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isoform_differentiation/Untitled2.ipynb
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{ | |
"cells": [ | |
{ | |
"cell_type": "code", | |
"execution_count": 2, | |
"metadata": {}, | |
"outputs": [], | |
"source": [ | |
"import pandas as pd\n", | |
"import numpy as np\n", | |
"from scipy.stats import ttest_ind_from_stats" | |
] | |
}, | |
{ | |
"cell_type": "code", | |
"execution_count": 3, | |
"metadata": {}, | |
"outputs": [], | |
"source": [ | |
"fn=\"/project/owlmayerTemporary/Sid/nanopore-analysis/Results_5_1/Quantification/all_counts_deseq2norm_stats.csv\"\n", | |
"df=pd.read_csv(fn)\n", | |
"conds = [\"day0\",\"day3\",\"day5\"]\n", | |
"for cond in conds: \n", | |
" df['mean'+cond]=df.filter(like=cond+'_').mean(1)\n", | |
" df['std'+cond]=df.filter(like=cond+'_').std(1)\n", | |
" df['stdn'+cond]=df.filter(like=cond+'_').std(1)/np.sqrt(2)\n", | |
" df['reps'+cond]=2\n", | |
" \n", | |
"for d in conds:\n", | |
" df['valMax'+str(d)] = (df.groupby(['gene_id'])['mean'+str(d)].transform(max)==df['mean'+str(d)])*1\n", | |
"potentialSwitches=set(df[(df.filter(like='valMax').sum(axis=1)>0)&(df.filter(like='valMax').sum(axis=1)<len(conds))]['gene_id'])\n", | |
"\n", | |
"df_genes=df.filter(like='gene').copy().drop_duplicates()\n", | |
"df_genes=df_genes[df_genes['gene_id'].isin(potentialSwitches)]\n", | |
"for d in conds:\n", | |
" df_genes['mainIso'+str(d)] = np.nan\n", | |
"df_genes=df_genes.set_index('gene_id')\n", | |
"\n", | |
"for gene in potentialSwitches:\n", | |
" data=df[df[\"gene_id\"]==gene]\n", | |
" if (data.shape[0] > 1):\n", | |
" for d in conds:\n", | |
" candidate=data[data['valMax'+str(d)]==1]\n", | |
" cmean=candidate['mean'+str(d)].values[0]\n", | |
" cstd=candidate['std'+str(d)].values[0]\n", | |
" creps=candidate['reps'+str(d)].values[0]\n", | |
" temp=data[data['transcript_id']!=candidate['transcript_id'].values[0]]\n", | |
"\n", | |
" if (temp.apply(lambda x: ttest_ind_from_stats(cmean, cstd, creps, x['mean'+str(d)],x['std'+str(d)], x['reps'+str(d)])[1],1)<0.05).all():\n", | |
" df_genes.loc[gene,'mainIso'+str(d)]=candidate['transcript_id'].values[0]\n", | |
"isoSwi=df_genes[df_genes.filter(like=\"mainIso\").nunique(axis=1)>1]\n", | |
"#isoSwi.to_csv('/project/Neurodifferentiation_System/IsoformsAll/isoformSwitches0_01.csv')\n", | |
"mainIsoforms=set(isoSwi.filter(like='mainIso').values.flatten()[~pd.isnull(isoSwi.filter(like='mainIso').values.flatten())])" | |
] | |
}, | |
{ | |
"cell_type": "code", | |
"execution_count": null, | |
"metadata": {}, | |
"outputs": [], | |
"source": [ | |
"fn='/project/Neurodifferentiation_System/IsoformsAll/stats_TPM.csv'\n", | |
"df=pd.read_csv(fn)\n", | |
"\n", | |
"days=list(set([int(x.split('transcript_mean')[1]) for x in df.filter(regex='transcript_mean').columns]))\n", | |
"for d in days:\n", | |
" df['valMax'+str(d)] = (df.groupby(['gene_id'])['transcript_mean'+str(d)].transform(max)==df['transcript_mean'+str(d)])*1\n", | |
"potentialSwitches=set(df[(df.filter(like='valMax').sum(axis=1)>0)&(df.filter(like='valMax').sum(axis=1)<len(days))]['gene_id'])\n", | |
"df_genes=df.filter(like='gene').copy().drop_duplicates()\n", | |
"df_genes=df_genes[df_genes['gene_id'].isin(potentialSwitches)]\n", | |
"for d in days:\n", | |
" df_genes['mainIso'+str(d)] = np.nan\n", | |
"df_genes=df_genes.set_index('gene_id')\n", | |
"for gene in potentialSwitches:\n", | |
" data=df[df[\"gene_id\"]==gene]\n", | |
" for d in days:\n", | |
" candidate=data[data['valMax'+str(d)]==1]\n", | |
" cmean=candidate['transcript_mean'+str(d)].values[0]\n", | |
