diff --git a/Untitled.ipynb b/Untitled.ipynb
deleted file mode 100644
index e8beb278a8f8fdfab608de7cd3c3c7b836094a33..0000000000000000000000000000000000000000
--- a/Untitled.ipynb
+++ /dev/null
@@ -1,850 +0,0 @@
-{
- "cells": [
- {
- "cell_type": "code",
- "execution_count": null,
- "id": "96ccbf23-4a46-4bae-bef2-fdf4c2466ad3",
- "metadata": {},
- "outputs": [],
- "source": []
- },
- {
- "cell_type": "code",
- "execution_count": 6,
- "id": "3157488c-08cf-4f10-95f6-745613382000",
- "metadata": {},
- "outputs": [],
- "source": [
- "from cdna.cdna import CDNAGen"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "id": "a6f5bc24-e454-49ad-b1e3-1f5b63c66ab2",
- "metadata": {},
- "outputs": [],
- "source": []
- },
- {
- "cell_type": "code",
- "execution_count": 7,
- "id": "ceb225a6-3a63-49e7-a0d3-a92256012261",
- "metadata": {},
- "outputs": [
- {
- "name": "stderr",
- "output_type": "stream",
- "text": [
- "INFO:root:Extracted GTF attributes: ['Accessibility_Energy', 'Hybridization_Energy', 'Interaction_Energy', 'Number_of_binding_sites', 'Binding_Probability']\n"
- ]
- },
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "\n",
- "Fasta file successfully written to: test_files/cDNA.fasta\n",
- "Copy number csv file successfully written to: test_files/cDNA.csv\n"
- ]
- }
- ],
- "source": [
- "test_path = \"/Users/ericboittier/Documents/github/cdna-generator/test_files/\"\n",
- "gtf = test_path+\"Example_GTF_Input.gtf\"\n",
- "cpn = test_path+\"copy_number_input.csv\"\n",
- "fasta = test_path+\"yeast_example.fa\"\n",
- "\n",
- "G = CDNAGen(fasta, gtf, cpn, \"test_files/cDNA.fasta\", \"test_files/cDNA.csv\")"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 9,
- "id": "24976988-4a28-4932-8f53-d8ac7bb018f8",
- "metadata": {},
- "outputs": [
- {
- "data": {
- "text/html": [
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- " vertical-align: middle;\n",
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- " }\n",
- "\n",
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- " 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>seqname</th>\n",
- " <th>source</th>\n",
- " <th>feature</th>\n",
- " <th>start</th>\n",
- " <th>end</th>\n",
- " <th>score</th>\n",
- " <th>strand</th>\n",
- " <th>frame</th>\n",
- " <th>Accessibility_Energy</th>\n",
- " <th>Hybridization_Energy</th>\n",
- " <th>Interaction_Energy</th>\n",
- " <th>Number_of_binding_sites</th>\n",
- " <th>Binding_Probability</th>\n",
- " <th>Normalized_Binding_Probability</th>\n",
- " <th>Transcript_Copy_Number</th>\n",
- " <th>cdna_ID</th>\n",
- " <th>priming_site</th>\n",
- " <th>complement</th>\n",
- " </tr>\n",
- " </thead>\n",
- " <tbody>\n",
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- " <td>25</td>\n",
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- " </tr>\n",
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- " <td>5</td>\n",
- " <td>35</td>\n",
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- " <td>1.000000</td>\n",
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- " <td>None</td>\n",
- " <td>None</td>\n",
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- " <tr>\n",
- " <th>4</th>\n",
- " <td>Transcript_4</td>\n",
- " <td>RIBlast</td>\n",
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- " <td>None</td>\n",
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- " </tr>\n",
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- " <th>5</th>\n",
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- " <td>Transcript_5_0</td>\n",
- " <td>None</td>\n",
- " <td>None</td>\n",
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- " seqname source feature start end score strand frame \\\n",
