view filter_kw_val.py @ 0:8e3bb3153dc4 draft default tip

planemo upload

import argparse
import re

def options():
    """ 
    Parse arguments:
        -i, --input: Input file (text, tabular)
        -m, --match: For keyword filter, if we filter for exact
        --kw: keywords to filter out
        --kw_file: file containing keywords to filter out
        --value: value to filter 
        -o, --output: output filename, default is output.txt
        --trash_file: extra output file containing removed lines
    """
    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)
    
def isnumber(format, n):
    # Check if an element is integer or float
    float_format = re.compile("^[\-]?[1-9][0-9]*\.?[0-9]+$")
    int_format = re.compile("^[\-]?[1-9][0-9]*$")
    test = ""
    if format == "int":
        test = re.match(int_format, n)
    elif format == "float":
        test = re.match(float_format, n)
    if test:
        return True
    else:
        return False

def filters(args):
    """
    Extract filter arguments
    """
    
    # Read input file
    MQfilename = args.input.split(",")[0]
    header = args.input.split(",")[1]
    MQfile = readMQ(MQfilename)
    results = [MQfile, None]
    
    # Extract keyword arguments
    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])
            
    # Extract value arguments
    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("".join(results[0]))
    output.close()

    # Write deleted lines to trash_file
    trash = open(args.trash_file, "w")
    trash.write("".join(results[1]))
    trash.close()

def readOption(filename):
    """
    Read file containing keywords to filter out
    """
    f = open(filename, "r")
    file = f.read()
    filter_list = file.split("\n")
    filters = ""
    for i in filter_list:
        filters += i + ":"
    filters = filters[:-1]
    return filters

def readMQ(MQfilename):
    """
    Read input file and return list of file's lines
    """
    # Read input 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, kws, ncol, match):
    """
    Filter keywords
    """
    mq = MQfile
    
    # Check if column number is in right form 
    if isnumber("int", ncol.replace("c", "")):
        id_index = int(ncol.replace("c", "")) - 1 
    else:
        raise ValueError("Please specify the column where you would like to apply the filter with valid format")
    
    # Extract list of keywords to filter out
    kws = kws.upper().split(":")
    [kws.remove(blank) for blank in kws if blank.isspace() or blank == ""]
    
    # Separate header and content of input file
    if header == "true":
        header = mq[0]
        content = mq[1:]
    else:
        header = ""
        content = mq[:]
    
    # List of lines removed from input file
    if not filtered_lines: # In case there is already some filtered lines from other filters
        filtered_lines = []
        if header != "":
            filtered_lines.append(header)

    # Filter out the lines containing keywords
    for line in content:    
        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
        
        if match != "false":
            if any (pid.upper() in kws 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 kws):
                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):
    """
    Filter values
    """
    mq = MQfile
    
    # Check if column number is in right form
    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")
        
    # Separate header and content of input file
    if header == "true":
        header = mq[0]
        content = mq[1:]
    else:
        header = ""
        content = mq[:]
    
    # List of lines removed from input file
    if not filtered_prots: # In case there is already some filtered lines from other filters
        filtered_prots = []
        if header != "":
            filtered_prots.append(header)
    
    # Filter out the lines meet filter conditions    
    for prot in content:
        filter_value = float(filter_value)
        pep = prot.split("\t")[index].replace('"', "")
        if pep.replace(".", "", 1).isdigit():
            if opt == "<":
                if not float(pep) < filter_value:
                    filtered_prots.append(prot)
                    mq.remove(prot)
            elif opt == "<=":
                if not float(pep) <= filter_value:
                    filtered_prots.append(prot)
                    mq.remove(prot)
            elif opt == ">":
                if not float(pep) > filter_value:
                    filtered_prots.append(prot)
                    mq.remove(prot)
            elif opt == ">=":
                if not float(pep) >= filter_value:
                    filtered_prots.append(prot)
                    mq.remove(prot)
            else:
                if not float(pep) == filter_value:
                    filtered_prots.append(prot)
                    mq.remove(prot)
    return mq, filtered_prots 

if __name__ == "__main__":
    options()