comparison data_manager/install_primer_scheme_bedfiles.py @ 2:b3710e492ee4 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit 61b727022bd1b24a8843830a9c5f34ef66835694"

1:cce5d9327cd6

#!/usr/bin/env python

from __future__ import print_function, division

import argparse
import json
import os
import os.path
import re
import sys
import shutil

import requests

DATA_TABLE_NAME = "primer_scheme_bedfiles"


def fetch_artic_primers(output_directory, primers):
    primer_sets = {
        "SARS-CoV-2-ARTICv1": "https://raw.githubusercontent.com/artic-network/artic-ncov2019/master/primer_schemes/nCoV-2019/V1/nCoV-2019.bed",

                response.status_code,
                file=sys.stderr,
            )
            exit(response.status_code)
        bed_output_filename = os.path.join(output_directory, name + ".bed")
        open(bed_output_filename, "w").write(response.text)
        description = name[:-2] + " " + name[-2:] + " primer set"
        data.append(dict(value=name, path=bed_output_filename, description=description))
    return data


def install_primer_file(
    output_directory, input_filename, primer_name, primer_description
):
    name = re.sub(r"\W", "", str(primer_name).replace(" ", "_"))
    output_filename = os.path.join(output_directory, name + ".bed")
    shutil.copyfile(input_filename, output_filename)
    data = [dict(value=name, description=primer_description, path=output_filename)]
    return data


class SplitArgs(argparse.Action):

2:b3710e492ee4

#!/usr/bin/env python

from __future__ import division, print_function

import argparse
try:
    from io import StringIO
except ImportError:
    from StringIO import StringIO
import json
import os
import os.path
import re
import sys

import requests

DATA_TABLE_NAME = "primer_scheme_bedfiles"


def write_good_bed(input_file, bed_output_filename):
    with open(bed_output_filename, "w") as bed_output_file:
        for line in input_file:
            fields = line.split("\t")
            if len(fields) < 6:
                # too short to encode the strand format
                exit("invalid format in BED file: {}".format(line.rstrip()))
            try:
                # try and parse field 5 as a number
                float(fields[4])
            except ValueError:
                # ARTIC with broken BED, set field 5 to 60
                fields[4] = "60"
            bed_output_file.write("\t".join(fields))


def fetch_artic_primers(output_directory, primers):
    primer_sets = {
        "SARS-CoV-2-ARTICv1": "https://raw.githubusercontent.com/artic-network/artic-ncov2019/master/primer_schemes/nCoV-2019/V1/nCoV-2019.bed",

                response.status_code,
                file=sys.stderr,
            )
            exit(response.status_code)
        bed_output_filename = os.path.join(output_directory, name + ".bed")
        write_good_bed(StringIO(response.text), bed_output_filename)
        description = name[:-2] + " " + name[-2:] + " primer set"
        data.append(dict(value=name, path=bed_output_filename, description=description))
    return data


def install_primer_file(
    output_directory, input_filename, primer_name, primer_description
):
    name = re.sub(r"\W", "", str(primer_name).replace(" ", "_"))
    output_filename = os.path.join(output_directory, name + ".bed")
    with open(input_filename) as input_file:
        write_good_bed(input_file, output_filename)
    data = [dict(value=name, description=primer_description, path=output_filename)]
    return data


class SplitArgs(argparse.Action):