galaxy/tools/next_gen_conversion/solid2fastq.py

#!/usr/bin/env python

import optparse
import sqlite3
import sys
import tempfile

try:
    maketrans = str.maketrans
except AttributeError:
    from string import maketrans  # type: ignore[attr-defined,no-redef]


def stop_err(msg):
    sys.stderr.write(msg)
    sys.exit()


def solid2sanger(quality_string, min_qual=0):
    sanger = ""
    quality_string = quality_string.rstrip(" ")
    for qv in quality_string.split(" "):
        try:
            if int(qv) < 0:
                qv = "0"
            if int(qv) < min_qual:
                return False
                break
            sanger += chr(int(qv) + 33)
        except Exception:
            pass
    return sanger


def Translator(frm="", to="", delete=""):
    if len(to) == 1:
        to = to * len(frm)
    trans = maketrans(frm, to)

    def callable(s):
        return s.translate(trans, delete)

    return callable


def merge_reads_qual(
    f_reads,
    f_qual,
    f_out,
    trim_name=False,
    out="fastq",
    double_encode=False,
    trim_first_base=False,
    pair_end_flag="",
    min_qual=0,
    table_name=None,
):
    # Reads from two files f_csfasta (reads) and f_qual (quality values) and produces output in three formats depending on out parameter,
    # which can have three values: fastq, txt, and db
    # fastq = fastq format
    # txt = space delimited format with defline, reads, and qvs
    # dp = dump data into sqlite3 db.
    # IMPORTNAT! If out = db two optins must be provided:
    #   1. f_out must be a db connection object initialized with sqlite3.connect()
    #   2. table_name must be provided
    if out == "db":
        cursor = f_out.cursor()
        sql = "create table %s (name varchar(50) not null, read blob, qv blob)" % table_name
        cursor.execute(sql)

    lines = []
    line = " "
    while line:
        for f in [f_reads, f_qual]:
            line = f.readline().rstrip("\n\r")
            while line.startswith("#"):
                line = f.readline().rstrip("\n\r")
            lines.append(line)

        if lines[0].startswith(">") and lines[1].startswith(">"):
            if lines[0] != lines[1]:
                stop_err(
                    "Files reads and quality score files are out of sync and likely corrupted. Please, check your input data"
                )

            defline = lines[0][1:]
            if trim_name and (defline[len(defline) - 3 :] == "_F3" or defline[len(defline) - 3 :] == "_R3"):
                defline = defline[: len(defline) - 3]

        elif not lines[0].startswith(">") and not lines[1].startswith(">") and len(lines[0]) > 0 and len(lines[1]) > 0:
            if trim_first_base:
                lines[0] = lines[0][1:]
            if double_encode:
                de = Translator(frm="0123.", to="ACGTN")
                lines[0] = de(lines[0])
            qual = solid2sanger(lines[1], int(min_qual))
            if qual:
                if out == "fastq":
                    f_out.write("@%s%s\n%s\n+\n%s\n" % (defline, pair_end_flag, lines[0], qual))
                if out == "txt":
                    f_out.write("%s %s %s\n" % (defline, lines[0], qual))
                if out == "db":
                    cursor.execute('insert into %s values("%s","%s","%s")' % (table_name, defline, lines[0], qual))
        lines = []


def main():
    usage = "%prog --fr F3.csfasta --fq R3.csfasta --fout fastq_output_file [option]"
    parser = optparse.OptionParser(usage=usage)
    parser.add_option(
        "--fr", "--f_reads", metavar="F3_CSFASTA_FILE", dest="fr", help="Name of F3 file with color space reads"
    )
    parser.add_option(
        "--fq", "--f_qual", metavar="F3_QUAL_FILE", dest="fq", help="Name of F3 file with color quality values"
    )
    parser.add_option("--fout", "--f3_fastq_output", metavar="F3_OUTPUT", dest="fout", help="Name for F3 output file")
    parser.add_option(
        "--rr",
        "--r_reads",
        metavar="R3_CSFASTA_FILE",
        dest="rr",
        default=False,
        help="Name of R3 file with color space reads",
    )
    parser.add_option(
        "--rq",
        "--r_qual",
        metavar="R3_QUAL_FILE",
        dest="rq",
        default=False,
        help="Name of R3 file with color quality values",
    )
    parser.add_option("--rout", metavar="R3_OUTPUT", dest="rout", help="Name for F3 output file")
    parser.add_option(
        "-q",
        "--min_qual",
        dest="min_qual",
        default="-1000",
        help="Minimum quality threshold for printing reads. If a read contains a single call with QV lower than this value, it will not be reported. Default is -1000",
    )
    parser.add_option(
        "-t",
        "--trim_name",
        dest="trim_name",
        action="store_true",
        default=False,
        help="Trim _R3 and _F3 off read names. Default is False",
    )
    parser.add_option(
        "-f",
        "--trim_first_base",
        dest="trim_first_base",
        action="store_true",
        default=False,
        help="Remove the first base of reads in color-space. Default is False",
    )
    parser.add_option(
        "-d",
        "--double_encode",
        dest="de",
        action="store_true",
        default=False,
        help="Double encode color calls as nucleotides: 0123. becomes ACGTN. Default is False",
    )

    options, args = parser.parse_args()

    if not (options.fout and options.fr and options.fq):
        parser.error(
            """
        One or more of the three required paremetrs is missing:
        (1) --fr F3.csfasta file
        (2) --fq F3.qual file
        (3) --fout name of output file
        Use --help for more info
        """
        )

    fr = open(options.fr)
    fq = open(options.fq)
    f_out = open(options.fout, "w")

    if options.rr and options.rq:
        rr = open(options.rr)
        rq = open(options.rq)
        if not options.rout:
            parser.error("Provide the name for f3 output using --rout option. Use --help for more info")
        r_out = open(options.rout, "w")

        db = tempfile.NamedTemporaryFile()

        try:
            con = sqlite3.connect(db.name)
            cur = con.cursor()
        except Exception:
            stop_err("Cannot connect to %s\n") % db.name

        merge_reads_qual(
            fr,
            fq,
            con,
            trim_name=options.trim_name,
            out="db",
            double_encode=options.de,
            trim_first_base=options.trim_first_base,
            min_qual=options.min_qual,
            table_name="f3",
        )
        merge_reads_qual(
            rr,
            rq,
            con,
            trim_name=options.trim_name,
            out="db",
            double_encode=options.de,
            trim_first_base=options.trim_first_base,
            min_qual=options.min_qual,
            table_name="r3",
        )
        cur.execute("create index f3_name on f3( name )")
        cur.execute("create index r3_name on r3( name )")

        cur.execute("select * from f3,r3 where f3.name = r3.name")
        for item in cur:
            f_out.write("@%s%s\n%s\n+\n%s\n" % (item[0], "/1", item[1], item[2]))
            r_out.write("@%s%s\n%s\n+\n%s\n" % (item[3], "/2", item[4], item[5]))

    else:
        merge_reads_qual(
            fr,
            fq,
            f_out,
            trim_name=options.trim_name,
            out="fastq",
            double_encode=options.de,
            trim_first_base=options.trim_first_base,
            min_qual=options.min_qual,
        )

    f_out.close()


if __name__ == "__main__":
    main()