| Next changeset 1:f96cbb663aa9 (2020-02-28) |
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Commit message:
planemo upload for repository https://github.com/arpcard/rgi commit 7a78289be23c5a14ae39f454610fa8eca3f05188 |
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added:
README.rst data_managers/data_manager_conf.xml data_managers/data_manager_rgi_build_db/data_manager/.gitignore data_managers/data_manager_rgi_build_db/data_manager/import_data.py data_managers/data_manager_rgi_build_db/data_manager/rgi_database_builder.py data_managers/data_manager_rgi_build_db/data_manager/rgi_database_builder.xml data_managers/data_manager_rgi_build_db/tool-data/rgi_databases.loc.sample data_managers/data_manager_rgi_build_db/tool_data_table_conf.xml.sample rgi.xml test-data/test1.fasta |
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| diff -r 000000000000 -r 715bc9aeef69 README.rst --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Wed Feb 27 09:08:21 2019 -0500 |
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| @@ -0,0 +1,6 @@ +RGI wrapper +-------------------- + +This wrapper is used to run Resistance Gene Identifier (RGI) on galaxy environment. + +This tool is used together with data manager for RGI: `rgi_database_builder <https://github.com/arpcard/rgi_database_builder>`_. |
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| diff -r 000000000000 -r 715bc9aeef69 data_managers/data_manager_conf.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_managers/data_manager_conf.xml Wed Feb 27 09:08:21 2019 -0500 |
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| @@ -0,0 +1,24 @@ +<?xml version="1.0"?> +<data_managers> + <data_manager tool_file="data_manager_rgi_build_db/data_manager/rgi_database_builder.xml" id="rgi_database_builder" version="1.0.0"> + <!-- Defines a Data Table to be modified --> + <data_table name="rgi_databases"> + <!-- Handle the output of the Data Manager Tool --> + <output> + <!-- Columns that will be specified by the Data Manager Tool --> + <column name="value" /> + <column name="name" /> + <!-- The value of this column will be modified based upon data in "out_file" --> + <column name="path" output_ref="out_file" > + <!-- Moving a file from the extra files path of "out_file" --> + <move type="directory" relativize_symlinks="True"> + <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">rgi_databases/${value}/${path}</target> + </move> + <!-- Store this value in the final Data Table --> + <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/rgi_databases/${value}/${path}</value_translation> + <value_translation type="function">abspath</value_translation> + </column> + </output> + </data_table> + </data_manager> +</data_managers> |
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| diff -r 000000000000 -r 715bc9aeef69 data_managers/data_manager_rgi_build_db/data_manager/.gitignore --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_managers/data_manager_rgi_build_db/data_manager/.gitignore Wed Feb 27 09:08:21 2019 -0500 |
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| @@ -0,0 +1,1 @@ +*.pyc \ No newline at end of file |
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| diff -r 000000000000 -r 715bc9aeef69 data_managers/data_manager_rgi_build_db/data_manager/import_data.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_managers/data_manager_rgi_build_db/data_manager/import_data.py Wed Feb 27 09:08:21 2019 -0500 |
