Mercurial > repos > proteore > filter_keywords_values
view filter_kw_val.py @ 1:d29e469b6b20 draft
planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty
author | proteore |
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date | Fri, 16 Feb 2018 03:27:43 -0500 |
parents | 6a45ccfc0e4c |
children | 1e9911190142 |
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import argparse import re def options(): """ Parse options """ parser = argparse.ArgumentParser() parser.add_argument("-i", "--input", help="Input file", required=True) parser.add_argument("-m", "--match", help="Exact macth") parser.add_argument("--kw", nargs="+", action="append", help="") # parser.add_argument("--kw_file", nargs="+", action="append", help="") parser.add_argument("--value", nargs="+", action="append", help="") parser.add_argument("-o", "--output", default="output.txt") parser.add_argument("--trash_file", default="trash_MQfilter.txt") args = parser.parse_args() filters(args) # python filter2.py -i "/projet/galaxydev/galaxy/tools/proteore_uc1/proteinGroups_Maud.txt" # --protein_IDs "A2A288:A8K2U0" --peptides 2 "=" -o "test-data/output_MQfilter.txt" def isnumber(number_format, n): """ Check if a variable is a float or an integer """ float_format = re.compile("^[\-]?[1-9][0-9]*\.?[0-9]+$") int_format = re.compile("^[\-]?[1-9][0-9]*$") test = "" if number_format == "int": test = re.match(int_format, n) elif number_format == "float": test = re.match(float_format, n) if test: return True # else: # return False def filters(args): """ Filter the document """ MQfilename = args.input.split(",")[0] header = args.input.split(",")[1] MQfile = readMQ(MQfilename) results = [MQfile, None] if args.kw: keywords = args.kw for k in keywords: results = filter_keyword(results[0], header, results[1], k[0], k[1], k[2]) if args.kw_file: key_files = args.kw_file for kf in key_files: ids = readOption(kf[0]) results = filter_keyword(results[0], header, results[1], ids, kf[1], kf[2]) if args.value: for v in args.value: if isnumber("float", v[0]): results = filter_value(results[0], header, results[1], v[0], v[1], v[2]) else: raise ValueError("Please enter a number in filter by value") # Write results to output output = open(args.output, "w") output.write("\n".join(results[0])) output.close() # Write deleted lines to trash_file trash = open(args.trash_file, "w") trash.write("\n".join(results[1])) trash.close() def readOption(filename): f = open(filename, "r") file_content = f.read() filter_list = file_content.split("\n") filters = "" for i in filter_list: filters += i + ";" filters = filters[:-1] return filters def readMQ(MQfilename): # Read MQ file mqfile = open(MQfilename, "r") mq = mqfile.readlines() # Remove empty lines (contain only space or new line or "") [mq.remove(blank) for blank in mq if blank.isspace() or blank == ""] return mq def filter_keyword(MQfile, header, filtered_lines, ids, ncol, match): mq = MQfile if isnumber("int", ncol.replace("c", "")): id_index = int(ncol.replace("c", "")) - 1 #columns.index("Majority protein IDs") else: raise ValueError("Please specify the column where " "you would like to apply the filter " "with valid format") # Split list of filter IDs ids = ids.upper().split(";") # Remove blank IDs [ids.remove(blank) for blank in ids if blank.isspace() or blank == ""] # Remove space from 2 heads of IDs ids = [id.strip() for id in ids] if header == "true": header = mq[0] content = mq[1:] else: header = "" content = mq[:] if not filtered_lines: # In case there is already some filtered lines from other filters filtered_lines = [] if header != "": filtered_lines.append(header) for line in content: line = line.replace("\n", "") id_inline = line.split("\t")[id_index].replace('"', "").split(";") one_id_line = line.replace(line.split("\t")[id_index], id_inline[0]) # Take only first IDs line = line + "\n" if match != "false": # Filter protein IDs if any(pid.upper() in ids for pid in id_inline): filtered_lines.append(one_id_line) mq.remove(line) else: mq[mq.index(line)] = one_id_line else: if any(ft in pid.upper() for pid in id_inline for ft in ids): filtered_lines.append(one_id_line) mq.remove(line) else: mq[mq.index(line)] = one_id_line return mq, filtered_lines def filter_value(MQfile, header, filtered_prots, filter_value, ncol, opt): mq = MQfile if ncol and isnumber("int", ncol.replace("c", "")): #"Gene names" in columns: index = int(ncol.replace("c", "")) - 1 #columns.index("Gene names") else: raise ValueError("Please specify the column where " "you would like to apply the filter " "with valid format") if header == "true": header = mq[0] content = mq[1:] else: header = "" content = mq[:] if not filtered_prots: # In case there is already some filtered lines from other filters filtered_prots = [] if header != "": filtered_prots.append(header) for line in content: prot = line.replace("\n","") filter_value = float(filter_value) pep = prot.split("\t")[index].replace('"', "") if pep.replace(".", "", 1).isdigit(): if opt == "<": if float(pep) >= filter_value: filtered_prots.append(line) mq.remove(line) elif opt == "<=": if float(pep) > filter_value: filtered_prots.append(line) mq.remove(line) elif opt == ">": #print(prot.number_of_prots, filter_value, int(prot.number_of_prots) > filter_value) if float(pep) <= filter_value: filtered_prots.append(line) mq.remove(line) elif opt == ">=": if float(pep) < filter_value: filtered_prots.append(line) mq.remove(line) else: if float(pep) != filter_value: filtered_prots.append(line) mq.remove(line) return mq, filtered_prots #output, trash_file if __name__ == "__main__": options()