annotate yac.py @ 4:f7947c5a18b8 draft

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/yac_clipper commit 48768de9d682fb80c4981cd52ef724fdf8f6961e

#!/usr/bin/python
# yac = yet another clipper
# v 1.2.1 - 23-08-2014 - Support FastQ output
# v 1.1.0 - 23-08-2014 - argparse implementation
# Christophe Antoniewski <[e-mail]>

import argparse
from itertools import islice


def Parser():
    the_parser = argparse.ArgumentParser()
    the_parser.add_argument(
        '--input', action="store", nargs='+', help="input fastq files")
    the_parser.add_argument(
        '--output', action="store", type=str,
        help="output, clipped fasta file")
    the_parser.add_argument(
        '--output_format', action="store", type=str,
        help="output format, fasta or fastq")
    the_parser.add_argument(
        '--adapter_to_clip', action="store", type=str,
        help="adapter sequence to clip")
    the_parser.add_argument(
        '--min', action="store", type=int,
        help="minimal size of clipped sequence to keep")
    the_parser.add_argument(
        '--max', action="store", type=int,
        help="maximal size of clipped sequence to keep")
    the_parser.add_argument('--Nmode', action="store", type=str, choices=[
                            "accept", "reject"],
                            help="accept or reject Ns in clipped sequences")
    args = the_parser.parse_args()
    args.adapter_to_clip = args.adapter_to_clip.upper()
    return args


class Clip:

    def __init__(self, inputfile, outputfile, output_format,
                 adapter, minsize, maxsize, Nmode):
        self.inputfile = inputfile
        self.outputfile = outputfile
        self.output_format = output_format
        self.adapter = adapter
        self.minsize = int(minsize)
        self.maxsize = int(maxsize)
        self.Nmode = Nmode
        for line in open(inputfile):
            if line[0] == "@":
                self.inputformat = "fastq"
                break
            elif line[0] == ">":
                self.inputformat = "fasta"

        def motives(sequence):
            '''
            return a list of motives for perfect (6nt) or
            imperfect (7nt with one mismatch) search on import string module
            '''
            sequencevariants = [
                sequence[0:6]]  # initializes list with 6mer perfect match
            dicsubst = {"A": "TGCN", "T": "AGCN", "G": "TACN", "C": "GATN"}
            for pos in enumerate(sequence[:6]):
                for subst in dicsubst[pos[1]]:
                    sequencevariants.append(
                        sequence[:pos[0]] + subst + sequence[pos[0] + 1:7])
            return sequencevariants
        self.adaptmotifs = motives(self.adapter)

    def scanadapt(self, adaptmotives=[], sequence="", qscore=""):
        '''scans sequence for adapter motives'''
        match_position = sequence.rfind(adaptmotives[0])
        if qscore:
            if match_position != -1:
                return sequence[:match_position], qscore[:match_position]
            for motif in adaptmotives[1:]:
                match_position = sequence.rfind(motif)
                if match_position != -1:
                    return sequence[:match_position], qscore[:match_position]
            return sequence, qscore
        else:
            if match_position != -1:
                return sequence[:match_position]
            for motif in adaptmotives[1:]:
                match_position = sequence.rfind(motif)
                if match_position != -1:
                    return sequence[:match_position]
            return sequence

    def write_output(self, id, read, qscore, output):
        if self.output_format == "fasta":
            block = ">{0}\n{1}\n".format(id, read)
        else:
            block = "@HWI-{0}\n{1}\n+\n{2}\n".format(id, read, qscore)
        output.write(block)

    def fasta_in_write_output(self, id, read, output):
        output.write(">{0}\n{1}\n".format(id, read))

    def handle_io_fastq(self):
        '''Open input fastq file, pass read sequence and read qscore to
        scanadapt function. Pass clipped read and qscore to output function.'''
        id = 0
        output = open(self.outputfile, "a")
        with open(self.inputfile, "r") as input:
            block_gen = islice(input, 1, None, 2)
            for i, line in enumerate(block_gen):
                if i % 2:
                    qscore = line.rstrip()
                else:
                    read = line.rstrip()
                    continue
                try:
                    trimmed_read, trimmed_qscore = self.scanadapt(
                        self.adaptmotifs, read, qscore)
                except ValueError:
                    continue
                if self.minsize <= len(trimmed_read) <= self.maxsize:
                    if (self.Nmode == "reject") and ("N" in trimmed_read):
                        continue
                    id += 1
                    self.write_output(id, trimmed_read, trimmed_qscore, output)
        output.close()

    def handle_io_fasta(self):
        '''Open input fasta file, pass header and read sequence to scanadapt
        function. Pass clipped read and qscore to output function.'''
        id = 0
        output = open(self.outputfile, "a")
        with open(self.inputfile, "r") as input:
            block_gen = islice(input, 1, None, 2)
            for i, line in enumerate(block_gen):
                read = line.rstrip()
                trimmed_read = self.scanadapt(self.adaptmotifs, read)
                if self.minsize <= len(trimmed_read) <= self.maxsize:
                    if (self.Nmode == "reject") and ("N" in trimmed_read):
                        continue
                    id += 1
                    self.fasta_in_write_output(id, trimmed_read, output)
        output.close()


def main(*argv):
    instanceClip = Clip(*argv)
    if instanceClip.inputformat == "fasta":
        instanceClip.handle_io_fasta()
    else:
        instanceClip.handle_io_fastq()


if __name__ == "__main__":
    args = Parser()
    for inputfile in args.input:
        main(inputfile, args.output, args.output_format,
             args.adapter_to_clip, args.min, args.max, args.Nmode)