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Jon Palmer
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Mar 24, 2023
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,3 +1,3 @@ | ||
| VERSION = (1, 5, 5) | ||
| VERSION = (1, 6, 0) | ||
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| __version__ = ".".join(map(str, VERSION)) |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,10 @@ | ||
| { | ||
| "ITS": [ | ||
| "https://osf.io/kse82/download?version=2", | ||
| "https://osf.io/mx5gd/download?version=2" | ||
| ], | ||
| "16S": "https://osf.io/m7v5q/download?version=4", | ||
| "LSU": "https://osf.io/sqn5r/download?version=4", | ||
| "COI": "https://osf.io/pax79/download?version=5", | ||
| "PR2": "https://osf.io/6hjdq/download?version=2" | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,7 +1,6 @@ | ||
| #!/usr/bin/env python | ||
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| from __future__ import (absolute_import, division, | ||
| print_function, unicode_literals) | ||
| from __future__ import absolute_import, division, print_function, unicode_literals | ||
| import sys | ||
| import os | ||
| import argparse | ||
|
|
@@ -10,69 +9,117 @@ | |
| import json | ||
| import requests | ||
| import shutil | ||
| import subprocess | ||
| from amptk import amptklib | ||
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||
| try: | ||
| from urllib.request import urlopen | ||
| except ImportError: | ||
| from urllib2 import urlopen | ||
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| class MyFormatter(argparse.ArgumentDefaultsHelpFormatter): | ||
| def __init__(self,prog): | ||
| super(MyFormatter,self).__init__(prog,max_help_position=50) | ||
| def __init__(self, prog): | ||
| super(MyFormatter, self).__init__(prog, max_help_position=50) | ||
|
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|
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| def main(args): | ||
| parser=argparse.ArgumentParser(prog='amptk-install.py', | ||
| description='''Script to download preformatted databases''', | ||
| parser = argparse.ArgumentParser( | ||
| prog="amptk-install.py", | ||
| description="""Script to download preformatted databases""", | ||
| epilog="""Written by Jon Palmer (2019) [email protected]""", | ||
| formatter_class=MyFormatter) | ||
| parser.add_argument('-i','--input', nargs='+', required=True, choices=['ITS', '16S', 'LSU', 'COI', 'PR2'], help='Install Databases') | ||
| parser.add_argument('-f','--force', action='store_true', help='Overwrite existing databases') | ||
| parser.add_argument('-l','--local', action='store_true', help='Use local downloads.json for links') | ||
| args=parser.parse_args(args) | ||
| formatter_class=MyFormatter, | ||
| ) | ||
| parser.add_argument( | ||
| "-i", | ||
| "--input", | ||
| nargs="+", | ||
| required=True, | ||
| choices=["ITS", "16S", "LSU", "COI", "PR2"], | ||
| help="Install Databases", | ||
| ) | ||
| parser.add_argument( | ||
| "-f", "--force", action="store_true", help="Overwrite existing databases" | ||
| ) | ||
| parser.add_argument( | ||
| "-l", "--local", action="store_true", help="Use local downloads.json for links" | ||
| ) | ||
| args = parser.parse_args(args) | ||
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| parentdir = os.path.join(os.path.dirname(amptklib.__file__)) | ||
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| # downd from github to get most recent databases | ||
| if not args.local: | ||
| try: | ||
| print('Retrieving download links from GitHub Repo') | ||
| URL = json.loads(requests.get("https://raw.githubusercontent.com/nextgenusfs/amptk/master/amptk/downloads.json").text) | ||
| print("Retrieving download links from GitHub Repo") | ||
| URL = json.loads( | ||
| requests.get( | ||
