Mercurial > repos > iuc > data_manager_primer_scheme_bedfiles
diff 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"
author | iuc |
---|---|
date | Mon, 22 Jun 2020 18:26:10 -0400 |
parents | cce5d9327cd6 |
children | a2953ef09fe1 |
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--- a/data_manager/install_primer_scheme_bedfiles.py Fri Apr 24 16:10:30 2020 -0400 +++ b/data_manager/install_primer_scheme_bedfiles.py Mon Jun 22 18:26:10 2020 -0400 @@ -1,20 +1,39 @@ #!/usr/bin/env python -from __future__ import print_function, division +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 shutil 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", @@ -37,7 +56,7 @@ ) exit(response.status_code) bed_output_filename = os.path.join(output_directory, name + ".bed") - open(bed_output_filename, "w").write(response.text) + 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 @@ -48,7 +67,8 @@ ): name = re.sub(r"\W", "", str(primer_name).replace(" ", "_")) output_filename = os.path.join(output_directory, name + ".bed") - shutil.copyfile(input_filename, output_filename) + 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