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Tao Zhu
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| @@ -1,3 +1,3 @@ | ||
| # pysam | ||
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| # primer3-py | ||
| # flask |
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| #!/usr/bin/env python3 | ||
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| '''Here is the title | ||
| Here is the document | ||
| ''' | ||
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| __author__ = 'Tao Zhu' | ||
| __copyright__ = 'Copyright 2019' | ||
| __license__ = 'GPL' | ||
| __version__ = '0.1' | ||
| __email__ = '[email protected]' | ||
| __status__ = 'Development' | ||
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| import argparse | ||
| import re | ||
| import os | ||
| import json | ||
| import shutil | ||
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| from distutils.version import LooseVersion | ||
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| import make_sites, make_primers, design_primer, run_blast, sort_primers, output | ||
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| parser = argparse.ArgumentParser(description='PrimerServer2: a high-throughput primer \ | ||
| design and specificity-checking platform', formatter_class=argparse.ArgumentDefaultsHelpFormatter) | ||
| parser.add_argument('query', help='query file. (STDIN is acceptable)', type=argparse.FileType('r')) | ||
| parser.add_argument('template', help='template file in FASTA format') | ||
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| group = parser.add_mutually_exclusive_group() | ||
| group.add_argument('--no-specificity', help="Don't check specificity; Only design primers", action='store_true') | ||
| group.add_argument('--only-specificity', help="Only check specificity and skip primer designs", action='store_true') | ||
| parser.add_argument('--type', choices=['SEQUENCE_TARGET', 'SEQUENCE_INCLUDED_REGION', 'FORCE_END'],\ | ||
| help='primer types', default='SEQUENCE_TARGET') | ||
| parser.add_argument('-p', '--cpu', type=int, help='Used CPU number.', default=2) | ||
| parser.add_argument('-l', '--checking-size-min', type=int, help='Lower limit of the checking amplicon size range (bp).', \ | ||
| default=70) | ||
| parser.add_argument('-u', '--checking-size-max', type=int, help='Upper limit of the checking amplicon size range (bp).', \ | ||
| default=1000) | ||
| parser.add_argument('-r', '--primer-num-retain', type=int, help='The maximum number of primers for each site to return.', \ | ||
| default=10) | ||
| parser.add_argument('-a', '--report-amplicon-seqs', help="Get amplicon seqs (might be slow)", action='store_true') | ||
| parser.add_argument('--json-debug', help="Output debug information in JSON mode", action='store_true') | ||
| parser.add_argument('-o', '--out', help="Output primers in JSON format", type=argparse.FileType('w')) | ||
| parser.add_argument('-t', '--tsv', help="Output primers in TSV format", type=argparse.FileType('w')) | ||
| args = parser.parse_args() | ||
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| def error(msg): | ||
| if args.json_debug is True: | ||
| print(json.dumps({'ERROR': msg})) | ||
| raise Exception(msg) | ||
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| ############### Check Environments ############### | ||
| if shutil.which('samtools') is None: | ||
| error('No samtools detected in your system') | ||
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| samtools_version = os.popen('samtools --version').readlines()[0].strip().split(' ')[1] | ||
| if LooseVersion(samtools_version) < LooseVersion('1.9'): | ||
| error(f'Your samtools version is v{samtools_version}, but >=v1.9 is required') | ||
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| if shutil.which('blastn') is None: | ||
| error('No NCBI-BLAST+ (blastn) detected in your system') | ||
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| if shutil.which('makeblastdb') is None: | ||
| error('No NCBI-BLAST+ (makeblastdb) detected in your system') | ||
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| ############### Check Template File (FASTA) ####### | ||
| if os.path.isfile(args.template) is False: | ||
| error(f'File not found: {args.template}') | ||
| if os.path.isfile(args.template+'.fai') is False: | ||
| code = os.system(f'samtools faidx {args.template} 2>/dev/null') | ||
| if code != 0: | ||
| error(f'File {args.template} cannot be indexed by samtools faidx. Perhaps it is not in FASTA format') | ||
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| ############### Run ############################### | ||
| #### primers #### | ||
| query_string = args.query.read() | ||
| if args.only_specificity is True: | ||
| primers = make_primers.make_primers(query=query_string) | ||
| else: | ||
| sites = make_sites.build(query=query_string, template_file=args.template, primer_type=args.type) | ||
| primers = design_primer.multiple(sites, cpu=args.cpu) | ||
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| #### specificity #### | ||
| dbs = [args.template] | ||
| if args.no_specificity is False: | ||
| primers = run_blast.run_blast_parallel(primers=primers, dbs=dbs, cpu=args.cpu,\ | ||
| checking_size_max=args.checking_size_max, checking_size_min=args.checking_size_min, \ | ||
| report_amplicon_seq=args.report_amplicon_seqs) | ||
| primers = sort_primers.sort_rank(primers=primers, dbs=dbs, max_num_return=args.primer_num_retain) | ||
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| #### output ######### | ||
| if args.out is not None: | ||
| print(json.dumps(primers, indent=4), file=args.out) | ||
| else: | ||
| print(json.dumps(primers, indent=4)) | ||
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| if args.tsv is not None: | ||
| if args.no_specificity is False: | ||
| output.after_check(primers, dbs, file=args.tsv) |
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