| 1 | """MS/MS search engine results parsers. |
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| 2 | |
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| 3 | """ |
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| 4 | import sys |
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| 5 | import os |
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| 6 | import re |
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| 7 | import csv |
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| 8 | import urllib |
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| 9 | import fnmatch |
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| 10 | #from optparse import OptionParser |
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| 11 | from string import Template |
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| 12 | from collections import defaultdict |
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| 13 | from collections import namedtuple |
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| 14 | from itertools import izip, groupby |
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| 15 | |
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| 16 | SEPARATOR = '--gc0p4Jq0M2Yt08jU534c0p' |
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| 17 | # TODO: Use new style string formatting 2.6 and ditch Template |
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| 18 | SECTION_TEMPLATE = Template( |
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| 19 | r'Content-Type: application/x-Mascot; name="$section"') |
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| 20 | |
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| 21 | PEP_REGEX = re.compile(r'^q(\d+)' # nativeid |
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| 22 | '_p(\d+)' # rank |
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| 23 | '=\d+?' # missed cleavages |
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| 24 | ',([\.\d]+?)' # peptide mass |
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| 25 | ',([-\.\d]+?)' # delta mass |
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| 26 | ',\d+?' # n ions matches |
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| 27 | ',(\w+?)' # peptide string |
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| 28 | ',\d+?' # peaks used for Ions1 |
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| 29 | ',(\d+?)' # modstring |
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| 30 | ',([\.\d]+?)' # score |
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| 31 | ',\d+?' # ion series found |
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| 32 | ',\d+?' # peaks used for Ions2 |
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| 33 | ',\d+?' # peaks used for Ions3 |
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| 34 | ';(.+)$' # protein accessions string |
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| 35 | ) |
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| 36 | |
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| 37 | MascotPsm = namedtuple('MascotPsm', |
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| 38 | 'rank ' |
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| 39 | 'pep_mass ' |
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| 40 | 'delta_mass ' |
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| 41 | 'pep_seq ' |
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| 42 | 'score ' |
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| 43 | 'prot_ids' |
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| 44 | ) |
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| 45 | |
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| 46 | mascot_ptms = {'Acetyl (Protein N-term)': 'ac', |
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| 47 | 'Oxidation (M)': 'ox', |
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| 48 | 'Phospho (ST)': 'p', |
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| 49 | 'Dimethyl (K)': 'l', |
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| 50 | 'Dimethyl (N-term)': 'l', |
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| 51 | 'Dimethyl:2H(4) (K)': 'i', |
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| 52 | 'Dimethyl:2H(4) (N-term)': 'i', |
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| 53 | 'Dimethyl:2H(6)13C(2) (K)': 'h', |
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| 54 | 'Dimethyl:2H(6)13C(2) (N-term)': 'h', |
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| 55 | } |
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| 56 | |
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| 57 | class DatParser(object): |
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| 58 | """Mascot Dat Parser |
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| 59 | """ |
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| 60 | def __init__(self, |
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| 61 | protein_factory, |
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| 62 | peptide_factory, |
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| 63 | spectrum_factory, |
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| 64 | psm_factory, |
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| 65 | serparam_factory, |
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| 66 | scan_str=r'FinneganScanNumber%3a%20(\d+)', |
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| 67 | rawfn_str=r'(RawFile|period)%3a%20(.+raw)', |
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| 68 | decoy_str=r'^REV_.*', |
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| 69 | contaminant_str=r'^CON_.*', |
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| 70 | # XXX: Fix default factories |
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| 71 | ): |
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| 72 | self.scan_regex = re.compile(scan_str) |
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| 73 | decoy_regex = re.compile(decoy_str) |
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| 74 | contaminant_regex = re.compile(contaminant_str) |
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| 75 | # Contaminants are not exactly decoy psms |
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| 76 | self.non_target_regexes = (contaminant_regex, decoy_regex) |
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| 77 | self.rawfn_regex = re.compile(rawfn_str) |
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| 78 | self.protein_factory = protein_factory |
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| 79 | self.peptide_factory = peptide_factory |
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| 80 | self.spectrum_factory = spectrum_factory |
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| 81 | self.psm_factory = psm_factory |
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| 82 | self.serparam_factory = serparam_factory |
