@@ -329,20 +326,213 @@
},
{
"cell_type": "code",
- "execution_count": 3,
- "id": "0373e4dc",
+ "execution_count": 21,
+ "id": "e1588c54",
"metadata": {},
"outputs": [
{
- "ename": "NameError",
- "evalue": "name 'nt_prop' is not defined",
- "output_type": "error",
- "traceback": [
- "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
- "\u001b[0;31mNameError\u001b[0m Traceback (most recent call last)",
- "\u001b[0;32m<ipython-input-3-68f62b8d2117>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0mnt_prop\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
- "\u001b[0;31mNameError\u001b[0m: name 'nt_prop' is not defined"
- ]
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+ "text/plain": [
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+ "1 0 6 True [0.0, 2.25, 2.04] 214 -1 \n",
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+ "\n",
+ "[415 rows x 9 columns]"
+ ]
+ },
+ "execution_count": 21,
+ "metadata": {},
+ "output_type": "execute_result"
}
],
"source": [
@@ -352,7 +542,7 @@
{
"cell_type": "code",
"execution_count": 468,
- "id": "ff612c08",
+ "id": "156dcda2",
"metadata": {},
"outputs": [],
"source": [
@@ -363,7 +553,7 @@
{
"cell_type": "code",
"execution_count": 500,
- "id": "96ffa55b",
+ "id": "6413d856",
"metadata": {},
"outputs": [
{
@@ -384,7 +574,7 @@
{
"cell_type": "code",
"execution_count": 498,
- "id": "3ca0ce24",
+ "id": "fe8797db",
"metadata": {},
"outputs": [
{
@@ -406,7 +596,7 @@
{
"cell_type": "code",
"execution_count": 480,
- "id": "d11603b3",
+ "id": "9f1b975f",
"metadata": {},
"outputs": [
{
@@ -427,7 +617,7 @@
{
"cell_type": "code",
"execution_count": 549,
- "id": "e5731ae8",
+ "id": "a16f3fd0",
"metadata": {},
"outputs": [
{
@@ -459,7 +649,7 @@
{
"cell_type": "code",
"execution_count": 544,
- "id": "4a0bb208",
+ "id": "b9f25d41",
"metadata": {},
"outputs": [
{
@@ -483,7 +673,7 @@
{
"cell_type": "code",
"execution_count": 550,
- "id": "ea73aed6",
+ "id": "976095ce",
"metadata": {},
"outputs": [
{
@@ -513,7 +703,7 @@
{
"cell_type": "code",
"execution_count": 548,
- "id": "033ef083",
+ "id": "ac8f5067",
"metadata": {},
"outputs": [
{
@@ -537,7 +727,7 @@
{
"cell_type": "code",
"execution_count": 527,
- "id": "284c6b7a",
+ "id": "1006fc48",
"metadata": {},
"outputs": [
{
@@ -562,7 +752,7 @@
{
"cell_type": "code",
"execution_count": 503,
- "id": "70fafb27",
+ "id": "09c7e7d4",
"metadata": {},
"outputs": [
{
@@ -588,7 +778,7 @@
{
"cell_type": "code",
"execution_count": 537,
- "id": "08e4fe4a",
+ "id": "5f0c5266",
"metadata": {},
"outputs": [
{
@@ -637,7 +827,7 @@
{
"cell_type": "code",
"execution_count": 491,
- "id": "e12ead08",
+ "id": "fec987da",
"metadata": {},
"outputs": [
{
@@ -658,7 +848,7 @@
{
"cell_type": "code",
"execution_count": 493,
- "id": "6d7ca49f",
+ "id": "f332ad87",
"metadata": {},
"outputs": [
{
@@ -680,7 +870,7 @@
{
"cell_type": "code",
"execution_count": 4,
- "id": "e9ace3af",
+ "id": "dd3cd839",
"metadata": {},
"outputs": [],
"source": [
@@ -691,7 +881,7 @@
{
"cell_type": "code",
"execution_count": null,
- "id": "954df4d2",
+ "id": "41b3d9af",
"metadata": {},
