diff --git a/mrdna/readers/test.ipynb b/mrdna/readers/test.ipynb
index 207998d94578efcb8916ef58fcb29016ab1e6bd4..a3bd160b751ec4f98fab99afeb23a4076371dfd4 100644
--- a/mrdna/readers/test.ipynb
+++ b/mrdna/readers/test.ipynb
@@ -2,12 +2,20 @@
"cells": [
{
"cell_type": "code",
- "execution_count": 9,
+ "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",
@@ -55,8 +63,8 @@
},
{
"cell_type": "code",
- "execution_count": 6,
- "id": "4fc535bb",
+ "execution_count": 15,
+ "id": "3a134bd9-0d8c-40b2-bf71-7b2310e09802",
"metadata": {},
"outputs": [],
"source": [
@@ -71,11 +79,13 @@
" elif _gt == 2:\n",
" lattice_type = 'honeycomb'\n",
" else:\n",
- " print(\"WARNING: unable to determine cadnano part lattice type\")\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",
@@ -113,9 +123,10 @@
" 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_df\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",
@@ -139,136 +150,411 @@
" 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 rotationAboutAxis(np.array((0,0,1)),angle)\n",
+ " return angle\n",
"\n",
- "def nttype(scafs):\n",
- " def judge(i):\n",
- " if i ==[-1,-1,-1,-1]:\n",
- " return 0\n",
- " else: return 1\n",
- " n=np.array([judge(i) for i in scafs])\n",
- " return 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": 7,
- "id": "f83dff7d",
+ "execution_count": 18,
+ "id": "04c497ae",
"metadata": {},
"outputs": [],
"source": [
- "def gen_prop_table(json_file):\n",
- " part,vslist=read_json_file(json_file)\n",
- " props = part.getModelProperties().copy()\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",
- " 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",
+ "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",
- "\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",
+ " nt_prop[\"bp\"]=bp\n",
"\n",
- "\n",
- " return nt_prop\n"
+ " return nt_prop"
]
},
{
"cell_type": "code",
- "execution_count": 11,
- "id": "1d900942",
+ "execution_count": 19,
+ "id": "11b0f5de-80f6-4845-b97f-a9d31e7be90a",
"metadata": {},
"outputs": [
{
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "Found cadnano version 2 file\n"
- ]
- },
- {
- "name": "stderr",
- "output_type": "stream",
- "text": [
- "<ipython-input-7-d91c550125eb>:37: SettingWithCopyWarning: \n",
- "A value is trying to be set on a copy of a slice from a DataFrame\n",
- "\n",
- "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
- " nt_prop[\"bp\"][bp1]=bp2\n",
- "<ipython-input-7-d91c550125eb>:38: SettingWithCopyWarning: \n",
- "A value is trying to be set on a copy of a slice from a DataFrame\n",
- "\n",
- "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
- " nt_prop[\"bp\"][bp2]=bp1\n",
- "<ipython-input-7-d91c550125eb>:59: SettingWithCopyWarning: \n",
- "A value is trying to be set on a copy of a slice from a DataFrame\n",
- "\n",
- "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
- " nt_prop[\"stack\"][stackid.index[np.where(np.array(stackid)!=-1)]]=nt_prop[\"threeprime\"][stackid.index[np.where(np.array(stackid)!=-1)]]\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/test.json\")"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 23,
- "id": "04c497ae",
- "metadata": {},
- "outputs": [],
- "source": [
- "nt_prop.to_csv(\"test.csv\")"
+ "gen_prop_table(p)"
]
},
{
@@ -910,7 +1196,7 @@
},
{
"cell_type": "code",
- "execution_count": 358,
+ "execution_count": 13,
"id": "2fa31a78",
"metadata": {},
"outputs": [
@@ -924,16 +1210,16 @@
{
"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"
]
},
@@ -4437,7 +4723,7 @@
],
"metadata": {
"kernelspec": {
- "display_name": "Python 3",
+ "display_name": "Python 3 (ipykernel)",
"language": "python",
"name": "python3"
},
@@ -4451,7 +4737,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
- "version": "3.8.18"
+ "version": "3.8.19"
}
},
"nbformat": 4,