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| 83 | |
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| 84 | def _parse_params(self, dat_file): |
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| 85 | """Parses SER parameters and returns a SerParam object. |
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| 86 | """ |
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| 87 | for line in dat_file: |
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| 88 | if line.startswith("TOL="): |
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| 89 | prec_tol = line.strip().split('=')[1] |
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| 90 | prec_units = dat_file.next().strip().split('=')[1] |
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| 91 | elif line.startswith("ITOL="): |
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| 92 | frag_tol = line.strip().split('=')[1] |
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| 93 | frag_units = dat_file.next().strip().split('=')[1] |
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| 94 | elif line.startswith("DB="): |
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| 95 | db_name = line.strip().split('=')[1] |
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| 96 | elif line.startswith("CLE="): |
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| 97 | enzyme = line.strip().split('=')[1] |
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| 98 | elif line.startswith("FILE="): |
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| 99 | full_path = line.strip().split('=')[1] |
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| 100 | norm_path = full_path.replace('\\', '/') |
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| 101 | pkl_fn = norm_path.split("/")[-1] |
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| 102 | elif line.startswith("INSTRUMENT="): |
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| 103 | frag_line = line.strip().split('=')[1] |
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| 104 | if frag_line == "ETD-TRAP": |
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| 105 | frag_mode = 'ETD' |
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| 106 | elif frag_line == "ESI-TRAP": |
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| 107 | frag_mode = 'CID' |
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| 108 | elif line.startswith("QUANTITATION="): |
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| 109 | quantitation = line.strip().split('=')[1] |
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| 110 | return self.serparam_factory( |
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| 111 | prec_tol=(prec_tol, prec_units), |
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| 112 | frag_tol=(frag_tol, frag_units), |
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| 113 | db_name=db_name, |
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| 114 | enzyme=enzyme, |
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| 115 | pkl_fn=pkl_fn, |
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| 116 | quantitation=quantitation, |
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| 117 | frag_mode=frag_mode, |
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| 118 | ) |
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| 119 | |
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| 120 | def _parse_masses(self, dat_file): |
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| 121 | """Parses the modifications used by mascot |
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| 122 | """ |
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| 123 | ptms = [None] |
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| 124 | masses_section = SECTION_TEMPLATE.substitute(section="masses") |
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| 125 | for line in dat_file: |
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| 126 | if line.strip() == masses_section: |
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| 127 | break |
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| 128 | |
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| 129 | for line in dat_file: |
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| 130 | if line.startswith("delta"): |
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| 131 | m_ptm = line.strip().split('=')[1].split(',') |
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| 132 | ptm_sym = mascot_ptms[m_ptm[1]] |
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| 133 | ptm = (m_ptm[0], ptm_sym) |
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| 134 | ptms.append(ptm) |
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| 135 | elif line.strip() == SEPARATOR: |
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| 136 | return ptms |
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| 137 | |
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| 138 | def _parse_summary(self, dat_file): |
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| 139 | """Parse summary section |
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| 140 | """ |
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| 141 | summspec = list() |
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| 142 | summary_section = SECTION_TEMPLATE.substitute(section="summary") |
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| 143 | for line in dat_file: |
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| 144 | if line.strip() == summary_section: |
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| 145 | break |
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| 146 | for line in dat_file: |
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| 147 | if line.startswith('qexp'): |
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| 148 | r_mz, r_charge = line.strip().split('=')[1].split(',') |
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| 149 | mz = float(r_mz) |
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| 150 | charge = int(r_charge.rstrip('+')) |
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| 151 | summspec.append((mz, charge)) |
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| 152 | elif line.strip() == SEPARATOR: |
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| 153 | return summspec |
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| 154 | |
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| 155 | def _parse_psms(self, dat_file): |
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| 156 | """Parses the peptide section of mascot |
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| 157 | """ |
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| 158 | nativeid_psms = defaultdict(list) |
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| 159 | # Seek until Mascot peptide section |