"outputs": [],
"source": []
@@ -699,7 +889,7 @@
{
"cell_type": "code",
"execution_count": 18,
- "id": "7fcb7bd0",
+ "id": "9ec18edc",
"metadata": {},
"outputs": [],
"source": [
@@ -721,7 +911,7 @@
{
"cell_type": "code",
"execution_count": 358,
- "id": "e0d8b3ff",
+ "id": "2fa31a78",
"metadata": {},
"outputs": [
{
@@ -750,7 +940,7 @@
{
"cell_type": "code",
"execution_count": 441,
- "id": "6d351947",
+ "id": "64eb309f",
"metadata": {},
"outputs": [
{
@@ -933,7 +1123,7 @@
{
"cell_type": "code",
"execution_count": 199,
- "id": "a20c1429",
+ "id": "bda3cddd",
"metadata": {},
"outputs": [
{
@@ -954,7 +1144,7 @@
{
"cell_type": "code",
"execution_count": 434,
- "id": "39b7deb4",
+ "id": "a86cfa84",
"metadata": {},
"outputs": [],
"source": [
@@ -1022,7 +1212,7 @@
{
"cell_type": "code",
"execution_count": 442,
- "id": "83f49b07",
+ "id": "be5de5ba",
"metadata": {},
"outputs": [
{
@@ -1067,7 +1257,7 @@
{
"cell_type": "code",
"execution_count": 302,
- "id": "891a3222",
+ "id": "0ce6701d",
"metadata": {},
"outputs": [],
"source": [
@@ -1091,7 +1281,7 @@
{
"cell_type": "code",
"execution_count": 368,
- "id": "34a7d7b1",
+ "id": "9d0e49cf",
"metadata": {},
"outputs": [],
"source": [
@@ -1124,7 +1314,7 @@
{
"cell_type": "code",
"execution_count": 429,
- "id": "ec944c23",
+ "id": "c1d77642",
"metadata": {},
"outputs": [],
"source": [
@@ -1139,7 +1329,7 @@
{
"cell_type": "code",
"execution_count": 430,
- "id": "d67c5833",
+ "id": "2c2d1227",
"metadata": {},
"outputs": [
{
@@ -1174,7 +1364,7 @@
{
"cell_type": "code",
"execution_count": 431,
- "id": "eca06274",
+ "id": "e701d029",
"metadata": {},
"outputs": [
{
@@ -1195,7 +1385,7 @@
{
"cell_type": "code",
"execution_count": 433,
- "id": "1d66507f",
+ "id": "4a62f5d9",
"metadata": {},
"outputs": [
{
@@ -1216,7 +1406,7 @@
{
"cell_type": "code",
"execution_count": 167,
- "id": "c9ea70d5",
+ "id": "d80ab792",
"metadata": {},
"outputs": [],
"source": [
@@ -1228,7 +1418,7 @@
{
"cell_type": "code",
"execution_count": 360,
- "id": "02798620",
+ "id": "8e009bc9",
"metadata": {},
"outputs": [],
"source": [
@@ -1238,7 +1428,7 @@
{
"cell_type": "code",
"execution_count": 190,
- "id": "c39720e6",
+ "id": "3dc97f0d",
"metadata": {},
"outputs": [
{
@@ -1421,7 +1611,7 @@
{
"cell_type": "code",
"execution_count": 200,
- "id": "81cd15ec",
+ "id": "3d019b73",
"metadata": {},
"outputs": [],
"source": [
@@ -1457,7 +1647,7 @@
{
"cell_type": "code",
"execution_count": 201,
- "id": "719a89e5",
+ "id": "fb789ffb",
"metadata": {},
"outputs": [
{
@@ -1480,7 +1670,7 @@
{
"cell_type": "code",
"execution_count": 146,
- "id": "a8470ece",
+ "id": "98703867",
"metadata": {},
"outputs": [],
"source": [
@@ -1490,7 +1680,7 @@
{
"cell_type": "code",
"execution_count": 148,
- "id": "2ec8d095",
+ "id": "c316fead",
"metadata": {},
"outputs": [
{
@@ -1523,7 +1713,7 @@
{
"cell_type": "code",
"execution_count": 137,
- "id": "ab361dd6",
+ "id": "0718e41e",
"metadata": {},
"outputs": [],
"source": [
@@ -1540,7 +1730,7 @@
{
"cell_type": "code",
"execution_count": null,
- "id": "f3ecd95f",
+ "id": "1a61115e",
"metadata": {},
"outputs": [],
