diff --git a/mrdna/readers/.ipynb_checkpoints/test-checkpoint.ipynb b/mrdna/readers/.ipynb_checkpoints/test-checkpoint.ipynb
index f708f52415803193537b3354f3b54b9a7cd29e12..a3bd160b751ec4f98fab99afeb23a4076371dfd4 100644
--- a/mrdna/readers/.ipynb_checkpoints/test-checkpoint.ipynb
+++ b/mrdna/readers/.ipynb_checkpoints/test-checkpoint.ipynb
@@ -2,24 +2,59 @@
"cells": [
{
"cell_type": "code",
- "execution_count": 342,
- "id": "8abe7172",
+ "execution_count": 1,
+ "id": "03eb8540",
"metadata": {
"scrolled": true
},
- "outputs": [],
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "pip3 install termcolor\n"
+ ]
+ }
+ ],
"source": [
"import pandas as pd\n",
"import pickle\n",
- "import numpy as np"
+ "import numpy as np\n",
+ "import json\n",
+ "import re\n",
+ "import cadnano\n",
+ "from cadnano.document import Document\n"
]
},
{
"cell_type": "code",
- "execution_count": 343,
- "id": "a6c10574",
+ "execution_count": 2,
+ "id": "cb40f6b8",
"metadata": {},
"outputs": [],
+ "source": [
+ "from cadnano.views.pathview import pathstyles"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 1,
+ "id": "ea7e8da0",
+ "metadata": {},
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ " _\n",
+ " _____ ___ _| |___ ___\n",
+ "| | _| . | | .'|\n",
+ "|_|_|_|_| |___|_|_|__,| v1.0a.dev74 \n",
+ "it/its\n",
+ "\n"
+ ]
+ }
+ ],
"source": [
"import cadnano\n",
"from cadnano.document import Document\n",
@@ -28,98 +63,536 @@
},
{
"cell_type": "code",
- "execution_count": 553,
- "id": "1322927e",
+ "execution_count": 15,
+ "id": "3a134bd9-0d8c-40b2-bf71-7b2310e09802",
"metadata": {},
"outputs": [],
"source": [
- "def gen_prop_table(json_file):\n",
- " part,vslist=read_json_file(json_file)\n",
- " props = part.getModelProperties().copy()\n",
+ "def get_lattice(part):\n",
+ " lattice_type = None\n",
+ " _gt = part.getGridType()\n",
" try:\n",
- " if props.get('point_type') == PointType.ARBITRARY:\n",
- " # TODO add code to encode Parts with ARBITRARY point configurations\n",
- " raise NotImplementedError(\"Not implemented\")\n",
+ " lattice_type = _gt.name.lower()\n",
" except:\n",
- " try:\n",
- " vh_props, origins = part.helixPropertiesAndOrigins()\n",
- " except:\n",
- " origins = {hid:part.getVirtualHelixOrigin(hid)[:2] for hid in part.getidNums()}\n",
- " scaf_id=[nttype(vslist['scaf'][i]) for i in vslist.index]\n",
- " stap_id=[nttype(vslist['stap'][i]) for i in vslist.index]\n",
- " cad_bps=part.getIndices(0)\n",
- " vslist[\"scafnt\"]=np.sum(np.array(scaf_id),axis=1)\n",
- " vslist[\"stapnt\"]=np.sum(np.array(stap_id),axis=1)\n",
- " totnt=np.sum(vslist[\"scafnt\"])+np.sum(vslist[\"stapnt\"])\n",
- " is_scaf=np.zeros(totnt,dtype=bool)\n",
- " is_scaf[0:np.sum(vslist[\"scafnt\"])]=1\n",
- " nt_prop=pd.DataFrame(index=range(totnt),columns=[\"vh\",\"zid\",\"is_scaf\",\"r\",\"bp\",\"stack\",\"threeprime\",\"seq\",\"orientation\"])\n",
- " nt_prop[\"is_scaf\"]=is_scaf\n",
- " tot_id=scaf_id+stap_id\n",
- " vhi,zidi=np.where(np.array(scaf_id)==1)\n",
- " vhj,zidj=np.where(np.array(stap_id)==1)\n",
- " vhi=vslist.index[vhi]\n",
- " vhj=vslist.index[vhj]\n",
- " nt_prop[\"vh\"]=list(vhi)+list(vhj)\n",
- " nt_prop[\"zid\"]=list(zidi)+list(zidj)\n",
+ " if _gt == 1:\n",
+ " lattice_type = 'square'\n",
+ " elif _gt == 2:\n",
+ " lattice_type = 'honeycomb'\n",
+ " else:\n",
+ " print(lattice_type)\n",
+ " return lattice_type\n",
+ "\n",
+ "\n",
+ "def read_json_file(filename):\n",
+ " import cadnano\n",
+ " from cadnano.document import Document\n",
+ "\n",
+ " try:\n",
+ " with open(filename) as ch:\n",
+ " json_data = json.load(ch)\n",
+ " except:\n",
+ " with open(filename) as ch:\n",
+ " content = \"\"\n",
+ " for l in ch:\n",
+ " l = re.sub(r\"'\", r'\"', l)\n",
+ " # https://stackoverflow.com/questions/4033633/handling-lazy-json-in-python-expecting-property-name\n",
+ " # l = re.sub(r\"{\\s*(\\w)\", r'{\"\\1', l)\n",
+ " # l = re.sub(r\",\\s*(\\w)\", r',\"\\1', l)\n",
+ " # l = re.sub(r\"(\\w):\", r'\\1\":', l)\n",
+ " content += l+\"\\n\"\n",
+ " json_data = json.loads(content)\n",
+ "\n",
+ " try:\n",
+ " doc = Document()\n",
+ " cadnano.fileio.v3decode.decode(doc, json_data)\n",
+ " decoder = 3\n",
+ " except:\n",
+ " doc = Document()\n",
+ " cadnano.fileio.v2decode.decode(doc, json_data)\n",
+ " decoder = 2\n",
+ "\n",
+ " parts = [p for p in doc.getParts()]\n",
+ " if len(parts) != 1:\n",
+ " raise Exception(\"Only documents containing a single cadnano part are implemented at this time.\")\n",
+ " part = parts[0]\n",
+ "\n",
+ " if decoder == 2:\n",
+ " \"\"\" It seems cadnano2.5 (as of ce6ff019) does not set the EulerZ for square lattice structures correctly, doing so here \"\"\"\n",
