def main():
args = app.parse_args()
data_path, metadata_source, sites_file = args.csv_file, args.metadata, args.site_file
prediction_results = convert_csv_to_nested(data_path)
if metadata_source is not None:
reader = csv.DictReader(open(metadata_source))
glycans = get_glycan_identities(reader.fieldnames)
prediction_results.metadata["glycan_identities"] = glycans
if sites_file is not None:
site_list = [line.strip() for line in open(sites_file, "r")]
site_list = list(map(int, site_list))
prediction_results.metadata["site_list"] = site_list
outfile = try_get_outfile(data_path, "json")
prediction_results.serialize(outfile)
print(outfile)
return outfile
def main(db_file, output_file=None):
'''
Scores observed fragment to theoretical ion pairings, eliminates ambiguity using tandem MS2 data
:param db_file: Path to file created by match_ions.py, matching theoretical ions to observed spectra
:param output_file: Path to file to write results to. Defaults to `db_file` + ".processed"
'''
matched_ions = sqlitedict.SqliteDict(db_file, tablename="matched_ions")
scored_results = []
did_not_match = []
metadata = sqlitedict.SqliteDict(db_file, tablename="metadata")
metadata['db_file_name'] = db_file
glycan_identities = metadata["glycan_identities"]
if output_file is None:
output_file = try_get_outfile(db_file, "processed")
else:
output_file += ".processed"
logger.info("Output file %s", output_file)
for row in matched_ions.values():
total_bare_b = float(row["total_b_ions"])
total_bare_y = float(row["total_y_ions"])
all_b_found = (row["b_ion_coverage"])
num_b_found = float(len(all_b_found))
percent_b = (num_b_found / total_bare_b)
all_y_found = row["y_ion_coverage"]
num_y_found = float(len(all_y_found))
percent_y = (num_y_found / total_bare_y)
b_HexNAc = row["b_ions_with_HexNAc"]
b_HexNAc_found = len(b_HexNAc)
total_possible_b_HexNAc = float(row["possible_b_ions_HexNAc"])
if total_possible_b_HexNAc == 0:
percent_b_HexNAc = 0
else:
percent_b_HexNAc = b_HexNAc_found / total_possible_b_HexNAc
y_HexNAc = row["y_ions_with_HexNAc"]
y_HexNAc_found = len(y_HexNAc)
total_possible_y_HexNAc = float(
row["possible_y_ions_HexNAc"])
if total_possible_y_HexNAc == 0:
percent_y_HexNAc = 0
else:
percent_y_HexNAc = y_HexNAc_found / total_possible_y_HexNAc
stubs = row["Stub_ions"]
Oxoniums = row["Oxonium_ions"]
glycan_lib.parse_glycan_pack_string(row["Glycan"], glycan_identities)
glycans = glycan_lib.parse_glycan_pack_string(row["Glycan"], glycan_identities)
NeuAc = glycans.get("NeuAc", 0)
bad_oxonium_ions = []
if NeuAc != 0:
pass
else:
try:
bad_oxonium_ions.extend(d for d in Oxoniums if d['key'] in {"NeuAC", "NeuAc-H2O"})
except:
bad_oxonium_ions.extend(d for d in Oxoniums if d['key'] == 274.092 or d["key"] == 292.1026)
if (all_y_found + all_b_found) != 0:
scored_results.append({"MS1_Score": row["MS1_Score"],
"Obs_Mass": row["Obs_Mass"],
"Calc_mass": row["Calc_mass"],
"ppm_error": row["ppm_error"],
"Peptide": row["Peptide"],
"Peptide_mod": row["Peptide_mod"],
"Glycan": row["Glycan"],
"vol": row["vol"],
"glyco_sites": row["glyco_sites"],
"startAA": row["startAA"],
"endAA": row["endAA"],
"Seq_with_mod": row["Seq_with_mod"],
"Glycopeptide_identifier": row["Seq_with_mod"] + row["Glycan"],
"Oxonium_ions": Oxoniums,
"bare_b_ions": row["bare_b_ions"],
"total_b_ions_possible": total_bare_b,
"bare_y_ions": row["bare_y_ions"],
"total_y_ions_possible": total_bare_y,
"b_ions_with_HexNAc": b_HexNAc,
"y_ions_with_HexNAc": y_HexNAc,
"b_ion_coverage": all_b_found,
"y_ion_coverage": all_y_found,
"Stub_ions": stubs,
"percent_b_ion_with_HexNAc_coverage": percent_b_HexNAc,
"percent_y_ion_with_HexNAc_coverage": percent_y_HexNAc,
"percent_b_ion_coverage": percent_b,
"percent_y_ion_coverage": percent_y,
"scan_id": row['scan_id'],
"scan_id_range": row["scan_id_range"],
"bad_oxonium_ions": bad_oxonium_ions,
"glycan_composition": glycans,
"protein_id": row.get("protein_id")
})
else:
did_not_match.append(row["Glycopeptide_identifier"])
results = {
"metadata": dict(metadata),
"predictions": scored_results,
"intact_mass_no_fragments": did_not_match
}
if output_file:
f = open(output_file + ".json", 'wb')
for chunk in json.JSONEncoder().iterencode(results):
f.write(chunk)
f.close()
return (output_file + '.json', results)
else:
return None, results