| "https://raw.githubusercontent.com/nextgenusfs/amptk/master/amptk/downloadsv1.6.0.json" | ||
| ).text | ||
| ) | ||
| except: | ||
| print('Unable to download links from GitHub, using funannotate version specific links') | ||
| with open(os.path.join(os.path.dirname(__file__), 'downloads.json')) as infile: | ||
| print( | ||
| "Unable to download links from GitHub, using funannotate version specific links" | ||
| ) | ||
| with open( | ||
| os.path.join(os.path.dirname(__file__), "downloadsv1.6.0.json") | ||
| ) as infile: | ||
| URL = json.load(infile) | ||
| else: | ||
| with open(os.path.join(os.path.dirname(__file__), 'downloads.json')) as infile: | ||
| with open( | ||
| os.path.join(os.path.dirname(__file__), "downloadsv1.6.0.json") | ||
| ) as infile: | ||
| URL = json.load(infile) | ||
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| for x in args.input: | ||
| udbfile = os.path.join(parentdir, 'DB', x+'.udb') | ||
| udbfile = os.path.join(parentdir, "DB", x + ".udb") | ||
| if os.path.isfile(udbfile): | ||
| if not args.force: | ||
| print("A formated database was found, to overwrite use '--force'. You can add more custom databases by using the `amptk database` command.") | ||
| print( | ||
| "A formated database was found, to overwrite use '--force'. You can add more custom databases by using the `amptk database` command." | ||
| ) | ||
| sys.exit(1) | ||
| #download | ||
| # download | ||
| if not x in URL: | ||
| if args.force: | ||
| continue | ||
| print("%s not valid, choices are ITS, 16S, LSU, COI, PR2" % x) | ||
| sys.exit(1) | ||
| print("Downloading %s pre-formatted database" % x) | ||
| # getting where some files need to be split, so check here if is a list or not | ||
| # list of tar.gz files must be in proper order | ||
| address = URL.get(x) | ||
| if not os.path.isfile(x+'.amptk.tar.gz'): | ||
| amptklib.download(address, x+'.amptk.tar.gz') | ||
| tfile = tarfile.open(x+'.amptk.tar.gz', 'r:gz') | ||
| if isinstance(address, list): | ||
| dloads = [] | ||
| for i, addy in enumerate(address): | ||
| dloadname = "{}.part{}.tar.gz".format(x, i + 1) | ||
| if not os.path.isfile(dloadname): | ||
| amptklib.download(addy, dloadname) | ||
| dloads.append(dloadname) | ||
| concat_cmd = ["cat"] + dloads | ||
| with open(x + ".amptk.tar.gz", "wb") as outfile: | ||
| subprocess.call(concat_cmd, stdout=outfile) | ||
| for f in dloads: | ||
| os.remove(f) | ||
| elif isinstance(address, str): | ||
| if not os.path.isfile(x + ".amptk.tar.gz"): | ||
| amptklib.download(address, x + ".amptk.tar.gz") | ||
| # now extract and install | ||
| tfile = tarfile.open(x + ".amptk.tar.gz", "r:gz") | ||
| tfile.extractall(x) | ||
| for file in os.listdir(x): | ||
| shutil.move(os.path.join(x,file), os.path.join(parentdir, 'DB', file)) | ||
| shutil.move(os.path.join(x, file), os.path.join(parentdir, "DB", file)) | ||
| shutil.rmtree(x) | ||
| os.remove(x+'.amptk.tar.gz') | ||
| print('Extracting FASTA files for {:}'.format(x)) | ||
| extracted = os.path.join(parentdir, 'DB', x+'.extracted.fa') | ||
| cmd = ['vsearch', '--udb2fasta', udbfile, '--output', extracted] | ||
| os.remove(x + ".amptk.tar.gz") | ||
| print("Extracting FASTA files for {:}".format(x)) | ||
| extracted = os.path.join(parentdir, "DB", x + ".extracted.fa") | ||
| cmd = ["vsearch", "--udb2fasta", udbfile, "--output", extracted] | ||
| amptklib.runSubprocess5(cmd) | ||
| print("{:} taxonomy database installed to {:}".format(x, os.path.join(parentdir, 'DB'))) | ||
| print( | ||
| "{:} taxonomy database installed to {:}".format( | ||
| x, os.path.join(parentdir, "DB") | ||
| ) | ||
| ) | ||
|
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|
|
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| if __name__ == "__main__": | ||
|
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