+ " l = get_lattice(part)\n",
+ " if l == 'square':\n",
+ " for id_num in part.getIdNums():\n",
+ " if part.vh_properties.loc[id_num,'eulerZ'] == 0:\n",
+ " part.vh_properties.loc[id_num,'eulerZ'] = 360*(6/10.5)\n",
+ " df=pd.DataFrame(json_data[\"vstrands\"])\n",
+ " n_df=df.set_index(\"num\")\n",
+ " return part\n",
+ "\n",
+ "def get_helix_angle(part, helix_id, indices):\n",
+ " \"\"\" Get \"start_orientation\" for helix \"\"\"\n",
+ " # import ipdb\n",
+ " # ipdb.set_trace()\n",
+ "\n",
+ " \"\"\" FROM CADNANO2.5\n",
+ " + angle is CCW\n",
+ " - angle is CW\n",
+ " Right handed DNA rotates clockwise from 5' to 3'\n",
+ " we use the convention the 5' end starts at 0 degrees\n",
+ " and it's pair is minor_groove_angle degrees away\n",
+ " direction, hence the minus signs. eulerZ\n",
+ " \"\"\"\n",
+ "\n",
+ " hp, bpr, tpr, eulerZ, mgroove = part.vh_properties.loc[helix_id,\n",
+ " ['helical_pitch',\n",
+ " 'bases_per_repeat',\n",
+ " 'turns_per_repeat',\n",
+ " 'eulerZ',\n",
+ " 'minor_groove_angle']]\n",
+ " twist_per_base = tpr*360./bpr\n",
+ " # angle = eulerZ - twist_per_base*indices + 0.5*mgroove + 180\n",
+ " angle = eulerZ + twist_per_base*indices - 0.5*mgroove\n",
+ " return angle\n",
+ "\n",
+ "def gen_id_series(strand,part):\n",
+ " df=pd.DataFrame(columns=[\"vh\",\"zid\",\"fwd\",\"stack_tuple\",\"threeprime_tuple\",\"x\",\"y\",\"z\"],index=range(strand.totalLength()),dtype=object)\n",
+ " df[\"vh\"]=strand._id_num\n",
+ " df[\"fwd\"]=strand.isForward()\n",
+ " df[\"x\"]=part.getVirtualHelixOrigin(strand._id_num)[0]*10\n",
+ " df[\"y\"]=part.getVirtualHelixOrigin(strand._id_num)[1]*10\n",
+ " id_lo,id_hi=strand.idxs()\n",
+ " zids=[str(i) for i in range(id_lo,id_hi+1)]\n",
+ " insert_dict={}\n",
+ " insert_dict=dict([(j.idx(),j.length()) for j in strand.insertionsOnStrand()])\n",
+ " z=np.arange(id_lo,id_hi+1)\n",
+ " zids=[str(i) for i in range(id_lo,id_hi+1)]\n",
+ " z=list(np.arange(id_lo,id_hi+1))\n",
+ " zids=[str(i) for i in range(id_lo,id_hi+1)]\n",
+ " for insert_base in insert_dict:\n",
+ " z_ind=zids.index(str(insert_base))\n",
+ " z_val=insert_dict[insert_base]\n",
+ " z_pos_ind=z.index(insert_base)\n",
+ " zids.pop(z_ind)\n",
+ " z.pop(z_pos_ind)\n",
+ " if z_val!=-1:\n",
+ " #l=[str(insert_base)+\".\"+str(i) for i in range(z_val+1)]\n",
+ " l=list(range(z_val+1))\n",
+ " l.reverse()\n",
+ " for k in l: \n",
+ " zids.insert(z_ind,str(insert_base)+\".\"+str(k))\n",
+ " z.insert(z_pos_ind,insert_base+k/(z_val+1))\n",
+ " df[\"zid\"]=zids\n",
+ " df[\"z\"]=np.array(z)*3.4\n",
+ " \n",
+ " \n",
+ " L=[(df[\"vh\"][i],df[\"zid\"][i],df[\"fwd\"][i]) for i in df.index]\n",
+ " if strand.isForward()==True:\n",
+ " df[\"stack_tuple\"]=L[1:]+[-1]\n",
+ " if strand.connection3p() is None:\n",
+ " df[\"threeprime_tuple\"]=L[1:]+[-1]\n",
+ " else:\n",
+ " df[\"threeprime_tuple\"]=L[1:]+[(strand.connection3p().idNum(),str(strand.connection3p().idx5Prime()),strand.connection3p().isForward())]\n",
+ " \n",
+ " \n",
+ " else:\n",
+ " df[\"stack_tuple\"]=[-1]+L[0:-1]\n",
+ " if strand.connection3p() is None:\n",
+ " df[\"threeprime_tuple\"]=[-1]+L[0:-1]\n",
+ " else:\n",
+ " df[\"threeprime_tuple\"]=[(strand.connection3p().idNum(),str(strand.connection3p().idx5Prime()),strand.connection3p().isForward())]+L[0:-1]\n",
+ " ## cadnano 3.1 sequence assign is wrong if there is insertion or deletion. \n",
+ " df[\"r\"]=[np.array([df[\"x\"][i],df[\"y\"][i],df[\"z\"][i]],dtype=np.float32) for i in df.index]\n",
+ " \n",
+ " return [pd.Series(df.loc[i]) for i in df.index]\n",
+ "\n"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 18,
+ "id": "04c497ae",
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "def gen_prop_table(part):\n",
+ " strand_set=[]\n",
+ " for i in part.getidNums():\n",
+ " fwd,rev=part.getStrandSets(i)\n",
+ " [strand_set.append(i) for i in fwd.strands()]\n",
+ " [strand_set.append(i) for i in rev.strands()]\n",
+ " id_series=[]\n",
+ " for i in strand_set:\n",
+ " id_series=id_series+gen_id_series(i,part)\n",
+ " \n",
+ " nt_prop=pd.DataFrame(id_series)\n",
+ " nt_prop.reset_index(inplace=True)\n",
+ " nt_prop[\"seq\"]=-1\n",
+ " ind_tuple=list(zip(nt_prop[\"vh\"],nt_prop[\"zid\"],nt_prop[\"fwd\"]))\n",
+ " stacks=[]\n",
+ " for i in list(nt_prop[\"stack_tuple\"]):\n",
+ " if i ==-1:\n",
+ " stacks.append(i)\n",
+ " else:\n",
+ " stacks.append(ind_tuple.index(i))\n",
+ " nt_prop[\"stack\"]=stacks\n",
+ " tprime=[]\n",
+ " for i in list(nt_prop[\"threeprime_tuple\"]):\n",
+ " if i ==-1:\n",
+ " tprime.append(i)\n",
+ " else:\n",
+ " tprime.append(ind_tuple.index(i))\n",
+ " nt_prop[\"threeprime\"]=tprime\n",
" vhzid=list(zip(nt_prop[\"vh\"],nt_prop[\"zid\"]))\n",
