def msb_filter(proj_dir, msb_out_dir, pq_path):
"""
Filter the pepquant output by keeping only values with spectral counts in
the msblender output.
"""
proj_name = ut.shortname(proj_dir)
msb_quant_file = os.path.join(msb_out_dir, proj_name+MSB_EXT)
assert os.path.exists(msb_quant_file), "No filter elution found: %s" % msb_quant_file
pq_elut, msb_elut = [el.load_elution(f) for f in pq_path,
msb_quant_file]
pq_elut.mat = el.filter_matching_elution(pq_elut, msb_elut)
pq_filt_path = pq_path.replace(PQ_CLEAN, PQ_FILT)
el.write_elution(pq_elut, pq_filt_path)
return pq_filt_path
def merge(proj_dir, dirnames, pq_new_path):
"""
Combine pepquant quantitation from project_1 (etc) PQ_FILE into
project+PQ_NEW.
"""
if not os.path.exists(proj_dir):
os.mkdir(proj_dir)
proj_name = ut.shortname(proj_dir)
assert not os.path.exists(pq_new_path), "%s exists. Exiting." % pq_new_path
dirnames = ut.i0(sort_numbered(dirnames))
#print "Sorted dirnames:", dirnames
pq_files = [os.path.join(d,PQ_FILE) for d in dirnames]
for f in pq_files:
if not os.path.exists(f):
print "No Elution File:", f
eluts = (el.load_elution(f) for f in pq_files if os.path.exists(f))
merged = reduce(el.combine_elutions, eluts)
el.write_elution(merged, pq_new_path)
def elut_clean_prots(fin,fout):
elut = el.load_elution(fin)
elut.prots = [p.strip('>') for p in elut.prots]
el.write_elution(elut, fout)