- "0 Transcript_1 RIBlast Priming_site 10 25 NaN + 0 \n",
- "1 Transcript_1 RIBlast Priming_site 640 655 NaN + 0 \n",
- "2 Transcript_2 RIBlast Priming_site 3 18 NaN + 0 \n",
- "3 Transcript_3 RIBlast Priming_site 5 35 NaN + 0 \n",
- "4 Transcript_4 RIBlast Priming_site 5 35 NaN + 0 \n",
- "5 Transcript_5 RIBlast Priming_site 5 35 NaN + 0 \n",
- "\n",
- " Accessibility_Energy Hybridization_Energy Interaction_Energy \\\n",
- "0 1.49 -9.76 -8.74 \n",
- "1 1.71 -9.12 -8.34 \n",
- "2 1.21 -5.12 -2.34 \n",
- "3 1.21 -5.12 -2.34 \n",
- "4 1.21 -5.12 -2.34 \n",
- "5 1.21 -5.12 -2.34 \n",
- "\n",
- " Number_of_binding_sites Binding_Probability \\\n",
- "0 2 0.12 \n",
- "1 2 0.05 \n",
- "2 1 0.15 \n",
- "3 1 0.25 \n",
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- "4 None \n",
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- "\n",
- " complement \n",
- "0 TTACAACTTTAGTTCTTTTAATATACTAGAAGCCAGCTCTTTATAC... \n",
- "1 TTACAACTTTAGTTCTTTTAATATACTAGAAGCCAGCTCTTTATAC... \n",
- "2 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATTAAA... \n",
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- "4 None \n",
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- "execution_count": 9,
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- " <th>3</th>\n",
- " <td>Transcript_3</td>\n",
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- " <td>Priming_site</td>\n",
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- " <td>35</td>\n",
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- " <td>1.000000</td>\n",
- " <td>33.0</td>\n",
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- " <td>None</td>\n",
- " <td>None</td>\n",
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- " <tr>\n",
- " <th>4</th>\n",
- " <td>Transcript_4</td>\n",
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- " <td>Priming_site</td>\n",
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- " <td>35</td>\n",
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- " <td>11.0</td>\n",
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- " <td>35</td>\n",
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- " seqname source feature start end score strand frame \\\n",
- "0 Transcript_1 RIBlast Priming_site 10 25 NaN + 0 \n",
- "1 Transcript_1 RIBlast Priming_site 640 655 NaN + 0 \n",
- "2 Transcript_2 RIBlast Priming_site 3 18 NaN + 0 \n",
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- "5 Transcript_5 RIBlast Priming_site 5 35 NaN + 0 \n",
- "\n",
- " Accessibility_Energy Hybridization_Energy Interaction_Energy \\\n",
- "0 1.49 -9.76 -8.74 \n",
- "1 1.71 -9.12 -8.34 \n",
- "2 1.21 -5.12 -2.34 \n",
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- "4 1.21 -5.12 -2.34 \n",
- "5 1.21 -5.12 -2.34 \n",
- "\n",
- " Number_of_binding_sites Binding_Probability \\\n",
- "0 2 0.12 \n",
- "1 2 0.05 \n",
- "2 1 0.15 \n",
- "3 1 0.25 \n",
- "4 1 0.15 \n",
- "5 1 0.15 \n",
- "\n",
- " Normalized_Binding_Probability Transcript_Copy_Number cdna_ID \\\n",
- "0 0.705882 8.0 Transcript_1_0 \n",
- "1 0.294118 4.0 Transcript_1_1 \n",
- "2 1.000000 11.0 Transcript_2_0 \n",
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- "4 1.000000 11.0 Transcript_4_0 \n",
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- "\n",
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- "0 (T, T, T, T, T, T, T, T, T, A, T, G, G, A, T, ... \n",
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- "2 (T, T, T, T, T, T, T, T, T, T, T, T, T, T, T, ... \n",
- "3 None \n",
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- "5 None \n",
- "\n",
- " complement \n",
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- "2 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATTAAA... \n",