- " nt_prop[\"r\"]=[part.getCoordinate(helix_id, indices) for helix_id, indices in zip(nt_prop[\"vh\"],nt_prop[\"zid\"])]\n",
- " nt_prop[\"orientation\"]=[get_helix_angle(part, helix_id, indices) for helix_id,indices in zip(nt_prop[\"vh\"],nt_prop[\"zid\"])]\n",
+ " nt_prop[\"orientation\"]=[get_helix_angle(part, helix_id, int(float(indices))) for helix_id,indices in vhzid]\n",
" nt_prop=nt_prop.fillna(-1)\n",
- " for i in range(int(len(vhzid)/2)):\n",
+ " counter=-1\n",
+ " bp=-np.ones(len(nt_prop.index),dtype=int)\n",
+ " bp_map=dict(zip(ind_tuple,nt_prop.index))\n",
+ " for i,j,k in ind_tuple:\n",
+ " counter+=1\n",
" try:\n",
- " bp1,bp2=(i,1+i+vhzid[i+1:].index(vhzid[i]))\n",
- " nt_prop[\"bp\"][bp1]=bp2\n",
- " nt_prop[\"bp\"][bp2]=bp1\n",
+ " bp[counter]=bp_map[(i,j,not(k))]\n",
" except:\n",
" pass\n",
- " tprime_list=-np.ones(len(nt_prop.index),dtype=int)\n",
- " index2=list(zip(vhzid,nt_prop[\"is_scaf\"]))\n",
- " for i in range(len(nt_prop.index)):\n",
- " ((m,n),p)=list(zip(vhzid,nt_prop[\"is_scaf\"]))[i]\n",
- " if p==True:\n",
- " k,l=(vslist[\"scaf\"][m])[n][2:]\n",
- " if k!=-1 and l!=-1:\n",
- " n=index2.index(((k,l),True))\n",
- " tprime_list[i]=int(n)\n",
+ " nt_prop[\"bp\"]=bp\n",
"\n",
- " else:\n",
- " k,l=(vslist[\"stap\"][m])[n][2:]\n",
- " if k!=-1 and l!=-1:\n",
- " n=index2.index(((k,l),False))\n",
- " tprime_list[i]=int(n)\n",
- " nt_prop[\"threeprime\"]=tprime_list\n",
- " (n,)=np.where(nt_prop[\"threeprime\"]==-1)\n",
- " stackid=nt_prop[\"bp\"][[list(nt_prop[\"threeprime\"]).index(i) for i in n]]\n",
- " nt_prop[\"stack\"][stackid.index[np.where(np.array(stackid)!=-1)]]=nt_prop[\"threeprime\"][stackid.index[np.where(np.array(stackid)!=-1)]]\n",
- " ## Todo: sequence \n",
- "\n",
- "\n",
- " return nt_prop\n"
+ " return nt_prop"
]
},
{
"cell_type": "code",
- "execution_count": 555,
- "id": "c787cb64",
+ "execution_count": 19,
+ "id": "11b0f5de-80f6-4845-b97f-a9d31e7be90a",
"metadata": {},
"outputs": [
{
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "Found cadnano version 2 file\n"
- ]
+ "data": {
+ "text/html": [
+ "<div>\n",
+ "<style scoped>\n",
+ " .dataframe tbody tr th:only-of-type {\n",
+ " vertical-align: middle;\n",
+ " }\n",
+ "\n",
+ " .dataframe tbody tr th {\n",
+ " vertical-align: top;\n",
+ " }\n",
+ "\n",
+ " .dataframe thead th {\n",
+ " text-align: right;\n",
+ " }\n",
+ "</style>\n",
+ "<table border=\"1\" class=\"dataframe\">\n",
+ " <thead>\n",
+ " <tr style=\"text-align: right;\">\n",
+ " <th></th>\n",
+ " <th>index</th>\n",
+ " <th>vh</th>\n",
+ " <th>zid</th>\n",
+ " <th>fwd</th>\n",
+ " <th>stack_tuple</th>\n",
+ " <th>threeprime_tuple</th>\n",
+ " <th>x</th>\n",
+ " <th>y</th>\n",
+ " <th>z</th>\n",
+ " <th>r</th>\n",
+ " <th>seq</th>\n",
+ " <th>stack</th>\n",
+ " <th>threeprime</th>\n",
+ " <th>orientation</th>\n",
+ " <th>bp</th>\n",
+ " </tr>\n",
+ " </thead>\n",
+ " <tbody>\n",
+ " <tr>\n",
+ " <th>0</th>\n",
+ " <td>0</td>\n",
+ " <td>0</td>\n",
+ " <td>5</td>\n",
+ " <td>True</td>\n",
+ " <td>(0, 6, True)</td>\n",
+ " <td>(0, 6, True)</td>\n",
+ " <td>0.000000</td>\n",
+ " <td>22.50</td>\n",
+ " <td>17.0</td>\n",
+ " <td>[0.0, 22.5, 17.0]</td>\n",
+ " <td>-1</td>\n",
+ " <td>1</td>\n",
+ " <td>1</td>\n",
+ " <td>81.428571</td>\n",
+ " <td>38</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>1</th>\n",
+ " <td>1</td>\n",
+ " <td>0</td>\n",
+ " <td>6</td>\n",
+ " <td>True</td>\n",
+ " <td>(0, 7, True)</td>\n",
+ " <td>(0, 7, True)</td>\n",
+ " <td>0.000000</td>\n",
+ " <td>22.50</td>\n",
+ " <td>20.4</td>\n",
+ " <td>[0.0, 22.5, 20.4]</td>\n",
+ " <td>-1</td>\n",
+ " <td>2</td>\n",
+ " <td>2</td>\n",
+ " <td>115.714286</td>\n",
+ " <td>39</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>2</th>\n",
+ " <td>2</td>\n",
+ " <td>0</td>\n",
+ " <td>7</td>\n",
+ " <td>True</td>\n",
+ " <td>(0, 8, True)</td>\n",
+ " <td>(0, 8, True)</td>\n",
+ " <td>0.000000</td>\n",
+ " <td>22.50</td>\n",
+ " <td>23.8</td>\n",
+ " <td>[0.0, 22.5, 23.8]</td>\n",
+ " <td>-1</td>\n",
+ " <td>3</td>\n",
+ " <td>3</td>\n",
+ " <td>150.000000</td>\n",
+ " <td>40</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>3</th>\n",
+ " <td>3</td>\n",
+ " <td>0</td>\n",
+ " <td>8</td>\n",
+ " <td>True</td>\n",
+ " <td>(0, 9, True)</td>\n",
+ " <td>(0, 9, True)</td>\n",
+ " <td>0.000000</td>\n",
+ " <td>22.50</td>\n",
+ " <td>27.2</td>\n",
+ " <td>[0.0, 22.5, 27.2]</td>\n",
+ " <td>-1</td>\n",
+ " <td>4</td>\n",
+ " <td>4</td>\n",
+ " <td>184.285714</td>\n",
+ " <td>41</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>4</th>\n",
+ " <td>4</td>\n",
+ " <td>0</td>\n",
+ " <td>9</td>\n",
+ " <td>True</td>\n",
+ " <td>(0, 10, True)</td>\n",
