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POefficient way to compare elements between very long lists
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copied!<p>I have two lists in files: File 1 has 200000 rows and looks like</p> <pre><code>MAP2K4 FLNC MYPN ACTN2 ACVR1 FNTA UGT2A1 HPGDS RPA2 STAT3 ARF1 GGA3 ARF3 ARFIP2 ARF3 ARFIP1 AKR1A1 EXOSC4 RPA2 GAS7 APP APPBP2 APLP1 DAB1 CITED2 TFAP2A EP300 TFAP2A APOB MTTP ARRB2 RALGDS ARRB2 ZNF807 </code></pre> <p>File 2 has 700000 rows and looks like:</p> <pre><code>MAP2K4 FLNC MAP2K4 rs10036867 MAP2K4 ACTN2 MAP2K4 TEP1 ACTN2 MYPN UGT2A1 NDUFAF6 RPA2 rs10109257 RPA2 rs10151961 GAS7 RPA2 APOB PDZRN4 APOB BICD1 ARRB2 ZNF807 ARRB2 FAM107B </code></pre> <p>I need to get the matching rows between these two lists despite the order of the elements. For instance in the above example it should look like:</p> <pre><code>MAP2K4 FLNC ACTN2 MYPN RPA2 GAS7 ARRB2 ZNF807 </code></pre> <p>I wrote the following, but this seems to take forever!</p> <pre><code>col0_file1 = [] col1_file1 = [] col0_file2 = [] col1_file2 = [] with open('File1') as f1, open('File2') as f2: for line in f1: col0,col1 = line.split() col0_file1.append(col0) col1_file1.append(col1) for line in f2: col0,col1 = line.split() col0_file2.append(col0) col1_file2.append(col1) result = [] for x in range(len(col0_file1)): for i, j in map(None, col0_file2, col1_file2): if i == col0_file1[x] and j == col1_file1[x]: result.append([i,j]) elif j == col0_file1[x] and i == col1_file[x]: result.append([i,j]) with open('matching', 'w') as out: for elem in result: out.write('{a} \n'.format(a = '\t'.join(elem))) </code></pre> <p>Any way I could simplify the complexity? or Better means of doing it?</p>

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