" cstd=candidate['transcript_std'+str(d)].values[0]\n", | |
" creps=candidate['number_reps'+str(d)].values[0]\n", | |
" temp=data[data['transcript_id']!=candidate['transcript_id'].values[0]]\n", | |
" if (temp.apply(lambda x: ttest_ind_from_stats(cmean, cstd, creps, x['transcript_mean'+str(d)],x['transcript_std'+str(d)], x['number_reps'+str(d)])[1],1)<0.01).all():\n", | |
" df_genes.loc[gene,'mainIso'+str(d)]=candidate['transcript_id'].values[0]\n", | |
"isoSwi=df_genes[df_genes.filter(like=\"mainIso\").nunique(axis=1)>1]\n", | |
"isoSwi.to_csv('/project/Neurodifferentiation_System/IsoformsAll/isoformSwitches0_01.csv')\n", | |
"mainIsoforms=set(isoSwi.filter(like='mainIso').values.flatten()[~pd.isnull(isoSwi.filter(like='mainIso').values.flatten())])" | |
] | |
}, | |
{ | |
"cell_type": "code", | |
"execution_count": 4, | |
"metadata": {}, | |
"outputs": [], | |
"source": [ | |
"fn=\"/project/owlmayerTemporary/Sid/nanopore-analysis/Results_5_1/Quantification/all_counts_deseq2norm.txt\"\n", | |
"df=pd.read_csv(fn)\n", | |
"conds = [\"day0\",\"day3\",\"day5\"]\n", | |
"for cond in conds: \n", | |
" df['mean'+cond]=df.filter(like=cond+'_').mean(1)\n", | |
" df['std'+cond]=df.filter(like=cond+'_').std(1)\n", | |
" df['stdn'+cond]=df.filter(like=cond+'_').std(1)/np.sqrt(2)\n", | |
" df['reps'+cond]=2\n", | |
" \n", | |
"for d in conds:\n", | |
" df['valMax'+str(d)] = (df.groupby(['gene_id'])['mean'+str(d)].transform(max)==df['mean'+str(d)])*1\n", | |
"#df.to_csv(\"/project/owlmayerTemporary/Sid/nanopore-analysis/Results_5_1/Quantification/all_counts_deseq2norm_stats.csv\")" | |
] | |
}, | |
{ | |
"cell_type": "code", | |
"execution_count": 5, | |
"metadata": {}, | |
"outputs": [ | |
{ | |
"name": "stdout", | |
"output_type": "stream", | |
"text": [ | |
"ADAM12\n", | |
"AL596087.2\n", | |
"CLCN1\n", | |
"COX11\n", | |
"DNMBP\n", | |
"EPB41L5\n", | |
"ERBB2\n", | |
"ERGIC3\n", | |
"F2RL1\n", | |
"FKBP11\n", | |
"GAB3\n", | |
"GABRB1\n", | |
"IQSEC2\n", | |
"LAGE3\n", | |
"LINC00623\n", | |
"MXRA7\n", | |
"NCAM1\n", | |
"NHLH1\n", | |
"NKAIN4\n", | |
"PFN2\n", | |
"PLXNA2\n", | |
"PPM1E\n", | |
"PSMD14\n", | |
"PTRH1\n", | |
"RDM1P5\n", | |
"RFC5\n", | |
"RNF24\n", | |
"RPS24\n", | |
"SEPTIN6\n", | |
"SEPTIN8\n", | |
"SHD\n", | |
"SMC5\n", | |
"SNORA40\n", | |
"STMN2\n", | |
"TFDP2\n", | |
"TRAF3IP2\n", | |
"UNC45B\n", | |
"VEPH1\n", | |
"WDR37\n", | |
"ZNRD2\n", | |
"40\n" | |
] | |
} | |
], | |
"source": [ | |
"count =0\n", | |
"for i in sorted(isoSwi[\"gene_name\"].values):\n", | |
" print(i)\n", | |
" count += 1\n", | |
"print(count)\n" | |
] | |
}, | |
{ | |
"cell_type": "code", | |
"execution_count": 6, | |
"metadata": {}, | |
"outputs": [ | |
{ | |
"data": { | |
"text/plain": [ | |
"2353" | |
] | |
}, | |
"execution_count": 6, | |
"metadata": {}, | |
"output_type": "execute_result" | |
} | |
], | |
"source": [ | |
"len(potentialSwitches)" | |
] | |
}, | |
{ | |
"cell_type": "code", | |
"execution_count": 1, | |
"metadata": {}, | |
"outputs": [ | |
{ | |
"ename": "NameError", | |
"evalue": "name 'potentialSwitches' 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-1-261a0e621f00>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0mpotentialSwitches\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m", | |
"\u001b[0;31mNameError\u001b[0m: name 'potentialSwitches' is not defined" | |
] | |
} | |
], | |
"source": [ | |
"potentialSwitches" | |
] | |
} | |
], | |
"metadata": { | |
"kernelspec": { | |
"display_name": "Python 3", | |
"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": "3.7.4" | |
} | |
}, | |
"nbformat": 4, | |
"nbformat_minor": 2 | |
} |