+ " <td>(0, 10, True)</td>\n",
+ " <td>0.000000</td>\n",
+ " <td>22.50</td>\n",
+ " <td>30.6</td>\n",
+ " <td>[0.0, 22.5, 30.6]</td>\n",
+ " <td>-1</td>\n",
+ " <td>5</td>\n",
+ " <td>5</td>\n",
+ " <td>218.571429</td>\n",
+ " <td>42</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>...</th>\n",
+ " <td>...</td>\n",
+ " <td>...</td>\n",
+ " <td>...</td>\n",
+ " <td>...</td>\n",
+ " <td>...</td>\n",
+ " <td>...</td>\n",
+ " <td>...</td>\n",
+ " <td>...</td>\n",
+ " <td>...</td>\n",
+ " <td>...</td>\n",
+ " <td>...</td>\n",
+ " <td>...</td>\n",
+ " <td>...</td>\n",
+ " <td>...</td>\n",
+ " <td>...</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>410</th>\n",
+ " <td>12</td>\n",
+ " <td>5</td>\n",
+ " <td>35</td>\n",
+ " <td>False</td>\n",
+ " <td>(5, 34, False)</td>\n",
+ " <td>(5, 34, False)</td>\n",
+ " <td>19.485574</td>\n",
+ " <td>11.25</td>\n",
+ " <td>119.0</td>\n",
+ " <td>[19.485573, 11.25, 119.0]</td>\n",
+ " <td>-1</td>\n",
+ " <td>409</td>\n",
+ " <td>409</td>\n",
+ " <td>1110.000000</td>\n",
+ " <td>375</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>411</th>\n",
+ " <td>13</td>\n",
+ " <td>5</td>\n",
+ " <td>36</td>\n",
+ " <td>False</td>\n",
+ " <td>(5, 35, False)</td>\n",
+ " <td>(5, 35, False)</td>\n",
+ " <td>19.485574</td>\n",
+ " <td>11.25</td>\n",
+ " <td>122.4</td>\n",
+ " <td>[19.485573, 11.25, 122.4]</td>\n",
+ " <td>-1</td>\n",
+ " <td>410</td>\n",
+ " <td>410</td>\n",
+ " <td>1144.285714</td>\n",
+ " <td>376</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>412</th>\n",
+ " <td>14</td>\n",
+ " <td>5</td>\n",
+ " <td>37</td>\n",
+ " <td>False</td>\n",
+ " <td>(5, 36, False)</td>\n",
+ " <td>(5, 36, False)</td>\n",
+ " <td>19.485574</td>\n",
+ " <td>11.25</td>\n",
+ " <td>125.8</td>\n",
+ " <td>[19.485573, 11.25, 125.8]</td>\n",
+ " <td>-1</td>\n",
+ " <td>411</td>\n",
+ " <td>411</td>\n",
+ " <td>1178.571429</td>\n",
+ " <td>377</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>413</th>\n",
+ " <td>15</td>\n",
+ " <td>5</td>\n",
+ " <td>38</td>\n",
+ " <td>False</td>\n",
+ " <td>(5, 37, False)</td>\n",
+ " <td>(5, 37, False)</td>\n",
+ " <td>19.485574</td>\n",
+ " <td>11.25</td>\n",
+ " <td>129.2</td>\n",
+ " <td>[19.485573, 11.25, 129.2]</td>\n",
+ " <td>-1</td>\n",
+ " <td>412</td>\n",
+ " <td>412</td>\n",
+ " <td>1212.857143</td>\n",
+ " <td>378</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>414</th>\n",
+ " <td>16</td>\n",
+ " <td>5</td>\n",
+ " <td>39</td>\n",
+ " <td>False</td>\n",
+ " <td>(5, 38, False)</td>\n",
+ " <td>(5, 38, False)</td>\n",
+ " <td>19.485574</td>\n",
+ " <td>11.25</td>\n",
+ " <td>132.6</td>\n",
+ " <td>[19.485573, 11.25, 132.6]</td>\n",
+ " <td>-1</td>\n",
+ " <td>413</td>\n",
+ " <td>413</td>\n",
+ " <td>1247.142857</td>\n",
+ " <td>379</td>\n",
+ " </tr>\n",
+ " </tbody>\n",
+ "</table>\n",
+ "<p>415 rows × 15 columns</p>\n",
+ "</div>"
+ ],
+ "text/plain": [
+ " index vh zid fwd stack_tuple threeprime_tuple x y \\\n",
+ "0 0 0 5 True (0, 6, True) (0, 6, True) 0.000000 22.50 \n",
+ "1 1 0 6 True (0, 7, True) (0, 7, True) 0.000000 22.50 \n",
+ "2 2 0 7 True (0, 8, True) (0, 8, True) 0.000000 22.50 \n",
+ "3 3 0 8 True (0, 9, True) (0, 9, True) 0.000000 22.50 \n",
+ "4 4 0 9 True (0, 10, True) (0, 10, True) 0.000000 22.50 \n",
+ ".. ... .. .. ... ... ... ... ... \n",
+ "410 12 5 35 False (5, 34, False) (5, 34, False) 19.485574 11.25 \n",
+ "411 13 5 36 False (5, 35, False) (5, 35, False) 19.485574 11.25 \n",
+ "412 14 5 37 False (5, 36, False) (5, 36, False) 19.485574 11.25 \n",
+ "413 15 5 38 False (5, 37, False) (5, 37, False) 19.485574 11.25 \n",
+ "414 16 5 39 False (5, 38, False) (5, 38, False) 19.485574 11.25 \n",
+ "\n",
+ " z r seq stack threeprime orientation \\\n",
+ "0 17.0 [0.0, 22.5, 17.0] -1 1 1 81.428571 \n",
+ "1 20.4 [0.0, 22.5, 20.4] -1 2 2 115.714286 \n",
+ "2 23.8 [0.0, 22.5, 23.8] -1 3 3 150.000000 \n",
+ "3 27.2 [0.0, 22.5, 27.2] -1 4 4 184.285714 \n",
+ "4 30.6 [0.0, 22.5, 30.6] -1 5 5 218.571429 \n",
+ ".. ... ... ... ... ... ... \n",
+ "410 119.0 [19.485573, 11.25, 119.0] -1 409 409 1110.000000 \n",
+ "411 122.4 [19.485573, 11.25, 122.4] -1 410 410 1144.285714 \n",
+ "412 125.8 [19.485573, 11.25, 125.8] -1 411 411 1178.571429 \n",
+ "413 129.2 [19.485573, 11.25, 129.2] -1 412 412 1212.857143 \n",
+ "414 132.6 [19.485573, 11.25, 132.6] -1 413 413 1247.142857 \n",
+ "\n",
+ " bp \n",
+ "0 38 \n",
+ "1 39 \n",
+ "2 40 \n",
+ "3 41 \n",
+ "4 42 \n",
+ ".. ... \n",
+ "410 375 \n",
+ "411 376 \n",
+ "412 377 \n",
+ "413 378 \n",
+ "414 379 \n",
+ "\n",
+ "[415 rows x 15 columns]"
+ ]
+ },
+ "execution_count": 19,
+ "metadata": {},
+ "output_type": "execute_result"
}
],
"source": [