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| 160 | peptide_section = SECTION_TEMPLATE.substitute(section="peptides") |
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| 161 | for line in dat_file: |
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| 162 | if line.strip() == peptide_section: |
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| 163 | break |
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| 164 | for line in dat_file: |
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| 165 | match = re.match(PEP_REGEX, line) |
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| 166 | if match: |
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| 167 | nativeid = int(match.group(1)) |
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| 168 | rank = int(match.group(2)) |
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| 169 | pep_mass = float(match.group(3)) |
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| 170 | delta_mass = float(match.group(4)) |
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| 171 | aas = match.group(5) |
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| 172 | mods_str = match.group(6) |
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| 173 | pep_seq = apply_mods(aas, mods_str, self.m_ptms) |
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| 174 | score = float(match.group(7)) |
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| 175 | accs = match.group(8) |
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| 176 | prot_ids = get_prot_ids(accs) |
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| 177 | target_prots = filter_target_prots(prot_ids, |
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| 178 | self.non_target_regexes) |
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| 179 | if target_prots and (rank == 1 or rank == 2): |
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| 180 | mascot_psm = MascotPsm( |
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| 181 | rank=rank, |
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| 182 | pep_mass=pep_mass, |
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| 183 | delta_mass=delta_mass, |
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| 184 | pep_seq=pep_seq, |
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| 185 | score=score, |
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| 186 | prot_ids=target_prots |
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| 187 | ) |
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| 188 | nativeid_psms[nativeid].append(mascot_psm) |
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| 189 | elif line.strip() == SEPARATOR: |
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| 190 | return nativeid_psms |
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| 191 | |
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| 192 | def _parse_extraspec(self, dat_file): |
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| 193 | """Gets the data coming from the input file from Mascot dat |
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| 194 | format. |
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| 195 | """ |
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| 196 | extraspec = list() |
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| 197 | for line in dat_file: |
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| 198 | if line.startswith("title="): |
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| 199 | line = line.strip() |
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| 200 | try: |
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| 201 | quoted_rawfn = re.search(self.rawfn_regex, |
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| 202 | line).group(2) |
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| 203 | rawfn = urllib.unquote(quoted_rawfn) |
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| 204 | except AttributeError: |
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| 205 | sys.exit("It seems the raw regex is not valid. " |
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| 206 | "The line is: " + repr(line)) |
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| 207 | try: |
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| 208 | scan = int(re.search(self.scan_regex, line).group(1)) |
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| 209 | except AttributeError: |
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| 210 | sys.exit("Default scan regex for TITLE field" |
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| 211 | " doesn't match. TITLE: " + repr(line)) |
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| 212 | extraspec.append([rawfn, scan]) |
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| 213 | elif line.startswith("Ions1="): |
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| 214 | peaks = list() |
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| 215 | mascot_ions = line.strip().split("=")[1].split(",") |
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| 216 | for pair in mascot_ions: |
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| 217 | mz, inten = pair.split(':') |
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| 218 | peak = float(mz), float(inten) |
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| 219 | peaks.append(peak) |
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| 220 | extraspec[-1].append(tuple(peaks)) |
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| 221 | |
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| 222 | return extraspec |
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| 223 | |
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| 224 | def parse(self, dat_file, protid_sequence): |
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| 225 | """Takes a dat file and returns a dictionary of psms. |
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| 226 | """ |
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| 227 | serparams = self._parse_params(dat_file) |
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| 228 | self.m_ptms = self._parse_masses(dat_file) |
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| 229 | summspec = self._parse_summary(dat_file) |
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| 230 | nativeid_psms = self._parse_psms(dat_file) |
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| 231 | extraspec = self._parse_extraspec(dat_file) |
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| 232 | proteins = dict() |
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| 233 | spectra = dict() |
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| 234 | peptides = dict() |
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| 235 | psms = dict() |
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| 236 | # TODO: Take all these loops to other functions or methods |
