Mercurial > repos > rlegendre > ribo_tools
comparison get_codon_frequency.py @ 19:385fc64fa988 draft default tip
Uploaded
| author | rlegendre |
|---|---|
| date | Fri, 12 Jun 2015 11:32:59 -0400 |
| parents | c87c40e642af |
| children |
comparison
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| 18:a121cce43f90 | 19:385fc64fa988 |
|---|---|
| 366 expected = array(cond2_count) | 366 expected = array(cond2_count) |
| 367 observed = array(list(cond2.itervalues())) | 367 observed = array(list(cond2.itervalues())) |
| 368 | 368 |
| 369 # write result | 369 # write result |
| 370 with open(outfile, 'w') as out : | 370 with open(outfile, 'w') as out : |
| 371 out.write('Codon\tRaw_' + c1 + '\tRaw_' + c2 + '\tNorm_' + c1 + '\tNorm_' + c2 + '\tFC(Mut/WT)\n') | 371 out.write('Codon,Raw_' + c1 + ',Raw_' + c2 + ',Norm_' + c1 + ',Norm_' + c2 + ',FC(Mut/WT)\n') |
| 372 for i in codon_sorted: | 372 for i in codon_sorted: |
| 373 ## if global foldchange is equal to zero | 373 ## if global foldchange is equal to zero |
| 374 if cond1_norm[i] == 0 and cond2_norm[i] == 0: | 374 if cond1_norm[i] == 0 and cond2_norm[i] == 0: |
| 375 out.write(i + '\t' + str(cond1[i]) + '\t' + str(cond2[i]) + '\t' + str(cond1_norm[i]) + '\t' + str(cond2_norm[i]) + '\t1.0\n') | 375 out.write(i + ',' + str(cond1[i]) + ',' + str(cond2[i]) + ',' + str(cond1_norm[i]) + ',' + str(cond2_norm[i]) + ',1.0\n') |
| 376 elif cond1_norm[i] == 0 : | 376 elif cond1_norm[i] == 0 : |
| 377 out.write(i + '\t' + str(cond1[i]) + '\t' + str(cond2[i]) + '\t' + str(cond1_norm[i]) + '\t' + str(cond2_norm[i]) + '\t0.0\n') | 377 out.write(i + ',' + str(cond1[i]) + ',' + str(cond2[i]) + ',' + str(cond1_norm[i]) + ',' + str(cond2_norm[i]) + ',0.0\n') |
| 378 else: | 378 else: |
| 379 out.write(i + '\t' + str(cond1[i]) + '\t' + str(cond2[i]) + '\t' + str(cond1_norm[i]) + '\t' + str(cond2_norm[i]) + '\t' + str(cond2_norm[i] / cond1_norm[i]) + '\n') | 379 out.write(i + ',' + str(cond1[i]) + ',' + str(cond2[i]) + ',' + str(cond1_norm[i]) + ',' + str(cond2_norm[i]) + ',' + str(cond2_norm[i] / cond1_norm[i]) + '\n') |
| 380 with errstate(all='ignore'): | 380 with errstate(all='ignore'): |
| 381 chi = stats.chisquare(observed, expected) | 381 chi = stats.chisquare(observed, expected) |
| 382 out.write('Khi2 test\n') | 382 out.write('Khi2 test\n') |
| 383 out.write('T : ' + str(chi[0]) + '; p-value : ' + str(chi[1]) + '\n') | 383 out.write('T : ' + str(chi[0]) + '; p-value : ' + str(chi[1]) + '\n') |
| 384 | 384 |
| 476 pl.savefig(dirout + '/hist_amino_acid.png', format="png", dpi=340) | 476 pl.savefig(dirout + '/hist_amino_acid.png', format="png", dpi=340) |
| 477 pl.clf() | 477 pl.clf() |
| 478 | 478 |
| 479 # write result | 479 # write result |
| 480 with open(outfile, 'w') as out : | 480 with open(outfile, 'w') as out : |
| 481 out.write('Codon\tRaw_' + c1 + '\tRaw_' + c2 + '\tNorm_' + c1 + '\tNorm_' + c2 + '\tFC(Mut/WT)\n') | 481 out.write('Codon,Raw_' + c1 + ',Raw_' + c2 + ',Norm_' + c1 + ',Norm_' + c2 + ',FC(Mut/WT)\n') |
| 482 for i in codon_sorted: | 482 for i in codon_sorted: |
| 483 if cond1_norm[i] == 0 and cond2_norm[i] == 0: | 483 if cond1_norm[i] == 0 and cond2_norm[i] == 0: |
| 484 out.write(i + '\t' + str(cond1[i]) + '\t' + str(cond2[i]) + '\t' + str(cond1_norm[i]) + '\t' + str(cond2_norm[i]) + '\t1.0\n') | 484 out.write(i + ',' + str(cond1[i]) + ',' + str(cond2[i]) + ',' + str(cond1_norm[i]) + ',' + str(cond2_norm[i]) + ',1.0\n') |
| 485 elif cond1_norm[i] == 0 : | 485 elif cond1_norm[i] == 0 : |
| 486 out.write(i + '\t' + str(cond1[i]) + '\t' + str(cond2[i]) + '\t' + str(cond1_norm[i]) + '\t' + str(cond2_norm[i]) + '\t0.0\n') | 486 out.write(i + ',' + str(cond1[i]) + ',' + str(cond2[i]) + ',' + str(cond1_norm[i]) + ',' + str(cond2_norm[i]) + ',0.0\n') |
| 487 else: | 487 else: |
| 488 out.write(i + '\t' + str(cond1[i]) + '\t' + str(cond2[i]) + '\t' + str(cond1_norm[i]) + '\t' + str(cond2_norm[i]) + '\t' + str(cond2_norm[i] / cond1_norm[i]) + '\n') | 488 out.write(i + ',' + str(cond1[i]) + ',' + str(cond2[i]) + ',' + str(cond1_norm[i]) + ',' + str(cond2_norm[i]) + ',' + str(cond2_norm[i] / cond1_norm[i]) + '\n') |
| 489 out.write('Khi2 test\n') | 489 out.write('Khi2 test\n') |
| 490 with errstate(all='ignore'): | 490 with errstate(all='ignore'): |
| 491 chi = stats.chisquare(observed, expected) | 491 chi = stats.chisquare(observed, expected) |
| 492 out.write('T : ' + str(chi[0]) + '; p-value : ' + str(chi[1]) + '\n') | 492 out.write('T : ' + str(chi[0]) + '; p-value : ' + str(chi[1]) + '\n') |
| 493 | 493 |