From c8110260e90c3fb39f18693a1d1275a290bc5793 Mon Sep 17 00:00:00 2001
From: pinyili2 <pinyili2@illinois.edu>
Date: Tue, 6 Aug 2024 14:37:48 -0500
Subject: [PATCH] add
---
...no.py.swp => .nfs0000000000093fec000043e9} | Bin
mrdna/readers/segmentmodel_from_cadnano.py | 16 +-
mrdna/readers/test.ipynb | 172 ++++++++++--------
3 files changed, 112 insertions(+), 76 deletions(-)
rename mrdna/readers/{.segmentmodel_from_cadnano.py.swp => .nfs0000000000093fec000043e9} (100%)
diff --git a/mrdna/readers/.segmentmodel_from_cadnano.py.swp b/mrdna/readers/.nfs0000000000093fec000043e9
similarity index 100%
rename from mrdna/readers/.segmentmodel_from_cadnano.py.swp
rename to mrdna/readers/.nfs0000000000093fec000043e9
diff --git a/mrdna/readers/segmentmodel_from_cadnano.py b/mrdna/readers/segmentmodel_from_cadnano.py
index 676ff60..fe6b46c 100644
--- a/mrdna/readers/segmentmodel_from_cadnano.py
+++ b/mrdna/readers/segmentmodel_from_cadnano.py
@@ -109,7 +109,7 @@ def ntcount(scafs):
return 0
else: return 1
n=np.array([judge(i) for i in scafs])
- return np.sum(n)
+ return n
def mrdna_model_from_cadnano(json_data,**model_parameters):
@@ -124,12 +124,20 @@ def mrdna_model_from_cadnano(json_data,**model_parameters):
vh_props, origins = part.helixPropertiesAndOrigins()
except:
origins = {hid:part.getVirtualHelixOrigin(hid)[:2] for hid in part.getidNums()}
+ scaf_id=[ntcount(vslist['scaf'][i]) for i in vslist.index]
+ stap_id=[ntcount(vslist['stap'][i]) for i in vslist.index]
cad_bps=part.getIndices(0)
- vslist["scafnt"]=[ntcount(vslist['scaf'][i]) for i in vslist.index]
- vslist["stapnt"]=[ntcount(vslist['stap'][i]) for i in vslist.index]
+ vslist["scafnt"]=np.sum(scaf_id)
+ vslist["stapnt"]=np.sum(stap_id)
totnt=np.sum(vslist["scafnt"])+np.sum(vslist["stapnt"])
nt_prop=pd.DataFrame(index=range(totnt),columns=["vh","zid","r","bp","stack","threeprime","seq","orientation"])
-
+ ind=0
+ for vs in range(len(scaf_id)):
+ for j in range(len(vs)):
+ if j ==True
+ nt_prop.loc[ind]["vh"]=vs
+ nt_prop.loc[ind]["zid"]
+
model = model_from_basepair_stack_3prime( r, bp, stack, three_prime, seq, orientation, **model_parameters )
diff --git a/mrdna/readers/test.ipynb b/mrdna/readers/test.ipynb
index 34cdcbd..b039b19 100644
--- a/mrdna/readers/test.ipynb
+++ b/mrdna/readers/test.ipynb
@@ -3,7 +3,7 @@
{
"cell_type": "code",
"execution_count": 2,
- "id": "ab3deccf",
+ "id": "065c6b08",
"metadata": {
"scrolled": true
},
@@ -19,7 +19,7 @@
{
"cell_type": "code",
"execution_count": 7,
- "id": "0de414ce",
+ "id": "e2409533",
"metadata": {},
"outputs": [],
"source": [
@@ -30,7 +30,7 @@
{
"cell_type": "code",
"execution_count": 4,
- "id": "fdb603c1",
+ "id": "f3880b54",
"metadata": {},
"outputs": [],
"source": [
@@ -41,7 +41,7 @@
{
"cell_type": "code",
"execution_count": 5,
- "id": "6f322908",
+ "id": "5e4380bc",
"metadata": {},
"outputs": [
{
@@ -224,7 +224,7 @@
{
"cell_type": "code",
"execution_count": 14,
- "id": "f77c2bad",
+ "id": "6f670828",
"metadata": {},
"outputs": [
{
@@ -264,7 +264,7 @@
{
"cell_type": "code",
"execution_count": 18,