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| 237 | for summ, extra in izip(summspec, extraspec): |
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| 238 | spectrum = self.spectrum_factory( |
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| 239 | prec_mz=summ[0], |
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| 240 | prec_charge=summ[1], |
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| 241 | run=extra[0], |
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| 242 | scan=extra[1], |
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| 243 | peaks=extra[2], |
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| 244 | ) |
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| 245 | spectra['-'.join((str(spectrum.scan), |
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| 246 | spectrum.run))] = spectrum |
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| 247 | # XXX: Clean up this MESS |
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| 248 | for nativeid, m_psms in nativeid_psms.iteritems(): |
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| 249 | for m_psm in m_psms: |
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| 250 | run, spec, peaks = extraspec[nativeid - 1] |
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| 251 | spec_id = '-'.join((str(spec), run)) |
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| 252 | peptide = self.peptide_factory( |
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| 253 | sequence=m_psm.pep_seq, |
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| 254 | mass=m_psm.pep_mass |
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| 255 | ) |
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| 256 | psm = self.psm_factory( |
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| 257 | score=m_psm.score, |
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| 258 | rank=m_psm.rank, |
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| 259 | delta_mass=m_psm.delta_mass, |
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| 260 | pep_ref=peptide, |
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| 261 | spec_ref=spectra[spec_id], |
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| 262 | params_ref=serparams |
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| 263 | ) |
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| 264 | psms['--'.join((peptide.formatted_seq(), spec_id))] = psm |
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| 265 | spectra[spec_id].psm_refs.add(psm) |
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| 266 | if peptide.formatted_seq() not in peptides: |
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| 267 | peptide.psm_refs = set([psm]) |
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| 268 | peptides[peptide.formatted_seq()] = peptide |
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| 269 | else: |
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| 270 | peptide = peptides[peptide.formatted_seq()] |
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| 271 | peptide.psm_refs.add(psm) |
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| 272 | for prot_id in m_psm.prot_ids: |
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| 273 | if prot_id not in proteins: |
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| 274 | protein = self.protein_factory( |
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| 275 | native_id=prot_id, |
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| 276 | sequence=protid_sequence[prot_id][0], |
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| 277 | ext_ids = protid_sequence[prot_id][1], |
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| 278 | description=protid_sequence[prot_id][2], |
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| 279 | pep_refs=set([peptide]) |
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| 280 | ) |
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| 281 | proteins[prot_id] = protein |
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| 282 | else: |
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| 283 | proteins[prot_id].pep_refs.add(peptide) |
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| 284 | return proteins, peptides, spectra, psms |
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| 285 | |
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| 286 | def apply_mods(aas, mods_str, ptms): |
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| 287 | """Takes a naked peptides sequence, the mod string from Mascot and ptm |
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| 288 | map and returns a complete peptide sequence |
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| 289 | """ |
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| 290 | f_aas = ''.join(('.', aas, '.')) |
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| 291 | pep_seq = list() |
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| 292 | for a, m in izip(f_aas, mods_str): |
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| 293 | aa_m = (a, ptms[int(m)]) |
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| 294 | pep_seq.append(aa_m) |
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| 295 | return tuple(pep_seq) |
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| 296 | |
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| 297 | def get_prot_ids(accs): |
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| 298 | """From a Mascot accessions field return a tuple with all proteins |
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| 299 | ids. |
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| 300 | """ |
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| 301 | return tuple(x[1].strip('"') |
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| 302 | for x in (y.split(':') |
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| 303 | for y in accs.split(',"') |
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| 304 | ) |
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| 305 | ) |
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| 306 | |
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| 307 | def filter_target_prots(prot_ids, regexes): |
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| 308 | """Filters a list of protein ids for target protein ids |
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| 309 | """ |
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| 310 | target_prots = list() |
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| 311 | for prot_id in prot_ids: |
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| 312 | non_target_flag = True |
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| 313 | for regex in regexes: |
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| 314 | if re.match(regex, prot_id): |
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| 315 | non_target_flag = False |
