def test_readfile_content(self):
pepxml_file = pyopenms.PepXMLFile()
peps = []
prots = []
pepxml_file.load(self.filename, prots, peps)
assert len(prots) == 1
assert len(peps) == 3
assert peps[0].getHits()[0].getSequence().toString() == "LAPSAAEDGAFR"
def test_readfile_content(self):
pepxml_file = pyopenms.PepXMLFile()
peps = []
prots = []
pepxml_file.load(self.filename, prots, peps)
self.assertEqual( len(prots), 3)
self.assertEqual( len(peps), 19)
self.assertEqual( peps[0].getHits()[0].getSequence().toString(), b'(Glu->pyro-Glu)ELNKEMAAEKAKAAAG')
def test_readfile_content(self):
pepxml_file = pyopenms.PepXMLFile()
peps = []
prots = []
pepxml_file.load(self.filename, prots, peps)
self.assertEqual(len(prots), 1)
self.assertEqual(len(peps), 3)
self.assertEqual(peps[0].getHits()[0].getSequence().toString(),
"LAPSAAEDGAFR")
def get_peptides_protein_seq():
# Read in PepXML
protein_ids = []
peptide_ids = []
pyopenms.PepXMLFile().load(pepxml_file, protein_ids, peptide_ids)
peptides = [
pid.getHits()[0].getSequence().toString() for pid in peptide_ids
]
# Sequence could be from FASTA file (or just provided here)
sequence = "".join("""
MNKKKLGIRLLSLLALGGFVLANPVFADQNFARNEKEAKDSAITFIQKSAAIKAGARSAE
DIKLDKVNLGGELSGSNMYVYNISTGGFVIVSGDKRSPEILGYSTSGSFDANGKENIASF
MESYVEQIKENKKLDTTYAGTAEIKQPVVKSLLNSKGIHYNQGNPYNLLTPVIEKVKPGE
QSFVGQHAATGCVATATAQIMKYHNYPNKGLKDYTYTLSSNNPYFNHPKNLFAAISTRQY
NWNNILPTYSGRESNVQKMAISELMADVGISVDMDYGPSSGSAGSSRVQRALKENFGYNQ
SVHQINRSDFSKQDWEAQIDKELSQNQPVYYQGVGKVGGHAFVIDGADGRNFYHVNWGWG
GVSDGFFRLDALNPSALGTGGGAGGFNGYQSAVVGIKP
""".split())
return peptides, sequence
def test_readfile(self):
pepxml_file = pyopenms.PepXMLFile()
peps = []
prots = []
pepxml_file.load(self.filename, prots, peps)
pepxml_file = "data/sample_xtandem_output.pep.xml"
mzml_file = "data/sample_spectra.mzML"
output = "sample_ascore_output.csv"
fh = open(output, "w")
writer = csv.writer(fh)
# Cutoff for filtering peptide hits by their score
cutoff_score = 0.75
#
# Data I/O : load the pep.xml file and the mzXML file
#
protein_ids = []
peptide_ids = []
pyopenms.PepXMLFile().load(pepxml_file, protein_ids, peptide_ids)
exp = pyopenms.MSExperiment()
pyopenms.FileHandler().loadExperiment(mzml_file, exp)
def compute_spectrum_bins(exp):
rt_bins = {}
for s in exp:
if s.getMSLevel() == 1:
continue
tmp = rt_bins.get(int(s.getRT()), [])
tmp.append(s)
rt_bins[int(s.getRT())] = tmp
return rt_bins