- "id": "a1df854a",
+ "id": "ff3c11b6",
"metadata": {},
"outputs": [],
"source": [
@@ -286,7 +286,7 @@
{
"cell_type": "code",
"execution_count": 121,
- "id": "a88086bf",
+ "id": "40fffe7e",
"metadata": {},
"outputs": [],
"source": [
@@ -340,7 +340,7 @@
{
"cell_type": "code",
"execution_count": 44,
- "id": "221a82ed",
+ "id": "d640032c",
"metadata": {},
"outputs": [
{
@@ -362,7 +362,7 @@
{
"cell_type": "code",
"execution_count": 122,
- "id": "25accfa8",
+ "id": "7559115b",
"metadata": {
"scrolled": true
},
@@ -382,7 +382,7 @@
{
"cell_type": "code",
"execution_count": 52,
- "id": "5a0dec07",
+ "id": "1c4cd407",
"metadata": {},
"outputs": [
{
@@ -403,7 +403,7 @@
{
"cell_type": "code",
"execution_count": 83,
- "id": "413e3e88",
+ "id": "b85be77d",
"metadata": {},
"outputs": [],
"source": [
@@ -420,7 +420,7 @@
{
"cell_type": "code",
"execution_count": 84,
- "id": "e36edb50",
+ "id": "1b2f9268",
"metadata": {},
"outputs": [],
"source": [
@@ -431,7 +431,7 @@
{
"cell_type": "code",
"execution_count": 123,
- "id": "40764fb4",
+ "id": "5042c85d",
"metadata": {},
"outputs": [],
"source": [
@@ -446,7 +446,7 @@
{
"cell_type": "code",
"execution_count": 126,
- "id": "f6fc8912",
+ "id": "b91c2367",
"metadata": {},
"outputs": [
{
@@ -560,16 +560,30 @@
},
{
"cell_type": "code",
- "execution_count": null,
- "id": "9e5e1d1b",
+ "execution_count": 128,
+ "id": "3c1fc0c9",
"metadata": {},
- "outputs": [],
- "source": []
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "(array([0, 2]),)"
+ ]
+ },
+ "execution_count": 128,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "s=[True,False,True,False,False]\n",
+ "np.where(np.array(s)==True)"
+ ]
},
{
"cell_type": "code",
- "execution_count": 112,
- "id": "42d23cd4",
+ "execution_count": 127,
+ "id": "59833d98",
"metadata": {},
"outputs": [
{
@@ -593,6 +607,8 @@
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
+ " <th></th>\n",
+ " <th>r</th>\n",
" <th>bp</th>\n",
" <th>stack</th>\n",
" <th>threeprime</th>\n",
@@ -600,7 +616,9 @@
" <th>orientation</th>\n",
" </tr>\n",
" <tr>\n",
- " <th>r</th>\n",
+ " <th>vh</th>\n",
+ " <th>zid</th>\n",
+ " <th></th>\n",
" <th></th>\n",
" <th></th>\n",
" <th></th>\n",
@@ -610,7 +628,9 @@
" </thead>\n",
" <tbody>\n",
" <tr>\n",
- " <th>1.0</th>\n",
+ " <th>0</th>\n",
+ " <th>0</th>\n",
+ " <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
@@ -618,7 +638,9 @@
" <td>NaN</td>\n",
" </tr>\n",
" <tr>\n",
- " <th>1.0</th>\n",
+ " <th>1</th>\n",
+ " <th>3</th>\n",
+ " <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
@@ -626,7 +648,9 @@
" <td>NaN</td>\n",
" </tr>\n",
" <tr>\n",
- " <th>NaN</th>\n",
+ " <th>2</th>\n",
+ " <th>1</th>\n",
+ " <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
@@ -634,7 +658,9 @@
" <td>NaN</td>\n",
" </tr>\n",
" <tr>\n",
- " <th>NaN</th>\n",
+ " <th>3</th>\n",
+ " <th>2</th>\n",
+ " <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
@@ -642,7 +668,9 @@
" <td>NaN</td>\n",
" </tr>\n",
" <tr>\n",
- " <th>NaN</th>\n",
+ " <th>1</th>\n",
+ " <th>8</th>\n",