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| 316 | if non_target_flag: |
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| 317 | target_prots.append(prot_id) |
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| 318 | return target_prots |
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| 319 | |
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| 320 | def write_csv(psms, out_file): |
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| 321 | """Takes a dictionary of PSMs and writes a modified InsPecT output. |
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| 322 | """ |
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| 323 | fieldnames = ("#SpectraFile", |
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| 324 | "RawFile", |
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| 325 | "Fraction", |
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| 326 | "Scan", |
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| 327 | "Annotation", |
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| 328 | "Charge", |
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| 329 | "FragMode", |
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| 330 | "IsDecoy") |
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| 331 | header = dict() |
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| 332 | for fieldname in fieldnames: |
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| 333 | header[fieldname] = fieldname |
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| 334 | writer = csv.DictWriter(out_file, fieldnames, dialect='excel-tab') |
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| 335 | for psm in psms: |
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| 336 | writer.writerow(psm) |
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| 337 | |
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| 338 | def parse_fasta(fasta_fn): |
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| 339 | """Update protein sequence container from fasta file""" |
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| 340 | with open(fasta_fn, 'rb') as fasta_file: |
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| 341 | # Ditching the key of each iterator group because we know |
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| 342 | # the headers and sequence alternate all the time |
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| 343 | protid_sequence = defaultdict(str) |
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| 344 | groupgen = (i[1] for i in groupby(fasta_file, |
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| 345 | lambda l: l.startswith(">"))) |
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| 346 | for header in groupgen: |
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| 347 | header_line = header.next().strip() |
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| 348 | if header_line.startswith(">IPI:IPI"): |
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| 349 | ext_ids = dict() |
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| 350 | description = str() |
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| 351 | header_fields = header_line.split("|") |
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| 352 | prot_id = header_fields[0][5:] |
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| 353 | for field in header_fields[1:]: |
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| 354 | if not ' ' in field: |
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| 355 | db, db_id = field.split(':') |
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| 356 | ext_ids[db] = db_id |
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| 357 | else: |
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| 358 | trailing_fields = field.split(' ') |
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| 359 | for t_field in trailing_fields: |
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| 360 | if ":" in t_field: |
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| 361 | db, db_id = t_field.split(":") |
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| 362 | ext_ids[db] = db_id |
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| 363 | elif "=" in t_field: |
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| 364 | db, db_ids = t_field.split("=") |
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| 365 | # Take only 1st ID in case there are many |
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| 366 | db_id = db_ids.split(";")[0] |
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| 367 | ext_ids[db] = db_id |
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| 368 | else: |
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| 369 | description = " ".join((description[:], |
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| 370 | t_field)) |
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| 371 | sequence = "".join(s.strip() for s in groupgen.next()) |
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| 372 | protid_sequence[prot_id] = sequence, ext_ids, description |
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| 373 | return protid_sequence |
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| 374 | |
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| 375 | # XXX: Use better defaults for containers and factories |
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| 376 | def parse_dats(dats_dir, proteins_container=dict, peptides_container=dict, |
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| 377 | spectra_container=dict, psms_container=dict, |
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| 378 | protein_factory=dict, peptide_factory=dict, |
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| 379 | spectrum_factory=dict, psm_factory=dict, |
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| 380 | serparam_factory=dict): |
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| 381 | """Parses all the dat files in dats_dir |
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| 382 | """ |
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| 383 | proteins = proteins_container |
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| 384 | peptides = peptides_container |
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| 385 | spectra = spectra_container |
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| 386 | psms = psms_container |
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| 387 | dat_parser = DatParser(protein_factory=protein_factory, |
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| 388 | peptide_factory=peptide_factory, |
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| 389 | spectrum_factory=spectrum_factory, |
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| 390 | psm_factory=psm_factory, |
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| 391 | serparam_factory=serparam_factory) |