"source": []
@@ -1548,7 +1738,7 @@
{
"cell_type": "code",
"execution_count": 84,
- "id": "256fccfe",
+ "id": "12198835",
"metadata": {},
"outputs": [],
"source": [
@@ -1559,7 +1749,7 @@
{
"cell_type": "code",
"execution_count": 156,
- "id": "1ac95587",
+ "id": "1e5c9807",
"metadata": {},
"outputs": [
{
@@ -1685,7 +1875,7 @@
{
"cell_type": "code",
"execution_count": 157,
- "id": "c016cb03",
+ "id": "31c50f63",
"metadata": {},
"outputs": [
{
@@ -1802,7 +1992,7 @@
{
"cell_type": "code",
"execution_count": 128,
- "id": "11e1b98e",
+ "id": "67546136",
"metadata": {},
"outputs": [
{
@@ -1824,7 +2014,7 @@
{
"cell_type": "code",
"execution_count": 127,
- "id": "5a46d99d",
+ "id": "bad20d6a",
"metadata": {},
"outputs": [
{
@@ -1944,7 +2134,7 @@
{
"cell_type": "code",
"execution_count": 100,
- "id": "f6549e2c",
+ "id": "48225afa",
"metadata": {},
"outputs": [
{
@@ -1969,7 +2159,7 @@
{
"cell_type": "code",
"execution_count": 13,
- "id": "24b98917",
+ "id": "c75bd92f",
"metadata": {},
"outputs": [
{
@@ -1990,7 +2180,7 @@
{
"cell_type": "code",
"execution_count": 14,
- "id": "71923b7f",
+ "id": "00f1513e",
"metadata": {},
"outputs": [
{
@@ -2012,7 +2202,7 @@
{
"cell_type": "code",
"execution_count": 198,
- "id": "1307361f",
+ "id": "aaa65658",
"metadata": {},
"outputs": [
{
@@ -2034,7 +2224,7 @@
{
"cell_type": "code",
"execution_count": 15,
- "id": "3772e934",
+ "id": "cbddf07f",
"metadata": {},
"outputs": [
{
@@ -2055,7 +2245,7 @@
{
"cell_type": "code",
"execution_count": 173,
- "id": "5c1f341d",
+ "id": "fac8699e",
"metadata": {},
"outputs": [],
"source": [
@@ -2091,7 +2281,7 @@
{
"cell_type": "code",
"execution_count": 177,
- "id": "495b9e03",
+ "id": "308cd6c1",
"metadata": {},
"outputs": [],
"source": [
@@ -2127,7 +2317,7 @@
{
"cell_type": "code",
"execution_count": 187,
- "id": "c70f83b0",
+ "id": "bc032680",
"metadata": {},
"outputs": [
{
@@ -2354,7 +2544,7 @@
{
"cell_type": "code",
"execution_count": 142,
- "id": "df50d6fb",
+ "id": "29ff7990",
"metadata": {},
"outputs": [],
"source": [
@@ -2391,7 +2581,7 @@
{
"cell_type": "code",
"execution_count": 117,
- "id": "f6f7acb5",
+ "id": "3cb9542c",
"metadata": {},
"outputs": [],
"source": [
@@ -2412,7 +2602,7 @@
{
"cell_type": "code",
"execution_count": 116,
- "id": "8afcf746",
+ "id": "4219838b",
"metadata": {},
"outputs": [
{
@@ -2624,7 +2814,7 @@
{
"cell_type": "code",
"execution_count": 157,
- "id": "2132b521",
+ "id": "45168e4b",
"metadata": {},
"outputs": [
{
@@ -2648,7 +2838,7 @@
{
"cell_type": "code",
"execution_count": 152,
- "id": "539a2be6",
+ "id": "33e5c80d",
"metadata": {},
"outputs": [
{
@@ -2669,7 +2859,7 @@
{
"cell_type": "code",
"execution_count": 62,
- "id": "ba5ab701",
+ "id": "9b79e902",
"metadata": {},
"outputs": [
{
@@ -2897,7 +3087,7 @@
{
"cell_type": "code",
"execution_count": 3,
- "id": "0e988589",
+ "id": "cecd1c9f",
"metadata": {},
"outputs": [],
"source": [
@@ -3023,7 +3213,7 @@
{
"cell_type": "code",
"execution_count": 4,
- "id": "821ca309",
+ "id": "b4af37c1",
"metadata": {},
"outputs": [],
"source": [
@@ -3044,7 +3234,7 @@
{
"cell_type": "code",