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| b"@@ -0,0 +1,199 @@\n+import argparse\n+import datetime\n+import json\n+import os\n+import shutil\n+import sys\n+import tarfile\n+import urllib.request, urllib.error, urllib.parse\n+import zipfile\n+import logging\n+\n+path = os.path.join(os.getcwd(), 'rgi-database') \n+data_path = path\n+\n+level = logging.WARNING\n+logger = logging.getLogger(__name__)\n+logger.setLevel(level)\n+\n+def url_download(url, workdir):\n+ file_path = os.path.join(workdir, 'download.dat')\n+ if not os.path.exists(workdir):\n+ os.makedirs(workdir)\n+ src = None\n+ dst = None\n+ try:\n+ req = urllib.request.Request(url)\n+ src = urllib.request.urlopen(req)\n+ dst = open(file_path, 'wb')\n+ while True:\n+ chunk = src.read(2**10)\n+ if chunk:\n+ dst.write(chunk)\n+ else:\n+ break\n+ except Exception as e:\n+ print(str(e), file=sys.stderr)\n+ finally:\n+ if src:\n+ src.close()\n+ if dst:\n+ dst.close()\n+ if tarfile.is_tarfile(file_path):\n+ fh = tarfile.open(file_path, 'r:*')\n+ elif zipfile.is_zipfile(file_path):\n+ fh = zipfile.ZipFile(file_path, 'r')\n+ else:\n+ return\n+ # extract only one file : card.json\n+ for member in fh.getmembers():\n+ if member.isreg(): # skip if the TarInfo is not files\n+ member.name = os.path.basename(member.name) # remove the path by reset it\n+ if member.name == 'card.json':\n+ print('[import_data] extracting file: {}'.format(str(member.name)))\n+ fh.extract(member.name,workdir)\n+ os.remove(file_path)\n+\n+def checkKeyExisted(key, my_dict):\n+ try:\n+ nonNone = my_dict[key] is not None\n+ except KeyError:\n+ nonNone = False\n+ return nonNone\n+\n+def data_version():\n+ data_version = ''\n+ with open(os.path.join(data_path, 'card.json')) as json_file:\n+ json_data = json.load(json_file)\n+ for item in list(json_data.keys()):\n+ if item == '_version':\n+ data_version = json_data[item]\n+ json_file.close()\n+ return data_version\n+\n+def makeBlastDB():\n+ if os.path.isfile(os.path.join(path, 'proteindb.fsa')) == True:\n+ print('[import_data] create blast DB.')\n+ os.system('makeblastdb -in {}/proteindb.fsa -dbtype prot -out {}/protein.db > /dev/null 2>&1'.format(path, path))\n+\n+def makeDiamondDB():\n+ if os.path.isfile(os.path.join(path, 'proteindb.fsa')) == True:\n+ print('[import_data] create diamond DB.')\n+ os.system('diamond makedb --quiet --in {}/proteindb.fsa --db {}/protein.db'.format(path, path))\n+\n+def write_fasta_from_json():\n+\t\t'''Creates a fasta file from card.json file.'''\n+\t\tif os.path.isfile(os.path.join(path, 'proteindb.fsa')):\n+\t\t\treturn\n+\t\telse:\n+\t\t\ttry:\n+\t\t\t\twith open(os.path.join(data_path, 'card.json'), 'r') as jfile:\n+\t\t\t\t\tj = json.load(jfile)\n+\t\t\texcept Exception as e:\n+\t\t\t\tlogger.error(e)\n+\t\t\t\texit()\n+\n+\t\t\twith open(os.path.join(path, 'proteindb.fsa'), 'w') as fout:\n+\t\t\t\tfor i in j:\n+\t\t\t\t\tif i.isdigit():\n+\t\t \t# model_type: protein homolog model\n+\t\t\t\t\t\tif j[i]['model_type_id'] == '40292':\n+\t\t\t\t\t\t\ttry:\n+\t\t\t\t\t\t\t\tpass_bit_score = j[i]['model_param']['blastp_bit_score']['param_value']\n+\t\t\t\t\t\t\texcept KeyError:\n+\t\t\t\t\t\t\t\tlogger.warning('No bitscore for model (%s, %s). RGI will omit this model and keep running.' \\\n+\t\t\t\t\t\t\t\t\t% (j[i]['model_id'], j[i]['model_name']))\n+\t\t\t\t\t\t\t\tlogger.info('Please let the CARD Admins know! Email: card@mcmaster.ca')\n+\t\t\t\t\t\t\telse:\n+\t\t\t\t\t\t\t\ttry:\n+\t\t\t\t\t\t\t\t\tfor seq in j[i]['model_sequences']['sequence']:\n+\t\t\t\t\t\t\t\t\t\tfout.write('>%s_%s | model_type_id: 40292 | pass_bitscore: %s | %s\\n' % (i, seq, pass_bit_score, j[i]['ARO_name']))\n+\t\t\t\t\t\t\t\t\t\tfout.write('%s\\n' %(j[i]['model_sequences']['sequence'][seq]['protein_sequence']['sequence']))\n+\t\t\t\t\t\t\t\texcept Exception as e:\n+\t\t\t\t\t\t\t\t\tlogger.warning('No model sequences for model (%s, %s). RGI