def generate_protein_fdr(target, decoy, theader, dheader, headerfields):
tproteins = [x for x in reader.generate_tsv_proteins(target, theader)]
dproteins = [x for x in reader.generate_tsv_proteins(decoy, dheader)]
[x.update({'target_decoy': 'target'}) for x in tproteins]
[x.update({'target_decoy': 'decoy'}) for x in dproteins]
proteins = sorted(tproteins + dproteins, key=lambda x: get_score(x),
reverse=True)
fdrheader = headerfields['proteinfdr'][prottabledata.HEADER_QVAL][None]
for protein in qvalue_generator(fdrheader, proteins):
yield protein
def generate_accessionmaps(targetprot, decoyprot, theader, dheader):
t_scores, d_scores = {}, {}
for protein in reader.generate_tsv_proteins(targetprot, theader):
acc = protein[prottabledata.HEADER_PROTEIN]
t_scores[acc] = protein
t_scores[acc]['target_decoy'] = 'target'
for protein in reader.generate_tsv_proteins(decoyprot, dheader):
acc = protein[prottabledata.HEADER_PROTEIN]
d_scores[acc] = protein
d_scores[acc]['target_decoy'] = 'decoy'
return t_scores, d_scores
def create_td_assoc_map(tproteins, dproteins, theader, dheader):
tdmap = {}
for dprot in reader.generate_tsv_proteins(dproteins, dheader):
dprot = dprot[prottabledata.HEADER_PROTEIN]
faketprot = dprot.replace(mzidtsvdata.DECOY_PREFIX, '')
tdmap[faketprot] = dprot
for tprot in reader.generate_tsv_proteins(tproteins, theader):
tprot = tprot[prottabledata.HEADER_PROTEIN]
if not tdmap.get(tprot, False):
tdmap[tprot] = None
return tdmap
def generate_accessionmaps(targetprot, decoyprot, theader, dheader):
t_scores, d_scores = {}, {}
for protein in reader.generate_tsv_proteins(targetprot, theader):
acc = protein[prottabledata.HEADER_PROTEIN]
t_scores[acc] = protein
t_scores[acc]['target_decoy'] = 'target'
for protein in reader.generate_tsv_proteins(decoyprot, dheader):
acc = protein[prottabledata.HEADER_PROTEIN]
d_scores[acc] = protein
d_scores[acc]['target_decoy'] = 'decoy'
return t_scores, d_scores
def create_td_assoc_map(tproteins, dproteins, theader, dheader):
tdmap = {}
for dprot in reader.generate_tsv_proteins(dproteins, dheader):
dprot = dprot[prottabledata.HEADER_PROTEIN]
faketprot = dprot.replace(mzidtsvdata.DECOY_PREFIX, '')
tdmap[faketprot] = dprot
for tprot in reader.generate_tsv_proteins(tproteins, theader):
tprot = tprot[prottabledata.HEADER_PROTEIN]
if not tdmap.get(tprot, False):
tdmap[tprot] = None
return tdmap
def initialize_input(self):
super().initialize_input()
quantheader = reader.get_tsv_header(self.quantfile)
self.quantfields = reader.get_cols_in_file(self.quantcolpattern,
quantheader)
self.quantacc = reader.get_cols_in_file(self.quantacccolpattern,
quantheader, single_col=True)
self.quantpeptides = reader.generate_tsv_proteins(self.quantfile,
quantheader)
def initialize_input(self):
super().initialize_input()
quantheader = reader.get_tsv_header(self.quantfile)
self.quantfields = reader.get_cols_in_file(self.quantcolpattern,
quantheader)
self.quantacc = reader.get_cols_in_file(self.quantacccolpattern,
quantheader,
single_col=True)
self.quantfeatures = reader.generate_tsv_proteins(
self.quantfile, quantheader)
def output_to_target_accession_table(targetfn, featratios, channels):
#loop prottable, add ratios from dict, acc = key
theader = reader.get_tsv_header(targetfn)
acc_field = theader[0]
for feat in reader.generate_tsv_proteins(targetfn, theader):
try:
quants = featratios[feat[acc_field]]
except KeyError:
quants = {ch: 'NA' for ch in channels}
quants.update({get_no_psms_field(ch): 'NA' for ch in channels})
else:
quants.pop(ISOQUANTRATIO_FEAT_ACC)
feat.update(quants)
yield feat
def output_to_target_accession_table(targetfn, featratios, channels):
#loop prottable, add ratios from dict, acc = key
theader = reader.get_tsv_header(targetfn)
acc_field = theader[0]
for feat in reader.generate_tsv_proteins(targetfn, theader):
try:
quants = featratios[feat[acc_field]]
except KeyError:
quants = {ch: 'NA' for ch in channels}
quants.update({get_no_psms_field(ch): 'NA' for ch in channels})
else:
quants.pop(ISOQUANTRATIO_FEAT_ACC)
feat.update(quants)
yield feat
def initialize_input(self):
self.oldheader = reader.get_tsv_header(self.fn)
self.in_proteins = reader.generate_tsv_proteins(self.fn,
self.oldheader)
def initialize_input(self):
self.oldheader = reader.get_tsv_header(self.fn)
self.in_proteins = reader.generate_tsv_proteins(
self.fn, self.oldheader)