- "nt_prop=gen_prop_table(\"test/Na_liu.json\")"
+ "gen_prop_table(p)"
+ ]
+ },
+ {
+ "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": [
+ "(415,)"
+ ]
+ },
+ "execution_count": 29,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "np.array(list(nt_prop['bp'])).shape"
]
},
{
"cell_type": "code",
"execution_count": 560,
- "id": "927f76f3",
+ "id": "5ee54071",
"metadata": {},
"outputs": [
{
@@ -139,38 +612,223 @@
},
{
"cell_type": "code",
- "execution_count": 562,
- "id": "2093c036",
+ "execution_count": 21,
+ "id": "e1588c54",
"metadata": {},
"outputs": [
{
"data": {
+ "text/html": [
+ "<div>\n",
+ "<style scoped>\n",
+ " .dataframe tbody tr th:only-of-type {\n",
+ " vertical-align: middle;\n",
+ " }\n",
+ "\n",
+ " .dataframe tbody tr th {\n",
+ " vertical-align: top;\n",
+ " }\n",
+ "\n",
+ " .dataframe thead th {\n",
+ " text-align: right;\n",
+ " }\n",
+ "</style>\n",
+ "<table border=\"1\" class=\"dataframe\">\n",
+ " <thead>\n",
+ " <tr style=\"text-align: right;\">\n",
+ " <th></th>\n",
+ " <th>vh</th>\n",
+ " <th>zid</th>\n",
+ " <th>is_scaf</th>\n",
+ " <th>r</th>\n",
+ " <th>bp</th>\n",
+ " <th>stack</th>\n",
+ " <th>threeprime</th>\n",
+ " <th>seq</th>\n",
+ " <th>orientation</th>\n",
+ " </tr>\n",
+ " </thead>\n",
+ " <tbody>\n",
+ " <tr>\n",
+ " <th>0</th>\n",
+ " <td>0</td>\n",
+ " <td>5</td>\n",
+ " <td>True</td>\n",
+ " <td>[0.0, 2.25, 1.7000000000000002]</td>\n",
+ " <td>213</td>\n",
+ " <td>-1</td>\n",
+ " <td>1</td>\n",
+ " <td>-1</td>\n",
+ " <td>[[0.14904226617617466, -0.9888308262251284, 0....</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>1</th>\n",
+ " <td>0</td>\n",
+ " <td>6</td>\n",
+ " <td>True</td>\n",
+ " <td>[0.0, 2.25, 2.04]</td>\n",
+ " <td>214</td>\n",
+ " <td>-1</td>\n",
+ " <td>2</td>\n",
+ " <td>-1</td>\n",
+ " <td>[[-0.4338837391175583, -0.900968867902419, 0.0...</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>2</th>\n",
+ " <td>0</td>\n",
+ " <td>7</td>\n",
+ " <td>True</td>\n",
+ " <td>[0.0, 2.25, 2.3800000000000003]</td>\n",
+ " <td>215</td>\n",
+ " <td>-1</td>\n",
+ " <td>3</td>\n",
+ " <td>-1</td>\n",
+ " <td>[[-0.8660254037844388, -0.49999999999999994, 0...</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>3</th>\n",
+ " <td>0</td>\n",
+ " <td>8</td>\n",
+ " <td>True</td>\n",
+ " <td>[0.0, 2.25, 2.72]</td>\n",
+ " <td>216</td>\n",
+ " <td>-1</td>\n",
+ " <td>4</td>\n",
+ " <td>-1</td>\n",
+ " <td>[[-0.9972037971811805, 0.07473009358642399, 0....</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>4</th>\n",
+ " <td>0</td>\n",
+ " <td>9</td>\n",
+ " <td>True</td>\n",
+ " <td>[0.0, 2.25, 3.06]</td>\n",
+ " <td>217</td>\n",
+ " <td>-1</td>\n",
+ " <td>5</td>\n",
+ " <td>-1</td>\n",
+ " <td>[[-0.7818314824680299, 0.6234898018587334, 0.0...</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>...</th>\n",
+ " <td>...</td>\n",
+ " <td>...</td>\n",
+ " <td>...</td>\n",
+ " <td>...</td>\n",
+ " <td>...</td>\n",
+ " <td>...</td>\n",
+ " <td>...</td>\n",
+ " <td>...</td>\n",
+ " <td>...</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>410</th>\n",
+ " <td>5</td>\n",
+ " <td>35</td>\n",
+ " <td>False</td>\n",
+ " <td>[1.948557375, 1.125, 11.9]</td>\n",
+ " <td>205</td>\n",
+ " <td>-1</td>\n",
+ " <td>411</td>\n",
+ " <td>-1</td>\n",
+ " <td>[[0.8660254037844375, -0.5000000000000019, 0.0...</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>411</th>\n",
+ " <td>5</td>\n",
+ " <td>36</td>\n",
+ " <td>False</td>\n",
+ " <td>[1.948557375, 1.125, 12.24]</td>\n",
+ " <td>206</td>\n",
+ " <td>-1</td>\n",
+ " <td>412</td>\n",
+ " <td>-1</td>\n",
+ " <td>[[0.4338837391175605, -0.900968867902418, 0.0]...</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>412</th>\n",
+ " <td>5</td>\n",
+ " <td>37</td>\n",
+ " <td>False</td>\n",
+ " <td>[1.948557375, 1.125, 12.58]</td>\n",
+ " <td>-1</td>\n",
+ " <td>-1</td>\n",
+ " <td>413</td>\n",
+ " <td>-1</td>\n",
+ " <td>[[-0.14904226617617078, -0.9888308262251292, 0...</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>413</th>\n",
+ " <td>5</td>\n",
+ " <td>38</td>\n",
+ " <td>False</td>\n",
+ " <td>[1.948557375, 1.125, 12.920000000000002]</td>\n",
+ " <td>-1</td>\n",
+ " <td>-1</td>\n",
+ " <td>414</td>\n",
+ " <td>-1</td>\n",
+ " <td>[[-0.6801727377709186, -0.7330518718298275, 0....</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>414</th>\n",
+ " <td>5</td>\n",
+ " <td>39</td>\n",
+ " <td>False</td>\n",
+ " <td>[1.948557375, 1.125, 13.260000000000002]</td>\n",
+ " <td>-1</td>\n",
+ " <td>-1</td>\n",
+ " <td>-1</td>\n",
+ " <td>-1</td>\n",
+ " <td>[[-0.9749279121818233, -0.222520933956317, 0.0...</td>\n",
+ " </tr>\n",
+ " </tbody>\n",
+ "</table>\n",
+ "<p>415 rows × 9 columns</p>\n",
