+
−import argparse
+
−import csv
+
−import os
+
−import shutil
+
−
+
−
+
−parser = argparse.ArgumentParser()
+
−parser.add_argument("--input")
+
−parser.add_argument("--db_local")
+
−parser.add_argument("--num_highest")
+
−parser.add_argument("--ppm_db")
+
−parser.add_argument("--ppm_mass_tol")
+
−parser.add_argument("--abs_mass_tol")
+
−parser.add_argument("--polarity")
+
−parser.add_argument("--score_type")
+
−parser.add_argument("--results")
+
−parser.add_argument("--tool_directory")
+
−
+
−args = parser.parse_args()
+
−print(args)
+
−
+
−# Example
+
−# python cfmid.py --abs_mass_tol='0.01' --db_local='test-data/demo_db.tsv' --input='test-data/input.msp' --num_highest='10' --polarity='pos' --ppm_db='10.0' --ppm_mass_tol='10.0' --results='results.txt' --score_type='Jaccard' --tool_directory='/home/rw/Documents/cfm-galaxy/tools/cfm'
+
−
+
−id2info = {}
+
−mz2id = []
+
−# store DB in dicts
+
−with open(args.db_local) as csvfile:
+
−    csvreader = csv.DictReader(csvfile, delimiter="\t")
+
−    for row in csvreader:
+
−        id2info[row["Identifier"]] = row
+
−        mz2id.append((float(row["MonoisotopicMass"]), row["Identifier"]))
+
−
+
−name_tmp = "tmp"
+
−if os.path.isdir(name_tmp):
+
−    shutil.rmtree(name_tmp)
+
−
+
−os.makedirs(name_tmp)
+
−with open(args.input, "r") as infile:
+
−    numlines = 0
+
−    for line in infile:
+
−        line = line.strip()
+
−        if numlines == 0:
+
−            print(line)
+
−            if "NAME" in line:
+
−                featid = line.split("NAME: ")[1]
+
−            if "PRECURSORMZ" in line:
+
−                mz = float(line.split("PRECURSORMZ: ")[1])
+
−                if args.polarity == "pos":
+
−                    mz2 = mz - 1.007276
+
−                else:
+
−                    mz2 = mz + 1.007276
+
−            if "Num Peaks" in line:
+
−                numlines = int(line.split("Num Peaks: ")[1])
+
−                linesread = 0
+
−                peaklist = []
+
−        else:
+
−            if linesread == numlines:
+
−                numlines = 0
+
−                cand_id_list = []
+
−                mz_ranges = (float(args.ppm_db) * mz2) / 1e6
+
−                mz_ranges = (mz2 - mz_ranges, mz2 + mz_ranges)
+
−                # check hits
+
−                for t in mz2id:
+
−                    if (t[0] > mz_ranges[0]) and (t[0] < mz_ranges[1]):
+
−                        cand_id_list.append(t[1])
+
−                # run only if we got candidates
+
−                if len(cand_id_list) > 0:
+
−                    # write spec file
+
−                    with open("./tmpspec.txt", "w") as outfile:
+
−                        for e in ["low", "mid", "high"]:
+
−                            outfile.write(e + "\n")
+
−                            for p in peaklist:
+
−                                outfile.write(p[0] + "\t" + p[1] + "\n")
+
−                    # write candidates file
+
−                    with open("./tmpcand.txt", "w") as outfile:
+
−                        for c in cand_id_list:
+
−                            outfile.write(
+
−                                "{0} {1}\n".format(c, id2info[c]["InChI"])
+
−                            )  # TODO: Use InChI or SMILES
+
−
+
−                    # create command line call
+
−                    outi = os.path.join(name_tmp, "cfm_" + featid + ".txt")
+
−                    cmd_command = "cfm-id tmpspec.txt {0} tmpcand.txt ".format(featid)
+
−                    cmd_command += "{0} {1} {2} {3} ".format(
+
−                        args.num_highest,
+
−                        args.ppm_db,
+
−                        args.ppm_mass_tol,
+
−                        args.abs_mass_tol,
+
−                    )
+
−                    if args.polarity == "pos":
+
−                        cmd_command += (
+
−                            os.path.join(
+
−                                args.tool_directory,
+
−                                "data",
+
−                                "positive_metab_se_cfm",
+
−                                "param_output0.log",
+
−                            )
+
−                            + " "
+
−                        )
+
−                        cmd_command += (
+
−                            os.path.join(
+
−                                args.tool_directory,
+
−                                "data",
+
−                                "positive_metab_se_cfm",
+
−                                "param_config.txt",
+
−                            )
+
−                            + " "
+
−                        )
+
−                    else:
+
−                        cmd_command += (
+
−                            os.path.join(
+
−                                args.tool_directory,
+
−                                "data",
+
−                                "negative_metab_se_cfm/param_output0.log",
+
−                            )
+
−                            + " "
+
−                        )
+
−                        cmd_command += (
+
−                            os.path.join(
+
−                                args.tool_directory,
+
−                                "data",
+
−                                "negative_metab_se_cfm/param_config.txt",
+
−                            )
+
−                            + " "
+
−                        )
+
−                    cmd_command += "{0} 1 {1}".format(args.score_type, outi)
+
−                    # run
+
−                    print(cmd_command)
+
−                    os.system(cmd_command)
+
−            else:
+
−                line = tuple(line.split("\t"))
+
−                linesread += 1
+
−                peaklist.append(line)
+
−
+
−
+
−# merge outputs
+
−outfiles = os.listdir(name_tmp)
+
−outfiles.sort(key=lambda x: os.path.getmtime(os.path.join(name_tmp, x)))
+
−with open(args.results, "w") as outfile:
+
−    outfile.write("UID\tRank\tScore\tIdentifier\tInChI\n")
+
−    for fname in outfiles:
+
−        fileid = os.path.basename(fname)
+
−        fileid = fileid.split("_")[1]
+
−        fileid = fileid.split(".txt")[0]
+
−        with open(os.path.join(name_tmp, fname)) as infile:
+
−            for line in infile:
+
−                line = line.replace(" ", "\t")
+
−                outfile.write(fileid + "\t" + line)