will omit this model and keep running.' \\\n+\t\t\t\t\t\t\t\t\t\t% ("..b"l: card@mcmaster.ca')\n+\n+\n+\t\t \t# model_type: protein variant model\n+\t\t\t\t\t\telif j[i]['model_type_id'] == '40293':\n+\t\t\t\t\t\t\ttry:\n+\t\t\t\t\t\t\t\tpass_bit_score = j[i]['model_param']['blastp_bit_score']['param_value']\n+\t\t\t\t\t\t\texcept KeyError:\n+\t\t\t\t\t\t\t\tlogger.warning('No bitscore for model (%s, %s). RGI will omit this model and keep running.' \\\n+\t\t\t\t\t\t\t\t\t% (j[i]['model_id'], j[i]['model_name']))\n+\t\t\t\t\t\t\t\tlogger.info('Please let the CARD Admins know! Email: card@mcmaster.ca')\n+\t\t\t\t\t\t\telse:\n+\t\t\t\t\t\t\t\ttry:\n+\t\t\t\t\t\t\t\t\tsnpList = [j[i]['model_param']['snp']['param_value'][k] for k in j[i]['model_param']['snp']['param_value']]\n+\t\t\t\t\t\t\t\texcept Exception as e:\n+\t\t\t\t\t\t\t\t\tlogger.warning('No snp for model (%s, %s). RGI will omit this model and keep running.' \\\n+\t\t\t\t\t\t\t\t\t\t% (j[i]['model_id'], j[i]['model_name']))\n+\t\t\t\t\t\t\t\t\tlogger.info('Please let the CARD Admins know! Email: card@mcmaster.ca')\n+\n+\t\t\t\t\t\t\t\ttry:\n+\t\t\t\t\t\t\t\t\tfor seq in j[i]['model_sequences']['sequence']:\n+\t\t\t\t\t\t\t\t\t\tfout.write('>%s_%s | model_type_id: 40293 | pass_bit_score: %s | SNP: %s | %s\\n' \\\n+\t\t\t\t\t\t\t\t\t\t\t% (i, seq, pass_bit_score, ','.join(snpList), j[i]['ARO_name']))\n+\t\t\t\t\t\t\t\t\t\tfout.write('%s\\n' % (j[i]['model_sequences']['sequence'][seq]['protein_sequence']['sequence']))\n+\t\t\t\t\t\t\t\texcept Exception as e:\n+\t\t\t\t\t\t\t\t\tlogger.warning('No model sequences for model (%s, %s). RGI will omit this model and keep running.' \\\n+\t\t\t\t\t\t\t\t\t\t% (j[i]['model_id'], j[i]['model_name']))\n+\t\t\t\t\t\t\t\t\tlogger.info('Please let the CARD Admins know! Email: card@mcmaster.ca')\n+\n+\t\t \t# model_type: protein overexpression model\n+\t\t\t\t\t\telif j[i]['model_type_id'] == '41091':\n+\t\t\t\t\t\t\ttry:\n+\t\t\t\t\t\t\t\tpass_bit_score = j[i]['model_param']['blastp_bit_score']['param_value']\n+\t\t\t\t\t\t\texcept KeyError:\n+\t\t\t\t\t\t\t\tlogger.warning('No bitscore for model (%s, %s). RGI will omit this model and keep running.' \\\n+\t\t\t\t\t\t\t\t\t% (j[i]['model_id'], j[i]['model_name']))\n+\t\t\t\t\t\t\t\tlogger.info('Please let the CARD Admins know! Email: card@mcmaster.ca')\n+\t\t\t\t\t\t\telse:\n+\t\t\t\t\t\t\t\ttry:\n+\t\t\t\t\t\t\t\t\tsnpList = [j[i]['model_param']['snp']['param_value'][k] for k in j[i]['model_param']['snp']['param_value']]\n+\t\t\t\t\t\t\t\texcept Exception as e:\n+\t\t\t\t\t\t\t\t\tlogger.warning('No snp for model (%s, %s). RGI will omit this model and keep running.' \\\n+\t\t\t\t\t\t\t\t\t\t% (j[i]['model_id'], j[i]['model_name']))\n+\t\t\t\t\t\t\t\t\tlogger.info('Please let the CARD Admins know! Email: card@mcmaster.ca')\n+\n+\t\t\t\t\t\t\t\ttry:\n+\t\t\t\t\t\t\t\t\tfor seq in j[i]['model_sequences']['sequence']:\n+\t\t\t\t\t\t\t\t\t\tfout.write('>%s_%s | model_type_id: 41091 | pass_bit_score: %s | SNP: %s | %s\\n' \\\n+\t\t\t\t\t\t\t\t\t\t\t% (i, seq, pass_bit_score, ','.join(snpList), j[i]['ARO_name']))\n+\t\t\t\t\t\t\t\t\t\tfout.write('%s\\n' % (j[i]['model_sequences']['sequence'][seq]['protein_sequence']['sequence']))\n+\t\t\t\t\t\t\t\texcept Exception as e:\n+\t\t\t\t\t\t\t\t\tlogger.warning('No model sequences for model (%s, %s). RGI will omit this model and keep running.' \\\n+\t\t\t\t\t\t\t\t\t\t% (j[i]['model_id'], j[i]['model_name']))\n+\t\t\t\t\t\t\t\t\tlogger.info('Please let the CARD Admins know! Email: card@mcmaster.ca')\n+\n+def _main(args):\n+ if not os.path.exists(path):\n+ print('[import_data] mkdir: {}'.format(path))\n+ os.makedirs(path)\n+ print('[import_data] path: {}'.format(path))\n+ print(args)\n+\n+ if args.url == None:\n+ url = 'https://card.mcmaster.ca/latest/data'\n+ else:\n+ url = args.url\n+ print('[import_data] url: {}'.format(url))\n+ workdir = os.path.join(os.getcwd(), 'rgi-database')\n+ print('[import_data] working directory: {}'.format(workdir))\n+ url_download(url, workdir)\n+ write_fasta_from_json()\n+ makeBlastDB()\n+ makeDiamondDB()\n+ version = data_version()\n+ print('[import_data] data version: {}'.format(version))\n+ return version\n+\n+def run():\n+ parser = argparse.ArgumentParser(description='Create data manager json.')\n+ parser.add_argument('--url', dest='url', action='store', help='Url for CARD data')\n+ args = parser.parse_args()\n+ _main(args)\n+\n+if __name__ == '__main__':\n+ run()\n" |
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| diff -r 000000000000 -r 715bc9aeef69 data_managers/data_manager_rgi_build_db/data_manager/rgi_database_builder.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_managers/data_manager_rgi_build_db/data_manager/rgi_database_builder.py Wed Feb 27 09:08:21 2019 -0500 |
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| @@ -0,0 +1,47 @@ +import argparse +import datetime +import json +import os +import shutil +import sys +import tarfile +import urllib.request, urllib.error, urllib.parse +import zipfile +from import_data import run, _main + +parser = argparse.ArgumentParser(description='Create data manager json.') +parser.add_argument('--url', dest='url', action='store', help='Url for CARD data') +parser.add_argument('--out', dest='output', action='store', help='JSON filename') +parser.add_argument('--name', dest='name', action='store', default='CARD_data-' + str(datetime.datetime.now().strftime('%Y-%B-%d-%H:%M:%S')), help='Data table database name') +args = parser.parse_args() + +print('[rgi_database_builder] Importing...') + +_main(args) + +def main(args): + print('[rgi_database_builder] Building......') + + data_manager_entry = {} + data_manager_entry['value'] = args.name.lower() + data_manager_entry['name'] = args.name + data_manager_entry['path'] = '.' + + data_manager_json = dict(data_tables = dict(rgi_databases=data_manager_entry)) + + params = json.loads(open(args.output,'r').read()) + + target_directory = params['output_data'][0]['extra_files_path'] + os.mkdir(target_directory) + output_path = os.path.join(os.getcwd(), 'rgi-database') + + for filename in os.listdir(output_path): + print('[rgi_database_builder] move file: {} from {} to {}'.format(filename, output_path, target_directory)) + shutil.move(os.path.join(output_path, filename), target_directory) + + print(args.output) + print('[rgi_database_builder] write file: {}'.format(args.output)) + open(args.output, 'w').write(json.dumps(data_manager_json)) + +if __name__ == '__main__': + main(args) |
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| diff -r 000000000000 -r 715bc9aeef69 data_managers/data_manager_rgi_build_db/data_manager/rgi_database_builder.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_managers/data_manager_rgi_build_db/data_manager/rgi_database_builder.xml Wed Feb 27 09:08:21 2019 -0500 |
