proteins_df["Heavy/Medium"] = np.divide(proteins_df["Heavy/Light"],
proteins_df["Medium/Light"])
peptides_df = pd.ExcelFile(peptides).parse("Sheet1")
peptides_df = peptides_df[columns]
peptides_df["Heavy/Medium"] = np.divide(peptides_df["Heavy/Light"],
peptides_df["Medium/Light"])
peptides_df["isPhospho"] = pd.notnull(peptides_df["phosphoRS Isoform Probability"])
phospho_peptides = peptides_df[peptides_df["isPhospho"]==True].copy()
regular_peptides = peptides_df[peptides_df["isPhospho"]==False].copy()
# annotate sequence_window
cutils.add_seq_window(phospho_peptides, FASTA_dic)
#transform the ratios to log10
cutils.computelog(phospho_peptides)
cutils.computelog(regular_peptides)
cutils.computelog(proteins_df)
#add phosphosite plus site information
cutils.add_known_pssite(phospho_peptides, phosphositeDB, FASTA_dic)
#delete non-existing columns
del_columns = ['Medium/Light', 'Heavy/Medium', u'log10ML', u'log10HM']
for del_i, df_i in zip(del_columns, [peptides_df, phospho_peptides, regular_peptides]):
try:
del df_i[del_i]
except:
pass
#==========================================================================
peptides_df["isPhospho"] = pd.notnull(peptides_df["phosphoRS Isoform Probability"])
phospho_peptides = peptides_df[peptides_df["isPhospho"]==True].copy()
regular_peptides = peptides_df[peptides_df["isPhospho"]==False].copy()
if invert:
print "inverting ratios...."
phospho_peptides["Heavy/Light"] = 1 / phospho_peptides["Heavy/Light"]
regular_peptides["Heavy/Light"] = 1 / regular_peptides["Heavy/Light"]
# annotate sequence_window
cutils.add_seq_window(phospho_peptides, FASTA_dic)
#transform the ratios to log10
cutils.computelog(phospho_peptides, ratio_columns=["Heavy/Light"])
cutils.computelog(regular_peptides, ratio_columns=["Heavy/Light"])
cutils.computelog(proteins_df, ratio_columns=["Heavy/Light"])
#add phosphosite plus site information
cutils.add_known_pssite(phospho_peptides, phosphositeDB, FASTA_dic)
#delete non-existing columns
del_columns = ['Medium/Light', 'Heavy/Medium', u'log10ML', u'log10HM']
for del_i, df_i in zip(del_columns, [peptides_df, phospho_peptides, regular_peptides]):
try:
del df_i[del_i]
except:
pass
#==========================================================================