Mercurial > repos > rlegendre > ribo_tools
changeset 16:fcfdb2607cb8 draft
Uploaded
| author | rlegendre |
|---|---|
| date | Wed, 13 May 2015 04:34:59 -0400 |
| parents | 702e60e819c2 |
| children | c87c40e642af |
| files | get_codon_frequency.py |
| diffstat | 1 files changed, 16 insertions(+), 4 deletions(-) [+] |
line wrap: on
line diff
--- a/get_codon_frequency.py Mon May 11 09:53:08 2015 -0400 +++ b/get_codon_frequency.py Wed May 13 04:34:59 2015 -0400 @@ -325,7 +325,7 @@ # # cond2 = moyenne of replicats cond1divided by max cond2_val[i] = ((cond2_1[i] / sum21 + cond2_2[i] / sum22) / 2) cond2[i] = ((cond2_1[i] + cond2_2[i]) / 2) - # # standard deviation = absolute value of diffence between replicats of cond2 + # # standard deviation = absolute value of difference between replicats of cond2 std_cond2.append(std(array([((cond2_1[i]) * 100 / sum21), ((cond2_2[i]) * 100 / sum22)]))) # # max value for each codon max_val.append(max((cond1_1[i] / sum11 + cond1_2[i] / sum12) / 2, (cond2_1[i] / sum21 + cond2_2[i] / sum22) / 2)) @@ -379,9 +379,15 @@ # write result with open(outfile, 'w') as out : - out.write('Codon\tRaw_' + c1 + '\tRaw_' + c2 + '\tNorm_' + c1 + '\tNorm_' + c2 + '\tFC\tFC_' + c1 + '\tFC_' + c2 + '\n') + out.write('Codon\tRaw_' + c1 + '\tRaw_' + c2 + '\tNorm_' + c1 + '\tNorm_' + c2 + '\tFC(Mut/WT)\n') for i in codon_sorted: - 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]) + '\t' + str((cond2_1[i] / sum21) / (cond1_1[i] / sum11)) + '\t' + str((cond2_2[i] / sum22) / (cond1_1[i] / sum11)) + '\n') + ## if global foldchange is equal to zero + if cond1_norm[i] == 0 and cond2_norm[i] == 0: + out.write(i + '\t' + str(cond1[i]) + '\t' + str(cond2[i]) + '\t' + str(cond1_norm[i]) + '\t' + str(cond2_norm[i]) + '\t1.0\n') + elif cond1_norm[i] == 0 : + out.write(i + '\t' + str(cond1[i]) + '\t' + str(cond2[i]) + '\t' + str(cond1_norm[i]) + '\t' + str(cond2_norm[i]) + '\t0.0\n') + else: + 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') chi = stats.chisquare(observed, expected) out.write('Khi2 test\n') out.write('T : ' + str(chi[0]) + '; p-value : ' + str(chi[1]) + '\n') @@ -484,7 +490,12 @@ with open(outfile, 'w') as out : out.write('Codon\tRaw_' + c1 + '\tRaw_' + c2 + '\tNorm_' + c1 + '\tNorm_' + c2 + '\tFC(Mut/WT)\n') for i in codon_sorted: - 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') + if cond1_norm[i] == 0 and cond2_norm[i] == 0: + out.write(i + '\t' + str(cond1[i]) + '\t' + str(cond2[i]) + '\t' + str(cond1_norm[i]) + '\t' + str(cond2_norm[i]) + '\t1.0\n') + elif cond1_norm[i] == 0 : + out.write(i + '\t' + str(cond1[i]) + '\t' + str(cond2[i]) + '\t' + str(cond1_norm[i]) + '\t' + str(cond2_norm[i]) + '\t0.0\n') + else: + 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') out.write('Khi2 test\n') chi = stats.chisquare(observed, expected) out.write('T : ' + str(chi[0]) + '; p-value : ' + str(chi[1]) + '\n') @@ -606,6 +617,7 @@ pl.ylabel('Foldchange of codon occupancy') ax.yaxis.set_ticks_position('left') ax.xaxis.set_ticks_position('bottom') + pl.ylim(-1,3) pl.title(site+" site") pl.savefig(dirout + '/fc_codons.png', format="png", dpi=340)