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| @@ -0,0 +1,28 @@ +<?xml version="1.0"?> +<tool id="rgi_database_builder" name="RGI Database Builder" tool_type="manage_data" version="1.0.0"> + <description>Download and build the CARD database for RGI</description> + <requirements> + <requirement type="package" version="4.2.2">rgi</requirement> + </requirements> + <stdio> + <exit_code description="Error" level="fatal" range="1:" /> + </stdio> + <command interpreter="python3"> + <![CDATA[ + rgi_database_builder.py --out "${out_file}" + #if $name: + --name "${name}" + #end if + #if $url: + --url "${url}" + #end if + ]]> + </command> + <inputs> + <param name="name" type="text" value="" label="Database name" help="Name for this database, or leave blank for today's date" optional="True"/> + <param name="url" type="text" value="https://card.mcmaster.ca/latest/data" label="Url" help="Url for the CARD data e.g https://card.mcmaster.ca/lastest/data. Visit https://card.mcmaster.ca/download to see previous CARD releases." optional="True"/> + </inputs> + <outputs> + <data format="data_manager_json" name="out_file" label="${tool.name} (JSON)"/> + </outputs> +</tool> |
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| diff -r 000000000000 -r 715bc9aeef69 data_managers/data_manager_rgi_build_db/tool-data/rgi_databases.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_managers/data_manager_rgi_build_db/tool-data/rgi_databases.loc.sample Wed Feb 27 09:08:21 2019 -0500 |
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| @@ -0,0 +1,5 @@ +#This file lists the columns that will be specified by the RGI Data Manager tool. +# +#For example: +#<value> <name> <path> +#rgi_20181001 rgi_20181001 /galaxy-central/tool-data/rgi_databases/rgi_20181001 |
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| diff -r 000000000000 -r 715bc9aeef69 data_managers/data_manager_rgi_build_db/tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_managers/data_manager_rgi_build_db/tool_data_table_conf.xml.sample Wed Feb 27 09:08:21 2019 -0500 |
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| @@ -0,0 +1,8 @@ +<?xml version="1.0"?> +<tables> + <!-- Locations of RGI database in the required format --> + <table name="rgi_databases" comment_char="#"> + <columns>value, name, path</columns> + <file path="tool-data/rgi_databases.loc" /> + </table> +</tables> |
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| diff -r 000000000000 -r 715bc9aeef69 rgi.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rgi.xml Wed Feb 27 09:08:21 2019 -0500 |
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| b'@@ -0,0 +1,187 @@\n+<tool id="rgi" name="Resistance Gene Identifier (RGI)" version="4.2.2">\n+ <description>This tool predicts resistome(s) from protein or nucleotide data based on homology and SNP models.</description>\n+ <requirements>\n+ <requirement type="package" version="4.2.2">rgi</requirement>\n+ </requirements>\n+ <stdio>\n+ <exit_code range="1:" />\n+ </stdio>\n+ <command><![CDATA[\n+#if $db_opts.db_opts_selector != "default":\n+ rgi load\n+ #if $db_opts.db_opts_selector == "local":\n+ -i "${__tool_data_path__}/rgi_databases/$db_opts.rgi_db_local/card.json" \n+ #else:\n+ -i "$db_opts.rgi_db_hist"\n+ #end if\n+ --local\n+ &&\n+#end if\n+\n+rgi main\n+ -i \'$input_sequence\'\n+ -o out\n+ -t $input_type\n+ -a $alignment_tool\n+ -n "\\${GALAXY_SLOTS:-1}"\n+ $include_loose\n+ $low_quality\n+ -d $data\n+\n+#if $db_opts.db_opts_selector != "default":\n+ --local\n+#end if\n+ ]]></command>\n+ <inputs>\n+ <param argument="--input_sequence" type="data" format="fastq,fasta" label="Input sequence" help="input file must be in either FASTA (contig and protein) or gzip format e.g myFile.fasta, myFasta.fasta.gz"/>\n+ <param argument="--input_type" type="select" multiple="false" label="Input type" help="specify data input type (default = contig)">\n+ <option value="contig" selected="true">CONTIG (Nucleotide Sequence)</option>\n+ <option value="protein">PROTEIN (Protein Sequence)</option>\n+ </param>\n+ <param argument="--alignment_tool" type="select" label="Alignment tool" help="specify alignment tool (default = BLAST)">\n+ <option