- "3 None \n",
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- "5 None "
- ]
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- "execution_count": 4,
- "metadata": {},
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- "source": [
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- {
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- "execution_count": 5,
- "id": "0511af5c-780e-41ba-9fb2-17e6640c5822",
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- "source": [
- "G.write_csv()"
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- {
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- "execution_count": 6,
- "id": "9e7fe7be-d134-4c1e-8eea-55273c79e39d",
- "metadata": {},
- "outputs": [],
- "source": [
- "G.add_sequences()"
- ]
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- " <th>strand</th>\n",
- " <th>frame</th>\n",
- " <th>Accessibility_Energy</th>\n",
- " <th>Hybridization_Energy</th>\n",
- " <th>Interaction_Energy</th>\n",
- " <th>Number_of_binding_sites</th>\n",
- " <th>Binding_Probability</th>\n",
- " <th>Normalized_Binding_Probability</th>\n",
- " <th>Transcript_Copy_Number</th>\n",
- " <th>cdna_ID</th>\n",
- " <th>priming_site</th>\n",
- " <th>complement</th>\n",
- " </tr>\n",
- " </thead>\n",
- " <tbody>\n",
- " <tr>\n",
- " <th>0</th>\n",
- " <td>Transcript_1</td>\n",
- " <td>RIBlast</td>\n",
- " <td>Priming_site</td>\n",
- " <td>10</td>\n",
- " <td>25</td>\n",
- " <td>NaN</td>\n",
- " <td>+</td>\n",
- " <td>0</td>\n",
- " <td>1.49</td>\n",
- " <td>-9.76</td>\n",
- " <td>-8.74</td>\n",
- " <td>2</td>\n",
- " <td>0.12</td>\n",
- " <td>0.705882</td>\n",
- " <td>8.0</td>\n",
- " <td>Transcript_1_0</td>\n",
- " <td>(T, T, T, T, T, T, T, T, T, A, T, G, G, A, T, ...</td>\n",
- " <td>TTACAACTTTAGTTCTTTTAATATACTAGAAGCCAGCTCTTTATAC...</td>\n",
- " </tr>\n",
- " <tr>\n",
- " <th>1</th>\n",
- " <td>Transcript_1</td>\n",
- " <td>RIBlast</td>\n",
- " <td>Priming_site</td>\n",
- " <td>640</td>\n",
- " <td>655</td>\n",
- " <td>NaN</td>\n",
- " <td>+</td>\n",
- " <td>0</td>\n",
- " <td>1.71</td>\n",
- " <td>-9.12</td>\n",
- " <td>-8.34</td>\n",
- " <td>2</td>\n",
- " <td>0.05</td>\n",
- " <td>0.294118</td>\n",
- " <td>4.0</td>\n",
- " <td>Transcript_1_1</td>\n",
- " <td>(A, G, A, C, T, T, T, T, T, G, A, G, A, T, G, ...</td>\n",
- " <td>TTACAACTTTAGTTCTTTTAATATACTAGAAGCCAGCTCTTTATAC...</td>\n",
- " </tr>\n",
- " <tr>\n",
- " <th>2</th>\n",
- " <td>Transcript_2</td>\n",
- " <td>RIBlast</td>\n",
- " <td>Priming_site</td>\n",
- " <td>3</td>\n",
- " <td>18</td>\n",
- " <td>NaN</td>\n",
- " <td>+</td>\n",
- " <td>0</td>\n",
- " <td>1.21</td>\n",
- " <td>-5.12</td>\n",
- " <td>-2.34</td>\n",
- " <td>1</td>\n",
- " <td>0.15</td>\n",
- " <td>1.000000</td>\n",
- " <td>11.0</td>\n",
- " <td>Transcript_2_0</td>\n",
- " <td>(T, T, T, T, T, T, T, T, T, T, T, T, T, T, T, ...</td>\n",
- " <td>AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATTAAA...</td>\n",
- " </tr>\n",
- " <tr>\n",
- " <th>3</th>\n",
- " <td>Transcript_3</td>\n",
- " <td>RIBlast</td>\n",
- " <td>Priming_site</td>\n",
- " <td>5</td>\n",
- " <td>35</td>\n",
- " <td>NaN</td>\n",
- " <td>+</td>\n",
- " <td>0</td>\n",
- " <td>1.21</td>\n",
- " <td>-5.12</td>\n",
- " <td>-2.34</td>\n",
- " <td>1</td>\n",
- " <td>0.25</td>\n",
- " <td>1.000000</td>\n",
- " <td>33.0</td>\n",
- " <td>Transcript_3_0</td>\n",
- " <td>None</td>\n",
- " <td>None</td>\n",
- " </tr>\n",
- " <tr>\n",
- " <th>4</th>\n",
- " <td>Transcript_4</td>\n",
- " <td>RIBlast</td>\n",
- " <td>Priming_site</td>\n",
- " <td>5</td>\n",
- " <td>35</td>\n",
- " <td>NaN</td>\n",
- " <td>+</td>\n",
- " <td>0</td>\n",
- " <td>1.21</td>\n",
- " <td>-5.12</td>\n",
