def get_iTRAQ_pep_raw_XLS(f, iTRAQ_reporter_ions, entrez):
iTRAQ_data_raw = {}
with report.reader(f) as rdr:
for row in rdr:
seq, mods, acc = (row.seq, row.var_mods, row.acc)
acc = acc.replace(" ", "")
gene = entrez[acc].upper()
pep = functions.mz_pep_format(seq, mods)
#Raw Values
raw_counts = []
for ion in iTRAQ_reporter_ions:
raw_counts.append(float(row["Rep%d" % ion]))
raw_counts = array(raw_counts)
key = "%s_%s" % (gene, pep)
#Sum intensities per peptide per protein
if key in iTRAQ_data_raw:
iTRAQ_data_raw[key] += raw_counts
else:
iTRAQ_data_raw[key] = raw_counts
return iTRAQ_data_raw
def get_entrez_XLS(f):
#Store Entrez gene names
with report.reader(f, sheet_name='GenBank_Info') as genbank:
entrez = dict((row.acc, (row.gene).upper()) for row in genbank)
return entrez