+ " <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
@@ -654,16 +682,16 @@
"</div>"
],
"text/plain": [
- " bp stack threeprime seq orientation\n",
- "r \n",
- "1.0 NaN NaN NaN NaN NaN\n",
- "1.0 NaN NaN NaN NaN NaN\n",
- "NaN NaN NaN NaN NaN NaN\n",
- "NaN NaN NaN NaN NaN NaN\n",
- "NaN NaN NaN NaN NaN NaN"
+ " r bp stack threeprime seq orientation\n",
+ "vh zid \n",
+ "0 0 NaN NaN NaN NaN NaN NaN\n",
+ "1 3 NaN NaN NaN NaN NaN NaN\n",
+ "2 1 NaN NaN NaN NaN NaN NaN\n",
+ "3 2 NaN NaN NaN NaN NaN NaN\n",
+ "1 8 NaN NaN NaN NaN NaN NaN"
]
},
- "execution_count": 112,
+ "execution_count": 127,
"metadata": {},
"output_type": "execute_result"
}
@@ -675,7 +703,7 @@
{
"cell_type": "code",
"execution_count": 100,
- "id": "9ed6d92a",
+ "id": "1139214c",
"metadata": {},
"outputs": [
{
@@ -700,7 +728,7 @@
{
"cell_type": "code",
"execution_count": 13,
- "id": "41cad09e",
+ "id": "ca81ed00",
"metadata": {},
"outputs": [
{
@@ -721,7 +749,7 @@
{
"cell_type": "code",
"execution_count": 14,
- "id": "ee7a5b2f",
+ "id": "895861eb",
"metadata": {},
"outputs": [
{
@@ -743,7 +771,7 @@
{
"cell_type": "code",
"execution_count": 198,
- "id": "5308fd27",
+ "id": "82bc0749",
"metadata": {},
"outputs": [
{
@@ -765,7 +793,7 @@
{
"cell_type": "code",
"execution_count": 15,
- "id": "a173a0cc",
+ "id": "1f5791d0",
"metadata": {},
"outputs": [
{
@@ -786,7 +814,7 @@
{
"cell_type": "code",
"execution_count": 173,
- "id": "3ac307d0",
+ "id": "b36dc7e5",
"metadata": {},
"outputs": [],
"source": [
@@ -822,7 +850,7 @@
{
"cell_type": "code",
"execution_count": 177,
- "id": "6c3869e9",
+ "id": "e0f42e86",
"metadata": {},
"outputs": [],
"source": [
@@ -858,7 +886,7 @@
{
"cell_type": "code",
"execution_count": 187,
- "id": "a938b5d1",
+ "id": "0ca50f51",
"metadata": {},
"outputs": [
{
@@ -1085,7 +1113,7 @@
{
"cell_type": "code",
"execution_count": 142,
- "id": "28fa9e4a",
+ "id": "6b3a92fd",
"metadata": {},
"outputs": [],
"source": [
@@ -1122,7 +1150,7 @@
{
"cell_type": "code",
"execution_count": 117,
- "id": "5876b835",
+ "id": "09ac3efa",
"metadata": {},
"outputs": [],
"source": [
@@ -1143,7 +1171,7 @@
{
"cell_type": "code",
"execution_count": 116,
- "id": "b27560ea",
+ "id": "20b8e5fb",
"metadata": {},
"outputs": [
{
@@ -1355,7 +1383,7 @@
{
"cell_type": "code",
"execution_count": 157,
- "id": "c2ac4f18",
+ "id": "0978d11f",
"metadata": {},
"outputs": [
{
@@ -1379,7 +1407,7 @@
{
"cell_type": "code",
"execution_count": 152,
- "id": "11333080",
+ "id": "b9ffc57d",
"metadata": {},
"outputs": [
{
@@ -1400,7 +1428,7 @@
{
"cell_type": "code",
"execution_count": 62,
- "id": "c15af839",
+ "id": "91c8bda1",
"metadata": {},
"outputs": [
{
@@ -1628,7 +1656,7 @@
{
"cell_type": "code",
"execution_count": 3,
- "id": "eda2056d",
+ "id": "9d00775e",
"metadata": {},
"outputs": [],
"source": [
@@ -1754,7 +1782,7 @@
{
"cell_type": "code",
"execution_count": 4,
- "id": "f7efd378",
+ "id": "fe38ddd0",
"metadata": {},
"outputs": [],
"source": [
@@ -1775,7 +1803,7 @@
{
"cell_type": "code",
"execution_count": 20,
- "id": "1422eca5",
+ "id": "47af43f2",
"metadata": {},
