コード例 #1
0
def grab_ions(match_list, conf):
    '''Takes peptides and returns a sorted list of their predicted ions'''
    output = []
    for match in enumerate(match_list):
        consts = conf["other_constants"]
        masses = match[1]["orderedMasses"]
        bIons = PeptideDB.coarsen(PeptideDB.returnIons(masses, consts["B+"]))
        yIons = PeptideDB.coarsen(PeptideDB.returnIons(masses[::-1], consts["Y+"]))
        for bIon in bIons:
            output.append([int(bIon), int((match[0]*2)+1)])
        for yIon in yIons:
            output.append([int(yIon), int(match[0])*2])
    return sorted(output, key=lambda entry: entry[0])
コード例 #2
0
            else:
                peptides[(ions[match_index][1]+1)/2]["bCount"] += 1
                peptides[(ions[match_index][1]+1)/2]["bSum"] += int(peak[1])
            match_index += 1
            if match_index == len(ions):
                break
    output = []
    for entry in peptides:
        entry["spec"] = spectra["name"]
        output.append(entry)
    return output

configurations = configs.readConfigs("mascotStyle.cfg")
file_confs = configurations["data"]

peptide_set = PeptideDB.returnPeptides(configurations)
print "[+]"+str(len(peptide_set))+" mass entries generated."

spectra_file = file_confs["spectra_file"]
MGFFile = open(spectra_file, "rb")
spectra_gen = MGFParse.MGFReader(MGFFile, configurations)

score_mod = scorer.Score(configurations)

top_scores = []

for spectrum in spectra_gen:
    print ("[+]Searching %s. \r" % (spectrum["name"])),
    tol = configurations["search_options"]["initial_tolerance"]*spectrum["trueMass"]
    m1Matches = match_masses(peptide_set, spectrum["trueMass"], tol)
    counter = count_matches(m1Matches, spectrum, configurations)