def load_elution(fname, getname=True):
# expected file structure:
# first col: gene id
# second col: treat differently if 2nd col header is 'Total' or
# 'Description'
# remaining cols: elution profile data
lines = [l for l in ut.load_tab_file(fname)]
# final row: total count in msblender output; don't skip in cuihong's data
skip_final_row = (lines[-1][0][0] == '#')
rows = lines[1:-1] if skip_final_row else lines[1:]
fractions = [f for f in lines[0][1:]]
if fractions[0].lower() in ['total', 'totalcount', 'description']:
start_data_col = 2
fractions.remove(fractions[0])
else:
start_data_col = 1
mat = np.matrix([row[start_data_col:] for row in rows],dtype='float32')
prots = [row[0] for row in rows]
elut = Struct(mat=mat, prots=prots, fractions=fractions, filename=fname,
filename_original=fname)
if start_data_col == 2:
col2name_vals = [row[1] for row in rows]
elut.column2vals = col2name_vals
if getname: elut.name = os.path.basename(fname).split('.')[0]
return elut
def load_elution(fname, getname=True):
# expected file structure:
# first col: gene id
# second col: treat differently if 2nd col header is 'Total' or
# 'Description'
# remaining cols: elution profile data
lines = [l for l in ut.load_tab_file(fname)]
# final row: total count in msblender output; don't skip in cuihong's data
skip_final_row = lines[-1][0][0] == "#"
rows = lines[1:-1] if skip_final_row else lines[1:]
fractions = [f for f in lines[0][1:]]
if fractions[0].lower() in ["total", "totalcount", "description"]:
start_data_col = 2
fractions.remove(fractions[0])
else:
start_data_col = 1
mat = np.matrix([row[start_data_col:] for row in rows], dtype="float32")
prots = [row[0] for row in rows]
elut = Struct(mat=mat, prots=prots, fractions=fractions, filename=fname, filename_original=fname)
if start_data_col == 2:
col2name_vals = [row[1] for row in rows]
elut.column2vals = col2name_vals
if getname:
elut.name = os.path.basename(fname).split(".")[0]
return elut