"execution_count": 20,
- "id": "870c2661",
+ "id": "2fa89abc",
"metadata": {},
"outputs": [
{
@@ -3106,7 +3296,7 @@
{
"cell_type": "code",
"execution_count": 25,
- "id": "a6cb689d",
+ "id": "6e620d24",
"metadata": {},
"outputs": [
{
@@ -3168,7 +3358,7 @@
{
"cell_type": "code",
"execution_count": null,
- "id": "dd799008",
+ "id": "fef6094a",
"metadata": {},
"outputs": [],
"source": [
@@ -3181,7 +3371,7 @@
{
"cell_type": "code",
"execution_count": 13,
- "id": "df97d32a",
+ "id": "be089a18",
"metadata": {},
"outputs": [
{
@@ -3202,7 +3392,7 @@
{
"cell_type": "code",
"execution_count": 7,
- "id": "191c7b94",
+ "id": "6f75d365",
"metadata": {},
"outputs": [
{
@@ -3251,7 +3441,7 @@
{
"cell_type": "code",
"execution_count": 36,
- "id": "d1fb1c97",
+ "id": "8dfadf61",
"metadata": {},
"outputs": [
{
@@ -3313,7 +3503,7 @@
{
"cell_type": "code",
"execution_count": 1,
- "id": "aa4f5ed8",
+ "id": "ba097c82",
"metadata": {},
"outputs": [
{
@@ -3339,7 +3529,7 @@
{
"cell_type": "code",
"execution_count": null,
- "id": "cb9366dd",
+ "id": "1c4d4fa9",
"metadata": {},
"outputs": [],
"source": []
@@ -3347,7 +3537,7 @@
{
"cell_type": "code",
"execution_count": 3,
- "id": "2d779081",
+ "id": "d4ff1f83",
"metadata": {},
"outputs": [
{
@@ -3367,7 +3557,7 @@
{
"cell_type": "code",
"execution_count": 13,
- "id": "ad471f3d",
+ "id": "6f1dab46",
"metadata": {},
"outputs": [
{
@@ -3388,7 +3578,7 @@
{
"cell_type": "code",
"execution_count": 15,
- "id": "9d66b3aa",
+ "id": "615964fe",
"metadata": {},
"outputs": [
{
@@ -3458,7 +3648,7 @@
{
"cell_type": "code",
"execution_count": 16,
- "id": "50447f7e",
+ "id": "a71b0639",
"metadata": {},
"outputs": [],
"source": [
@@ -3469,7 +3659,7 @@
{
"cell_type": "code",
"execution_count": 26,
- "id": "145493e6",
+ "id": "2bb83a1e",
"metadata": {},
"outputs": [
{
@@ -3578,7 +3768,7 @@
{
"cell_type": "code",
"execution_count": 25,
- "id": "bda26a99",
+ "id": "86f5c21e",
"metadata": {},
"outputs": [
{
@@ -3599,7 +3789,7 @@
{
"cell_type": "code",
"execution_count": 10,
- "id": "21c76d05",
+ "id": "f3fae511",
"metadata": {},
"outputs": [
{
@@ -3630,7 +3820,7 @@
{
"cell_type": "code",
"execution_count": 1,
- "id": "49dad459",
+ "id": "07f3352b",
"metadata": {},
"outputs": [
{
@@ -4127,7 +4317,7 @@
{
"cell_type": "code",
"execution_count": 3,
- "id": "7badd9d8",
+ "id": "61be89c1",
"metadata": {},
"outputs": [
{
@@ -4161,7 +4351,7 @@
{
"cell_type": "code",
"execution_count": 4,
- "id": "a1ba34df",
+ "id": "a00c445c",
"metadata": {},
"outputs": [
{
@@ -4181,7 +4371,7 @@
{
"cell_type": "code",
"execution_count": 5,
- "id": "e7309034",
+ "id": "a648fae4",
"metadata": {},
"outputs": [],
"source": [
@@ -4191,7 +4381,7 @@
{
"cell_type": "code",
"execution_count": 6,
- "id": "705faaff",
+ "id": "9d100033",
"metadata": {},
"outputs": [
{
@@ -4212,7 +4402,7 @@
{
"cell_type": "code",
"execution_count": 7,
- "id": "75417690",
+ "id": "66d3eaf4",
"metadata": {},
"outputs": [
{
@@ -4239,7 +4429,7 @@
{
"cell_type": "code",
"execution_count": null,
- "id": "8ca5d402",
+ "id": "f60b0cdc",
"metadata": {},
"outputs": [],
"source": []