"outputs": [
{
@@ -1837,7 +1865,7 @@
{
"cell_type": "code",
"execution_count": 25,
- "id": "cf5a3dbd",
+ "id": "92ee5de3",
"metadata": {},
"outputs": [
{
@@ -1899,7 +1927,7 @@
{
"cell_type": "code",
"execution_count": null,
- "id": "98cb9b38",
+ "id": "e99ffa71",
"metadata": {},
"outputs": [],
"source": [
@@ -1912,7 +1940,7 @@
{
"cell_type": "code",
"execution_count": 13,
- "id": "ff952b38",
+ "id": "9f251d5c",
"metadata": {},
"outputs": [
{
@@ -1933,7 +1961,7 @@
{
"cell_type": "code",
"execution_count": 7,
- "id": "85083378",
+ "id": "ddff8ccc",
"metadata": {},
"outputs": [
{
@@ -1982,7 +2010,7 @@
{
"cell_type": "code",
"execution_count": 36,
- "id": "ded55624",
+ "id": "9bc201d2",
"metadata": {},
"outputs": [
{
@@ -2044,7 +2072,7 @@
{
"cell_type": "code",
"execution_count": 1,
- "id": "40a7b76d",
+ "id": "ab8da587",
"metadata": {},
"outputs": [
{
@@ -2070,7 +2098,7 @@
{
"cell_type": "code",
"execution_count": null,
- "id": "f994ff10",
+ "id": "4141882b",
"metadata": {},
"outputs": [],
"source": []
@@ -2078,7 +2106,7 @@
{
"cell_type": "code",
"execution_count": 3,
- "id": "5144726b",
+ "id": "ce1031ed",
"metadata": {},
"outputs": [
{
@@ -2098,7 +2126,7 @@
{
"cell_type": "code",
"execution_count": 13,
- "id": "5c836eac",
+ "id": "0f02b96f",
"metadata": {},
"outputs": [
{
@@ -2119,7 +2147,7 @@
{
"cell_type": "code",
"execution_count": 15,
- "id": "2c3ce8b1",
+ "id": "eb6d271c",
"metadata": {},
"outputs": [
{
@@ -2189,7 +2217,7 @@
{
"cell_type": "code",
"execution_count": 16,
- "id": "137db876",
+ "id": "db9fb42a",
"metadata": {},
"outputs": [],
"source": [
@@ -2200,7 +2228,7 @@
{
"cell_type": "code",
"execution_count": 26,
- "id": "8210cbee",
+ "id": "6e28886e",
"metadata": {},
"outputs": [
{
@@ -2309,7 +2337,7 @@
{
"cell_type": "code",
"execution_count": 25,
- "id": "4ef92d58",
+ "id": "8532c958",
"metadata": {},
"outputs": [
{
@@ -2330,7 +2358,7 @@
{
"cell_type": "code",
"execution_count": 10,
- "id": "57059a9e",
+ "id": "42c985e8",
"metadata": {},
"outputs": [
{
@@ -2361,7 +2389,7 @@
{
"cell_type": "code",
"execution_count": 1,
- "id": "001aef7e",
+ "id": "d26babc9",
"metadata": {},
"outputs": [
{
@@ -2858,7 +2886,7 @@
{
"cell_type": "code",
"execution_count": 3,
- "id": "8feaa1ca",
+ "id": "eacb35b4",
"metadata": {},
"outputs": [
{
@@ -2892,7 +2920,7 @@
{
"cell_type": "code",
"execution_count": 4,
- "id": "4455fa61",
+ "id": "0ff274ec",
"metadata": {},
"outputs": [
{
@@ -2912,7 +2940,7 @@
{
"cell_type": "code",
"execution_count": 5,
- "id": "605a19c2",
+ "id": "cb4b20bc",
"metadata": {},
"outputs": [],
"source": [
@@ -2922,7 +2950,7 @@
{
"cell_type": "code",
"execution_count": 6,
- "id": "c45d0282",
+ "id": "9694a3bb",
"metadata": {},
"outputs": [
{
@@ -2943,7 +2971,7 @@
{
"cell_type": "code",
"execution_count": 7,
- "id": "f0d25377",
+ "id": "d8dec327",
"metadata": {},
"outputs": [
{
@@ -2970,7 +2998,7 @@
{
"cell_type": "code",
"execution_count": null,
- "id": "bf3a74cf",
+ "id": "6af9f1ff",
"metadata": {},
"outputs": [],
"source": []
--
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