- " <td>-2.34</td>\n",
- " <td>1</td>\n",
- " <td>0.15</td>\n",
- " <td>1.000000</td>\n",
- " <td>11.0</td>\n",
- " <td>Transcript_4_0</td>\n",
- " <td>None</td>\n",
- " <td>None</td>\n",
- " </tr>\n",
- " <tr>\n",
- " <th>5</th>\n",
- " <td>Transcript_5</td>\n",
- " <td>RIBlast</td>\n",
- " <td>Priming_site</td>\n",
- " <td>5</td>\n",
- " <td>35</td>\n",
- " <td>NaN</td>\n",
- " <td>+</td>\n",
- " <td>0</td>\n",
- " <td>1.21</td>\n",
- " <td>-5.12</td>\n",
- " <td>-2.34</td>\n",
- " <td>1</td>\n",
- " <td>0.15</td>\n",
- " <td>1.000000</td>\n",
- " <td>55.0</td>\n",
- " <td>Transcript_5_0</td>\n",
- " <td>None</td>\n",
- " <td>None</td>\n",
- " </tr>\n",
- " </tbody>\n",
- "</table>\n",
- "</div>"
- ],
- "text/plain": [
- " seqname source feature start end score strand frame \\\n",
- "0 Transcript_1 RIBlast Priming_site 10 25 NaN + 0 \n",
- "1 Transcript_1 RIBlast Priming_site 640 655 NaN + 0 \n",
- "2 Transcript_2 RIBlast Priming_site 3 18 NaN + 0 \n",
- "3 Transcript_3 RIBlast Priming_site 5 35 NaN + 0 \n",
- "4 Transcript_4 RIBlast Priming_site 5 35 NaN + 0 \n",
- "5 Transcript_5 RIBlast Priming_site 5 35 NaN + 0 \n",
- "\n",
- " Accessibility_Energy Hybridization_Energy Interaction_Energy \\\n",
- "0 1.49 -9.76 -8.74 \n",
- "1 1.71 -9.12 -8.34 \n",
- "2 1.21 -5.12 -2.34 \n",
- "3 1.21 -5.12 -2.34 \n",
- "4 1.21 -5.12 -2.34 \n",
- "5 1.21 -5.12 -2.34 \n",
- "\n",
- " Number_of_binding_sites Binding_Probability \\\n",
- "0 2 0.12 \n",
- "1 2 0.05 \n",
- "2 1 0.15 \n",
- "3 1 0.25 \n",
- "4 1 0.15 \n",
- "5 1 0.15 \n",
- "\n",
- " Normalized_Binding_Probability Transcript_Copy_Number cdna_ID \\\n",
- "0 0.705882 8.0 Transcript_1_0 \n",
- "1 0.294118 4.0 Transcript_1_1 \n",
- "2 1.000000 11.0 Transcript_2_0 \n",
- "3 1.000000 33.0 Transcript_3_0 \n",
- "4 1.000000 11.0 Transcript_4_0 \n",
- "5 1.000000 55.0 Transcript_5_0 \n",
- "\n",
- " priming_site \\\n",
- "0 (T, T, T, T, T, T, T, T, T, A, T, G, G, A, T, ... \n",
- "1 (A, G, A, C, T, T, T, T, T, G, A, G, A, T, G, ... \n",
- "2 (T, T, T, T, T, T, T, T, T, T, T, T, T, T, T, ... \n",
- "3 None \n",
- "4 None \n",
- "5 None \n",
- "\n",
- " complement \n",
- "0 TTACAACTTTAGTTCTTTTAATATACTAGAAGCCAGCTCTTTATAC... \n",
- "1 TTACAACTTTAGTTCTTTTAATATACTAGAAGCCAGCTCTTTATAC... \n",
- "2 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATTAAA... \n",
- "3 None \n",
- "4 None \n",
- "5 None "
- ]
- },
- "execution_count": 7,
- "metadata": {},
- "output_type": "execute_result"
- }
- ],
- "source": [
- "G.df_input_GTF"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "id": "4a482960-0e05-4355-b91c-fc7f51c138c2",
- "metadata": {},
- "outputs": [],
- "source": []
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "id": "304fd031-524a-4fc3-9322-9b3dd55268fb",
- "metadata": {},
- "outputs": [],
- "source": [
- "# G.df_input_GTF[\"A\"] = G.df_input_GTF.apply(lambda row: foo(row), axis=1)"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "id": "a8f7a36d-d768-4daf-8705-4cab5e06b562",
- "metadata": {},
- "outputs": [],
- "source": [
- "G.df_input_GTF[G.df_input_GTF[\"seqname\"]==\"Transcript_1\"]"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "id": "b0d7f2e4-c590-49a9-89eb-b53144dba9e8",
- "metadata": {},
- "outputs": [],
- "source": []
- }
- ],
- "metadata": {
- "kernelspec": {
- "display_name": "Python 3 (ipykernel)",
- "language": "python",
- "name": "python3"
- },
- "language_info": {
- "codemirror_mode": {
- "name": "ipython",
- "version": 3
- },
- "file_extension": ".py",
- "mimetype": "text/x-python",
- "name": "python",
- "nbconvert_exporter": "python",
- "pygments_lexer": "ipython3",
- "version": "3.9.13"
- }
- },
- "nbformat": 4,
- "nbformat_minor": 5
-}