+ "</div>"
+ ],
"text/plain": [
- "vh 0\n",
- "zid 21\n",
- "is_scaf True\n",
- "r [0.0, 15.75, 7.140000000000001]\n",
- "bp 7560\n",
- "stack -1\n",
- "threeprime 13\n",
- "seq -1\n",
- "orientation [[-4.440892098500626e-16, 1.0, 0.0], [-1.0, -4...\n",
- "Name: 12, dtype: object"
+ " vh zid is_scaf r bp stack \\\n",
+ "0 0 5 True [0.0, 2.25, 1.7000000000000002] 213 -1 \n",
+ "1 0 6 True [0.0, 2.25, 2.04] 214 -1 \n",
+ "2 0 7 True [0.0, 2.25, 2.3800000000000003] 215 -1 \n",
+ "3 0 8 True [0.0, 2.25, 2.72] 216 -1 \n",
+ "4 0 9 True [0.0, 2.25, 3.06] 217 -1 \n",
+ ".. .. ... ... ... ... ... \n",
+ "410 5 35 False [1.948557375, 1.125, 11.9] 205 -1 \n",
+ "411 5 36 False [1.948557375, 1.125, 12.24] 206 -1 \n",
+ "412 5 37 False [1.948557375, 1.125, 12.58] -1 -1 \n",
+ "413 5 38 False [1.948557375, 1.125, 12.920000000000002] -1 -1 \n",
+ "414 5 39 False [1.948557375, 1.125, 13.260000000000002] -1 -1 \n",
+ "\n",
+ " threeprime seq orientation \n",
+ "0 1 -1 [[0.14904226617617466, -0.9888308262251284, 0.... \n",
+ "1 2 -1 [[-0.4338837391175583, -0.900968867902419, 0.0... \n",
+ "2 3 -1 [[-0.8660254037844388, -0.49999999999999994, 0... \n",
+ "3 4 -1 [[-0.9972037971811805, 0.07473009358642399, 0.... \n",
+ "4 5 -1 [[-0.7818314824680299, 0.6234898018587334, 0.0... \n",
+ ".. ... ... ... \n",
+ "410 411 -1 [[0.8660254037844375, -0.5000000000000019, 0.0... \n",
+ "411 412 -1 [[0.4338837391175605, -0.900968867902418, 0.0]... \n",
+ "412 413 -1 [[-0.14904226617617078, -0.9888308262251292, 0... \n",
+ "413 414 -1 [[-0.6801727377709186, -0.7330518718298275, 0.... \n",
+ "414 -1 -1 [[-0.9749279121818233, -0.222520933956317, 0.0... \n",
+ "\n",
+ "[415 rows x 9 columns]"
]
},
- "execution_count": 562,
+ "execution_count": 21,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
- "nt_prop.loc[12]"
+ "nt_prop"
]
},
{
"cell_type": "code",
"execution_count": 468,
- "id": "51b62714",
+ "id": "156dcda2",
"metadata": {},
"outputs": [],
"source": [
@@ -181,7 +839,7 @@
{
"cell_type": "code",
"execution_count": 500,
- "id": "66e9eacd",
+ "id": "6413d856",
"metadata": {},
"outputs": [
{
@@ -202,7 +860,7 @@
{
"cell_type": "code",
"execution_count": 498,
- "id": "ddecdaef",
+ "id": "fe8797db",
"metadata": {},
"outputs": [
{
@@ -224,7 +882,7 @@
{
"cell_type": "code",
"execution_count": 480,
- "id": "ea39cbd0",
+ "id": "9f1b975f",
"metadata": {},
"outputs": [
{
@@ -245,7 +903,7 @@
{
"cell_type": "code",
"execution_count": 549,
- "id": "5008fa72",
+ "id": "a16f3fd0",
"metadata": {},
"outputs": [
{
@@ -277,7 +935,7 @@
{
"cell_type": "code",
"execution_count": 544,
- "id": "7409a9a8",
+ "id": "b9f25d41",
"metadata": {},
"outputs": [
{
@@ -301,7 +959,7 @@
{
"cell_type": "code",
"execution_count": 550,
- "id": "7e3b3abc",
+ "id": "976095ce",
"metadata": {},
"outputs": [
{
@@ -331,7 +989,7 @@
{
"cell_type": "code",
"execution_count": 548,
- "id": "33c599fb",
+ "id": "ac8f5067",
"metadata": {},
"outputs": [
{
@@ -355,7 +1013,7 @@
{
"cell_type": "code",
"execution_count": 527,
- "id": "c781d982",
+ "id": "1006fc48",
"metadata": {},
"outputs": [
{
@@ -380,7 +1038,7 @@
{
"cell_type": "code",
"execution_count": 503,
- "id": "7efc3ee8",
+ "id": "09c7e7d4",
"metadata": {},
"outputs": [
{
@@ -406,7 +1064,7 @@
{
"cell_type": "code",
"execution_count": 537,
- "id": "0b3eaca4",
+ "id": "5f0c5266",
"metadata": {},
"outputs": [
{
@@ -455,7 +1113,7 @@
{
"cell_type": "code",
"execution_count": 491,
- "id": "99e544cd",
+ "id": "fec987da",
"metadata": {},
"outputs": [
{
@@ -476,7 +1134,7 @@
{
"cell_type": "code",
"execution_count": 493,
- "id": "264bc035",
+ "id": "f332ad87",
"metadata": {},
"outputs": [
{
@@ -498,7 +1156,7 @@
{
"cell_type": "code",
"execution_count": 4,
- "id": "4f596a68",
+ "id": "dd3cd839",
"metadata": {},
"outputs": [],
"source": [
@@ -509,7 +1167,7 @@
{
"cell_type": "code",
"execution_count": null,
- "id": "ce978dbf",
+ "id": "41b3d9af",
"metadata": {},
"outputs": [],
"source": []
@@ -517,7 +1175,7 @@
{
"cell_type": "code",
"execution_count": 18,
- "id": "e10006d7",
+ "id": "9ec18edc",
"metadata": {},
"outputs": [],
"source": [
@@ -538,8 +1196,8 @@
},
{
"cell_type": "code",
- "execution_count": 358,
- "id": "ed9e6b6f",
+ "execution_count": 13,
+ "id": "2fa31a78",
"metadata": {},
"outputs": [
{
@@ -552,23 +1210,23 @@
{
"data": {
"text/plain": [
- "NucleicAcidPart_-1_3904"
+ "NucleicAcidPart_-1_2800"
]
},
- "execution_count": 358,
+ "execution_count": 13,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
- "p,f=read_json_file(\"test.json\")\n",
+ "p=read_json_file(\"test/test.json\")\n",
"p"
]
},
{
"cell_type": "code",
"execution_count": 441,
- "id": "8ec446ce",
+ "id": "64eb309f",
"metadata": {},