value="blast" selected="true">BLAST</option>\n+ <option value="diamond">DIAMOND</option>\n+ </param>\n+ <param argument="--include_loose" type="boolean" checked="false" truevalue="--include_loose" falsevalue="" label="Include loose hits" help="include loose hits in addition to strict and perfect hits"/>\n+ <param argument="--low_quality" type="boolean" checked="false" truevalue="--low_quality" falsevalue="" label="Low quality" help="use for short contigs to predict partial genes"/>\n+ <param argument="--data" type="select" multiple="false" label="Data type" help="specify a data-type (default = NA)">\n+ <option value="wgs">WGS</option>\n+ <option value="plasmid">PLASMID</option>\n+ <option value="chromosome">CHROMOSOME</option>\n+ <option value="NA" selected="true">NA</option>\n+ </param>\n+ <conditional name="db_opts">\n+ <param name="db_opts_selector" type="select" label="Select an RGI database">\n+ <option value="default" selected="true">Default RGI database</option>\n+ <option value="local">Locally installed RGI database</option>\n+ <option value="hist">RGI database from your history</option>\n+ </param>\n+ <when value="default">\n+ <param name="rgi_db_local" type="hidden" value="" /> \n+ <param name="rgi_db_hist" type="hidden" value="" />\n+ </when>\n+ <when value="local">\n+ <param name="rgi_db_local" type="select" multiple="false" label="Locally installed RGI database">\n+ <options from_data_table="rgi_databases">\n+ <validator type="no_options" message="No databases are available built-in"/>\n+ </options>\n+ </param>\n+ <param name="rgi_db_hist" type="hidden" value="" />\n+ </when>\n+ <when value="hist">\n+ <param name="rgi_db_local" type="hidden" value="" />\n+ <param name="rgi_db_hist" type="data" format="json" label="RGI database from your history" />\n+ </when>\n+ </conditional>\n+ </inputs>\n+ <outputs>\n+ <data name="report" format="json" from_work_dir="out.json" label="${tool.name} '..b' | Contig | Start | Stop | Orientation | Cut_Off | Pass_Bitscore | Best_Hit_Bitscore | Best_Hit_ARO | Best_Identities | ARO | Model_type | SNPs_in_Best_Hit_ARO | Other_SNPs | Drug Class | Resistance Mechanism | AMR Gene Family | Predicted_DNA | Predicted_Protein | CARD_Protein_Sequence | Percentage Length of Reference Sequence | ID | Model_ID |\n++==========================================================================================================================+===============+=======+======+=============+==========+================+=====================+================+==================+==========+=======================+==========================+=============+============+=========================+======================+===========================+========================+===========================+=========================================+================================+===========+\n+| AY123251.1_6 # 3575 # 4489 # 1 # ID=1_6;partial=00;start_type=ATG;rbs_motif=None;rbs_spacer=None;gc_cont=0.399 | AY123251.1_6 | 3575 | 4489 | \\+ | Strict | 500 | 506.908 | CARB-7 | 83.68 | 3002246 | protein homolog model | n/a | n/a | penam | antibiotic inactivation | CARB beta-lactamase | ATGC | MLLYKMCDNQNYGVTYMKFLLV | MKSLLVFALLMPSVVFASSSKFQSV | 105.56 | gnl|BL_ORD_ID|589|hsp_num:0 | 1443 |\n++--------------------------------------------------------------------------------------------------------------------------+---------------+-------+------+-------------+----------+----------------+---------------------+----------------+------------------+----------+-----------------------+--------------------------+-------------+------------+-------------------------+----------------------+---------------------------+------------------------+---------------------------+-----------------------------------------+--------------------------------+-----------+\n+\n+report.json\n+^^^^^^^^^^^\n+\n+A json version of summary.txt.