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| 392 | import transaction |
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| 393 | for root, dirs, files in os.walk(dats_dir): |
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| 394 | for fn in files: |
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| 395 | if fnmatch.fnmatch(fn, '*.fasta'): |
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| 396 | protid_sequence = parse_fasta(os.path.join(root, fn)) |
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| 397 | for root, dirs, files in os.walk(dats_dir): |
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| 398 | for fn in files: |
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| 399 | if fnmatch.fnmatch(fn, '*.dat'): |
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| 400 | with open(os.path.join(root, fn)) as dat_file: |
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| 401 | ser_proteins, ser_peptides, \ |
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| 402 | ser_spectra, ser_psms = dat_parser.parse(dat_file, |
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| 403 | protid_sequence) |
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| 404 | proteins.update(ser_proteins) |
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| 405 | transaction.savepoint() |
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| 406 | for pep_id, pep in ser_peptides.items(): |
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| 407 | if not pep_id in peptides: |
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| 408 | peptides[str(pep_id)] = pep |
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| 409 | transaction.savepoint() |
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| 410 | for spec_id, spec in ser_spectra.items(): |
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| 411 | if spec_id not in spectra: |
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| 412 | spectra[str(spec_id)] = spec |
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| 413 | transaction.savepoint() |
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| 414 | for psm_id, psm in ser_psms.items(): |
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| 415 | if psm not in psms: |
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| 416 | psms[str(psm_id)] = psm |
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| 417 | transaction.savepoint() |
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| 418 | elif fnmatch.fnmatch(fn, '*.fasta'): |
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| 419 | fasta_path = os.path.join(root, fn) |
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| 420 | |
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| 421 | """ |
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| 422 | def main(): |
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| 423 | usage = "usage: %prog [options] mascotresult1.dat [mascotresult2.dat ...]" |
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| 424 | optparser = OptionParser(usage) |
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| 425 | optparser.add_option("-o", |
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| 426 | "--output", |
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| 427 | dest="out_fn", |
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| 428 | help="Output file [default: stdout]", |
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| 429 | metavar="FILE") |
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| 430 | optparser.add_option("-s", |
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| 431 | "--scans-in-title", |
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| 432 | dest="scans_in_title", |
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| 433 | type="int", |
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| 434 | default="1", |
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| 435 | help="1 to parse the scan number from the TITLE field, " |
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| 436 | "0 to parse the scan number from the SCAN field " |
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| 437 | "[default: %default]") |
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| 438 | optparser.add_option("-d", |
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| 439 | "--decoy-str", |
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| 440 | dest="decoy_str", |
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| 441 | default=r'^IPI:REV_:IPI', |
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| 442 | help="1 to parse the scan number from the TITLE field, " |
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| 443 | "0 to parse the scan number from the SCAN field " |
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| 444 | "[default: %default]") |
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| 445 | (options, args) = optparser.parse_args() |
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| 446 | |
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| 447 | if len(args) == 0: |
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| 448 | optparser.print_usage() |
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| 449 | |
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| 450 | else: |
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| 451 | for arg in args: |
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| 452 | if not arg.endswith(".dat"): |
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| 453 | optparser.error("Provide only mascot dat files") |
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| 454 | else: |
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| 455 | if options.out_fn: |
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| 456 | out_fn = options.out_file |
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| 457 | out_file = open(out_fn, 'wb') |
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| 458 | else: |
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| 459 | out_file = sys.stdout |
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| 460 | for arg in args: |
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| 461 | with open(arg) as in_file: |
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| 462 | dat_parser = DatParser(options.decoy_str, |
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| 463 | scans_in_title = options.scans_in_title) |
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| 464 | psms = dat_parser.parse(in_file) |
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| 465 | write_csv(psms, out_file) |
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| 466 | |
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| 467 | if __name__ == '__main__': |
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| 468 | main() |
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| 469 | """ |
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