"outputs": [
{
@@ -751,7 +1409,7 @@
{
"cell_type": "code",
"execution_count": 199,
- "id": "263415de",
+ "id": "bda3cddd",
"metadata": {},
"outputs": [
{
@@ -772,7 +1430,7 @@
{
"cell_type": "code",
"execution_count": 434,
- "id": "6e58a7e7",
+ "id": "a86cfa84",
"metadata": {},
"outputs": [],
"source": [
@@ -840,7 +1498,7 @@
{
"cell_type": "code",
"execution_count": 442,
- "id": "3ee34e17",
+ "id": "be5de5ba",
"metadata": {},
"outputs": [
{
@@ -885,7 +1543,7 @@
{
"cell_type": "code",
"execution_count": 302,
- "id": "72245714",
+ "id": "0ce6701d",
"metadata": {},
"outputs": [],
"source": [
@@ -909,7 +1567,7 @@
{
"cell_type": "code",
"execution_count": 368,
- "id": "c3891b4a",
+ "id": "9d0e49cf",
"metadata": {},
"outputs": [],
"source": [
@@ -942,7 +1600,7 @@
{
"cell_type": "code",
"execution_count": 429,
- "id": "b3fcb6ac",
+ "id": "c1d77642",
"metadata": {},
"outputs": [],
"source": [
@@ -957,7 +1615,7 @@
{
"cell_type": "code",
"execution_count": 430,
- "id": "2565f375",
+ "id": "2c2d1227",
"metadata": {},
"outputs": [
{
@@ -992,7 +1650,7 @@
{
"cell_type": "code",
"execution_count": 431,
- "id": "ecf2414e",
+ "id": "e701d029",
"metadata": {},
"outputs": [
{
@@ -1013,7 +1671,7 @@
{
"cell_type": "code",
"execution_count": 433,
- "id": "5bc1a2b8",
+ "id": "4a62f5d9",
"metadata": {},
"outputs": [
{
@@ -1034,7 +1692,7 @@
{
"cell_type": "code",
"execution_count": 167,
- "id": "5f500be3",
+ "id": "d80ab792",
"metadata": {},
"outputs": [],
"source": [
@@ -1046,7 +1704,7 @@
{
"cell_type": "code",
"execution_count": 360,
- "id": "d7f0b909",
+ "id": "8e009bc9",
"metadata": {},
"outputs": [],
"source": [
@@ -1056,7 +1714,7 @@
{
"cell_type": "code",
"execution_count": 190,
- "id": "686640b1",
+ "id": "3dc97f0d",
"metadata": {},
"outputs": [
{
@@ -1239,7 +1897,7 @@
{
"cell_type": "code",
"execution_count": 200,
- "id": "ff964cef",
+ "id": "3d019b73",
"metadata": {},
"outputs": [],
"source": [
@@ -1275,7 +1933,7 @@
{
"cell_type": "code",
"execution_count": 201,
- "id": "97bce4fa",
+ "id": "fb789ffb",
"metadata": {},
"outputs": [
{
@@ -1298,7 +1956,7 @@
{
"cell_type": "code",
"execution_count": 146,
- "id": "30246519",
+ "id": "98703867",
"metadata": {},
"outputs": [],
"source": [
@@ -1308,7 +1966,7 @@
{
"cell_type": "code",
"execution_count": 148,
- "id": "2b287b99",
+ "id": "c316fead",
"metadata": {},
"outputs": [
{
@@ -1341,7 +1999,7 @@
{
"cell_type": "code",
"execution_count": 137,
- "id": "781327b0",
+ "id": "0718e41e",
"metadata": {},
"outputs": [],
"source": [
@@ -1358,7 +2016,7 @@
{
"cell_type": "code",
"execution_count": null,
- "id": "91188f0a",
+ "id": "1a61115e",
"metadata": {},
"outputs": [],
"source": []
@@ -1366,7 +2024,7 @@
{
"cell_type": "code",
"execution_count": 84,
- "id": "a4317b6b",
+ "id": "12198835",
"metadata": {},
"outputs": [],
"source": [
@@ -1377,7 +2035,7 @@
{
"cell_type": "code",
"execution_count": 156,
- "id": "7154c666",
+ "id": "1e5c9807",
"metadata": {},
"outputs": [
{
@@ -1503,7 +2161,7 @@
{
"cell_type": "code",
"execution_count": 157,
- "id": "f82be5d8",
+ "id": "31c50f63",
"metadata": {},
"outputs": [
{
@@ -1620,7 +2278,7 @@
{
"cell_type": "code",
"execution_count": 128,
- "id": "4053cca5",
+ "id": "67546136",
"metadata": {},
"outputs": [
{
@@ -1642,7 +2300,7 @@
{
"cell_type": "code",
"execution_count": 127,
- "id": "2a012588",
+ "id": "bad20d6a",
"metadata": {},
"outputs": [
{
@@ -1762,7 +2420,7 @@
{
"cell_type": "code",
"execution_count": 100,
- "id": "acfa6f0c",
+ "id": "48225afa",
"metadata": {},
"outputs": [
{
@@ -1787,7 +2445,7 @@
{
"cell_type": "code",
"execution_count": 13,
- "id": "7e82631e",
+ "id": "c75bd92f",
"metadata": {},
"outputs": [
{
@@ -1808,7 +2466,7 @@
{
"cell_type": "code",
"execution_count": 14,
- "id": "c69e710a",
+ "id": "00f1513e",
"metadata": {},
"outputs": [
{
@@ -1830,7 +2488,7 @@
{
"cell_type": "code",
"execution_count": 198,
- "id": "c93f7b4b",
+ "id": "aaa65658",
"metadata": {},
"outputs": [
{
@@ -1852,7 +2510,7 @@
{
"cell_type": "code",
"execution_count": 15,
- "id": "f44d5593",
+ "id": "cbddf07f",
"metadata": {},
"outputs": [
{
@@ -1873,7 +2531,7 @@
{
"cell_type": "code",
"execution_count": 173,
- "id": "da99c2f2",
+ "id": "fac8699e",
"metadata": {},
"outputs": [],
"source": [
@@ -1909,7 +2567,7 @@
{
"cell_type": "code",
"execution_count": 177,
- "id": "bf41fbbe",
+ "id": "308cd6c1",
"metadata": {},
"outputs": [],
"source": [
@@ -1945,7 +2603,7 @@
{
"cell_type": "code",
"execution_count": 187,
- "id": "becc8ec8",
+ "id": "bc032680",
"metadata": {},
"outputs": [
{
@@ -2172,7 +2830,7 @@
{
"cell_type": "code",
"execution_count": 142,
- "id": "65d304e7",
+ "id": "29ff7990",
"metadata": {},
"outputs": [],
"source": [
@@ -2209,7 +2867,7 @@