\n+\n+Help\n+----\n+\n+**usage:**\n+ ``rgi main [-h] -i INPUT_SEQUENCE -o OUTPUT_FILE [-t {read,contig,protein,wgs}] [-a {DIAMOND,BLAST}] [-n THREADS] [--include_loose] [--local] [--clean] [--debug] [--low_quality] [-d {wgs,plasmid,chromosome,NA}] [-v]``\n+\n+**optional arguments:**\n+\n+- ``-h, --help``\n+ show this help message and exit\n+- ``-i INPUT_SEQUENCE, --input_sequence INPUT_SEQUENCE``\n+ input file must be in either FASTA (contig and protein) or gzip format e.g myFile.fasta, myFasta.fasta.gz\n+- ``-o OUTPUT_FILE, --output_file OUTPUT_FILE``\n+ output folder and base filename\n+- ``-t {read,contig,protein,wgs}, --input_type {read,contig,protein,wgs}``\n+ specify data input type (default = contig)\n+- ``-a {DIAMOND,BLAST}, --alignment_tool {DIAMOND,BLAST}``\n+ specify alignment tool (default = BLAST)\n+- ``-n THREADS, --num_threads THREADS``\n+ number of threads (CPUs) to use in the BLAST search (default=8)\n+- ``--include_loose``\n+ include loose hits in addition to strict and perfect hits\n+- ``--local``\n+ use local database (default: uses database in executable directory)\n+- ``--clean``\n+ removes temporary files\n+- ``--debug``\n+ debug mode\n+- ``--low_quality``\n+ use for short contigs to predict partial genes\n+- ``-d {wgs,plasmid,chromosome,NA}, --data {wgs,plasmid,chromosome,NA}``\n+ specify a data-type (default = NA)\n+- ``-v, --version``\n+ prints software version number\n+\n+Links\n+-----\n+\n+RGI: https://card.mcmaster.ca/analyze/rgi\n+\n+Github: https://github.com/arpcard/rgi\n+\n+CARD database: https://card.mcmaster.ca\n+ ]]>\n+ </help>\n+ <citations>\n+ <citation type="doi">10.1093/nar/gkw1004</citation>\n+ </citations>\n+</tool>\n' |
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| diff -r 000000000000 -r 715bc9aeef69 test-data/test1.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test1.fasta Wed Feb 27 09:08:21 2019 -0500 |
| b |
| @@ -0,0 +1,68 @@ +>AY123251.1 Salmonella enterica subsp. enterica serovar Typhi R-plasmid pST2301 class I integron aminoglycoside 6'-N-acetyltransferase (aacA4), chloramphenicol acetyltransferase (catB8), aminoglycoside 3'-adenyltransferase (aadA1), dihydrofolate reductase type I (dhfr1), aminoglycoside 6'-n-acetyltransferase (aac6-II), and CARB-8 beta-lactamase (blaCARB-8) genes, complete cds +TCATGGCTTGTTATGACTGTTTTTTTGTACAGTCTATGCCTCGGGCATCCAAGCAGCAAGCGCGTTACGC +CGTGGGTCGATGTTTGATGTTATGGAGCAGCAACGATGTTACGCAGCAGGGCAGTCGCCCTAAAACAAAG +TTAGGCATCACAAAGTACAGCATCGTGACCAACAGCAACGATTCCGTCACACTGCGCCTCATGACTGAGC +ATGACCTTGCGATGCTCTATGAGTGGCTAAATCGATCTCATATCGTCGAGTGGTGGGGCGGAGAAGAAGC +ACGCCCGACACTTGCTGACGTACAGGAACAGTACTTGCCAAGCGTTTTAGCGCAAGAGTCCGTCACTCCA +TACATTGCAATGCTGAATGGAGAGCCGATTGGGTATGCCCAGTCGTACGTTGCTCTTGGAAGCGGGGACG +GATGGTGGGAAGAAGAAACCGATCCAGGAGTACGCGGAATAGACCAGTCACTGGCGAATGCATCACAACT +GGGCAAAGGCTTGGGAACCAAGCTGGTTCGAGCTCTGGTTGAGTTGCTGTTCAATGATCCCGAGGTCACC +AAGATCCAAACGGACCCGTCGCCGAGCAACTTGCGAGCGATCCGATGCTACGAGAAAGCGGGGTTTGAGA +GGCAAGGTACCGTAACCACCCCAGATGGTCCAGCCGTGTACATGGTTCAAACACGCCAGGCATTCGAGCG +AACACGCAGTGTTGCCTAACCCTTCCATCGAGGGGGACGTCCAAGGGCTGGCGCCCTTGGCCGCCCCTCA +TGTCAAACGTTAGACGGCAAGAAAAGGTTCCACGAACTCTGATGAAAAACTACTTTAACAGCCCTTTCAA +AGGGGAACTTCTTTCTGAGCAAGTGAAAAATCCAAATATCAGAGTAGGCCGGTATAGCTATTACTCTGGC +TACTATCACGGGCACTCATTTGATGAATGCGCGCGATACTTGCTTCCAGATCGTGATGACGTTGATAAAT +TGATCATTGGCAGCTTTTGTTCTATAGGAAGCGGGGCTTCCTTCATCATGGCTGGCAATCAGGGGCATCG +GCATGACTGGGCATCATCCTTCCCCTTCTTCTATATGCAAGAGGAGCCTGCTTTCTCAAGAGCACTCGAC +GCCTTCCAAAGAGCAGGTGATACCGTCATTGGCAATGATGTCTGGATAGGCTCGGAGGCAATGATTATGC +CTGGCATCAAAATTGGAGACGGTGCCGTGATAGGTAGTCGCTCGTTGGTGACAAAAGATGTAGAGCCTTA +TGCCATCATCGGGGGAAATCCCGCAAAGCAAATTAAGAAGCGCTTCTCCGATGAGGAAATCTCATTGCTC +ATGGAGATGGAGTGGTGGAACTGGCCACTAGATAAAATTAAGACAGCAATGCCTCTGCTGTGCTCGTCAA +ATATTTTTGGTCTGCATAAGTATTGGCGCGAGTTTGCCGTCTAACAATTCATTCAAGCCGACGCCGCTTC +GCGGCACGGCTTAATTCTGGCGTTAAACATCATGAGGGAAGCGGTGATCGCCGAAGTATCGACTCAACTA +TCAGAGGTAGTTGGCGTCATCGAGCGCCATCTCGAACCGACGTTGCTGGCCGTACATTTGTACGGCTCCG +CAGTGGATGGCGGCCTGAAGCCACACAGTGATATTGATTTGCTGGTTACGGTGACCGTAAGGCTTGATGA +AACAACGCGGCGAGCTTTGATCAACGACCTTTTGGAAACTTCGGCTTCCCCTGGAGAGAGCGAGATTCTC +CGCGCTGTAGAAGTCACCATTGTTGTGCACGACGACATCATTCCGTGGCGTTATCCAGCTAAGCGCGAAC +TGCAATTTGGAGAATGGCAGCGCAATGACATTCTTGCAGGTATCTTCGAGCCAGCCACGATCGACATTGA +TCTGGCTATCTTGCTGACAAAAGCAAGAGAACATAGCGTTGCCTTGGTAGGTCCAGCGGCGGAGGAACTC +TTTGATCCGGTTCCTGAACAGGATCTATTTGAGGCGCTAAATGAAACCTTAACGCTATGGAACTCGCCGC +CCGACTGGGCTGGCGATGAGCGAAATGTAGTGCTTACGTTGTCCCGCATTTGGTACAGCGCAGTAACCGG +CAAAATCGCGCCGAAGGATGTCGCTGCCGACTGGGCAATGGAGCGCCTGCCGGCCCAGTATCAGCCCGTC +ATACTTGAAGCTAGACAGGCTTATCTTGGACAAGAAGAAGATCGCTTGGCCTCCCGCGCAGATCAGTTGG +AAGAATTTGTTCACTACGTGAAAGGCGAGATCACCAAGGTAGTCGGCAAATAATGTCTAACAATTCGTTC +AAGCCGACGCCGCTTCGCGGCGCGGCTTAACTCAAGCGTTAACCTCTGAGGAAGAATTGTGAAACTATCA +CTAATGGTAGCTATATCGAAGAATGGAGTTATCGGGAATGGCCCTGATATTCCATGGAGTGCCAAAGGTG +AACAGCTCCTGTTTAAAGCTATTACCTATAACCAATGGCTGTTGGTTGGACGCAAGACTTTTGAGTCAAT +GGGAGCATTACCCAACCGAAAGTATGCGGTCGTAACACGTTCAAGTTTTACATCTGACAATGAGAACGTA +GTGATCTTTCCATCAATTAAAGATGCTTTAACCAACCTAAAGAAAATAACGGATCATGTCATTGTTTCAG +GTGGTGGGGAGATATACAAAAGCCTGATCGATCAAGTAGATACACTACATATATCTACAATAGACATCGA +GCCGGAAGGTGATGTTTACTTTCCTGAAATCCCCAGCAATTTTAGGCCAGTTTTTACCCAAGACTTCGCC +TCTAACATAAATTATAGTTACCAAATCTGGCAAAAGGGTTAACAAGTGGCAGCAACGGATTCGCAAACCT +GTCACGCCTTTTGTACCAAAACCCGCGCCAGGTTTGCGATCCGCTGTGCCAGGCGTTAGGCAGCACAGAG +CGACCATTTCATGTCCGCGAGCACCCCCCCCATAACTCTTCGCCTCATGACCGAGCGCGACCTGCCGATG +CTCCATGATTGGCTCAACCGGCCGCACATCGTTGAGTGGTGGGGTGGTGACGAAGAGCGACCGACTCTTG +ATGAAGTGCTGGAACACTACCTGCCCAGAGCGATGGCGGAAGAGTCCGTAACACCGTACATCGCAATGCT +GGGCGAGGAACCGATCGGCTATGCTCAGTCGTACGTCGCGCTCGGAAGCGGTGATGGCTGGTGGGAAGAT +GAAACTGATCCAGGAGTGCGAGGAATAGACCAGTCTCTGGCTGACCCGACACAGTTGAACAAAGGCCTAG +GAACAAGGCTTGTCCGCGCTCTCGTTGAACTACTGTTCTCGGACCCCACCGTGACGAAGATTCAGACCGA +CCCGACTCCGAACAACCATCGAGCCATACGCTGCTATGAGAAGGCAGGATTCGTGCGGGAGAAGATCATC +ACCACGCCTGACGGGCCGGCGGTTTACATGGTTCAAACACGACAAGCCTTCGAGAGAAAGCGCGGTGTTG +CCTAACAACTCATTCAAGCCGACGCCGCTTCGCGGCGCGGCTTAATTCAGGTGTTAGCCATATTATGGAG +CCTCATGCTTTTATATAAAATGTGTGACAATCAAAATTATGGGGTTACTTACATGAAGTTTTTATTGGTA +TTTTCGCTTTTAATACCATCCGTGGTTTTTGCAAGTAGTTCAAAGTTTCGGCAAGTTGAACAAGACGTTA +AGGCAATTGAAGTTTCTCTTTCTGCTCGTATAGGTGTTTCCGTTCTTGATACTCAAAATGGAGAATACTG +GGATTACAATGGCAATCAGCGCTTCCCGTTGACAAGTACTTTTAAAACAATAGCTTGCGCTAAATTACTA +TATGATGCTGAGCAAGGAAAAGTTAATCCCAATAGTACAATCGAGATTAAGAAAGCAGATCTTGTGACCT +ATTCCCCTGTAATAGAAAAGCAAGTAGGGCAGGCAATCACACTCGATGATGCGTGCTTCGCAACTATGAC +TACAAGTGATAATACTGCGGCAAATATCATCCTAAGTGCTGTAGGTGGCTCCAAAGGCGTTACTGATTTT +TTAAGACAAATTGGGGACAAAGAGACTCGTCTAGACCGTATTGAGCCTGATTTAAATGAAGGTAAGCTCG +GTGATTTGAGGGATACGACAACTCCTAAGGCAATAGCCAGTACTTTGAATAAATTTTTATTTGGTTCAGC +GCTATCTGAAATGAACAAAAAAAAATTAGAGTCTTGGATGGTGAACAATCAAGTCACTGGTAATTTACTA +CGTTCAGTATTGCCGGCGGGATGGAACATTGCGGATCGTTCAGGTGCTGGCGGATTTGGTGCTCGGAGTA +TTACAGCAGTTGTGTGGAGTGAGCATCAAGCCCCAATTATTGTGAGCATCTATCTAGCTCAAACACAGGC +TTCAATGGCAGAGCGAAATGATGCGATTGTTAAAATTGGTCGTTCAATTTTTGACGTTTATACATCACAG +TCGCGCTGATAAGGCTAACAAGGCCATCAAGTTGACGGCTTTTCCGTCGCTTGTTTTGTGGCTTAACGCT +ACGCTACCACAAAACAATCAACTACAAAGCCGCAACTTATGGCGGCGTTAGATACACTAAGCACATAATT +GCTCACAGCCAAACTATCAGGTCAAGTCTGCTTTTATTATTTTTAAGCGTGCATAATAAGCCCTAC \ No newline at end of file |