{
"cell_type": "code",
"execution_count": 117,
- "id": "1102332d",
+ "id": "3cb9542c",
"metadata": {},
"outputs": [],
"source": [
@@ -2230,7 +2888,7 @@
{
"cell_type": "code",
"execution_count": 116,
- "id": "9349147e",
+ "id": "4219838b",
"metadata": {},
"outputs": [
{
@@ -2442,7 +3100,7 @@
{
"cell_type": "code",
"execution_count": 157,
- "id": "23c69dfb",
+ "id": "45168e4b",
"metadata": {},
"outputs": [
{
@@ -2466,7 +3124,7 @@
{
"cell_type": "code",
"execution_count": 152,
- "id": "c6e2518a",
+ "id": "33e5c80d",
"metadata": {},
"outputs": [
{
@@ -2487,7 +3145,7 @@
{
"cell_type": "code",
"execution_count": 62,
- "id": "bf85089c",
+ "id": "9b79e902",
"metadata": {},
"outputs": [
{
@@ -2715,7 +3373,7 @@
{
"cell_type": "code",
"execution_count": 3,
- "id": "3fd57867",
+ "id": "cecd1c9f",
"metadata": {},
"outputs": [],
"source": [
@@ -2841,7 +3499,7 @@
{
"cell_type": "code",
"execution_count": 4,
- "id": "014caa04",
+ "id": "b4af37c1",
"metadata": {},
"outputs": [],
"source": [
@@ -2862,7 +3520,7 @@
{
"cell_type": "code",
"execution_count": 20,
- "id": "95719bec",
+ "id": "2fa89abc",
"metadata": {},
"outputs": [
{
@@ -2924,7 +3582,7 @@
{
"cell_type": "code",
"execution_count": 25,
- "id": "f4034eb9",
+ "id": "6e620d24",
"metadata": {},
"outputs": [
{
@@ -2986,7 +3644,7 @@
{
"cell_type": "code",
"execution_count": null,
- "id": "b9adb4fe",
+ "id": "fef6094a",
"metadata": {},
"outputs": [],
"source": [
@@ -2999,7 +3657,7 @@
{
"cell_type": "code",
"execution_count": 13,
- "id": "ca67b08f",
+ "id": "be089a18",
"metadata": {},
"outputs": [
{
@@ -3020,7 +3678,7 @@
{
"cell_type": "code",
"execution_count": 7,
- "id": "86a7a627",
+ "id": "6f75d365",
"metadata": {},
"outputs": [
{
@@ -3069,7 +3727,7 @@
{
"cell_type": "code",
"execution_count": 36,
- "id": "63614edc",
+ "id": "8dfadf61",
"metadata": {},
"outputs": [
{
@@ -3131,7 +3789,7 @@
{
"cell_type": "code",
"execution_count": 1,
- "id": "177fe2f1",
+ "id": "ba097c82",
"metadata": {},
"outputs": [
{
@@ -3157,7 +3815,7 @@
{
"cell_type": "code",
"execution_count": null,
- "id": "0c4a7b82",
+ "id": "1c4d4fa9",
"metadata": {},
"outputs": [],
"source": []
@@ -3165,7 +3823,7 @@
{
"cell_type": "code",
"execution_count": 3,
- "id": "82b5073c",
+ "id": "d4ff1f83",
"metadata": {},
"outputs": [
{
@@ -3185,7 +3843,7 @@
{
"cell_type": "code",
"execution_count": 13,
- "id": "684cdf08",
+ "id": "6f1dab46",
"metadata": {},
"outputs": [
{
@@ -3206,7 +3864,7 @@
{
"cell_type": "code",
"execution_count": 15,
- "id": "95b9f60b",
+ "id": "615964fe",
"metadata": {},
"outputs": [
{
@@ -3276,7 +3934,7 @@
{
"cell_type": "code",
"execution_count": 16,
- "id": "da04d8df",
+ "id": "a71b0639",
"metadata": {},
"outputs": [],
"source": [
@@ -3287,7 +3945,7 @@
{
"cell_type": "code",
"execution_count": 26,
- "id": "fc9fa817",
+ "id": "2bb83a1e",
"metadata": {},
"outputs": [
{
@@ -3396,7 +4054,7 @@
{
"cell_type": "code",
"execution_count": 25,
- "id": "d030eea1",
+ "id": "86f5c21e",
"metadata": {},
"outputs": [
{
@@ -3417,7 +4075,7 @@
{
"cell_type": "code",
"execution_count": 10,
- "id": "6586e97f",
+ "id": "f3fae511",
"metadata": {},
"outputs": [
{
@@ -3448,7 +4106,7 @@
{
"cell_type": "code",
"execution_count": 1,
- "id": "f087752e",
+ "id": "07f3352b",
"metadata": {},
"outputs": [
{
@@ -3945,7 +4603,7 @@
{
"cell_type": "code",
"execution_count": 3,
- "id": "d548b882",
+ "id": "61be89c1",
"metadata": {},
"outputs": [
{
@@ -3979,7 +4637,7 @@
{
"cell_type": "code",
"execution_count": 4,
- "id": "bd65fa30",
+ "id": "a00c445c",
"metadata": {},
"outputs": [
{
@@ -3999,7 +4657,7 @@
{
"cell_type": "code",
"execution_count": 5,
- "id": "96fe4106",
+ "id": "a648fae4",
"metadata": {},
"outputs": [],
"source": [
@@ -4009,7 +4667,7 @@
{
"cell_type": "code",
"execution_count": 6,
- "id": "70b6c9a6",
+ "id": "9d100033",
"metadata": {},
"outputs": [
{
@@ -4030,7 +4688,7 @@
{
"cell_type": "code",
"execution_count": 7,
- "id": "fc17c5e7",
+ "id": "66d3eaf4",
"metadata": {},
"outputs": [
{
@@ -4057,7 +4715,7 @@
{
"cell_type": "code",
"execution_count": null,
- "id": "ba6c81e7",
+ "id": "f60b0cdc",
"metadata": {},
"outputs": [],
"source": []
@@ -4065,7 +4723,7 @@
],
"metadata": {
"kernelspec": {
- "display_name": "Python 3",
+ "display_name": "Python 3 (ipykernel)",
"language": "python",
"name": "python3"
},
@@ -4079,7 +4737,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
- "version": "3.8.18"
+ "version": "3.8.19"
}
},
"nbformat": 4,
diff --git a/mrdna/readers/segmentmodel_from_cadnano.bak.py b/mrdna/readers/test/segmentmodel_from_cadnano.bak.py
similarity index 100%
rename from mrdna/readers/segmentmodel_from_cadnano.bak.py
rename to mrdna/readers/test/segmentmodel_from_cadnano.bak.py