def main():
from zippylib import ascii_encode_dict
from zippylib import banner
print >> sys.stderr, banner(__version__)
parser = ArgumentParser(prog="zippy.py",
description='Zippy - Primer design and database')
parser.add_argument('--version', action='version', version='%(prog)s '+__version__+'('+__status__+')',\
help="Displays version")
# configuration files
global_group = parser.add_argument_group('Global options')
global_group.add_argument("-c", dest="config", default='zippy.json',metavar="JSON_FILE", \
help="configuration file [zippy.json]")
global_group.add_argument("--tiers", dest="tiers", default='0,1,2', \
help="Allowed design tiers (0,1,...,n)")
# run modes
subparsers = parser.add_subparsers(help='Help for subcommand')
## add primers
parser_add = subparsers.add_parser(
'add', help='Add previously designed primers to database')
parser_add.add_argument("primers", default=None, metavar="FASTA/TAB", \
help="Primers or locations to add to database")
parser_add.set_defaults(which='add')
## retrieve
parser_retrieve = subparsers.add_parser('get', help='Get/design primers')
parser_retrieve.add_argument("targets", default=None, metavar="VCF/BED/Interval/GenePred", \
help="File with intervals of interest or CHR:START-END (mandatory for gap-PCR)")
parser_retrieve.add_argument("--design", dest="design", default=False, action="store_true", \
help="Design primers if not in database")
parser_retrieve.add_argument("--gap", dest="gap", default=None, metavar="CHR:START-END", \
help="Second break point for gap-PCR")
parser_retrieve.add_argument("--nostore", dest="store", default=True, action='store_false', \
help="Do not store result in database")
parser_retrieve.add_argument("--outfile", dest="outfile", default='', type=str, \
help="Output file name")
parser_retrieve.set_defaults(which='get')
## query database for primers by name
parser_query = subparsers.add_parser(
'query',
help='Query database for primers with specified sub-string in name')
parser_query.add_argument("subString", default=None, metavar="Sub-string within name", \
help="String found within primer name")
parser_query.set_defaults(which='query')
## batch
parser_batch = subparsers.add_parser(
'batch', help='Batch design primers for sample list')
parser_batch.add_argument("targets", default=None, metavar="FILE1,FILE2,...", \
help="SNPpy result table(s) ")
parser_batch.add_argument("--predesign", dest="predesign", default=False, action="store_true", \
help="Design primers for all genes in batch")
parser_batch.add_argument("--nodesign", dest="design", default=True, action="store_false", \
help="Skip primer design if not in database")
parser_batch.add_argument("--tiers", dest="tiers", default='0,1,2', \
help="Allowed design tiers (0,1,...,n)")
parser_batch.add_argument("--outfile", dest="outfile", default='', type=str, \
help="Create worksheet PDF, order and robot CSV")
parser_batch.set_defaults(which='batch')
## update
parser_update = subparsers.add_parser(
'update', help='Update status and location of primers')
parser_update.add_argument('-l', dest="location", nargs=3, \
help="Update storage location of primer pair (primerid vessel well)")
parser_update.add_argument('-t', dest="locationtable", \
help="Batch update storage locations from TSV (primerid vessel well)")
parser_update.add_argument("--force", dest="force", default=False, action='store_true', \
help="Force Location update (resets existing)")
parser_update.add_argument('-b', dest="blacklist", type=str, \
help="Blacklist primer")
parser_update.set_defaults(which='update')
## dump specific datasets from database
parser_dump = subparsers.add_parser('dump', help='Data dump')
parser_dump.add_argument("--amplicons", dest="amplicons", default='', type=str, \
help="Retrieve amplicons of given size (eg. 10-1000)")
parser_dump.add_argument("--ordersheet", dest="ordersheet", default=False, action="store_true", \
help="IDT order sheet (primer pairs with no status marker)")
parser_dump.add_argument("--locations", dest="locations", default=False, action="store_true", \
help="Primer locations")
parser_dump.add_argument("--redundancies", dest="redundancies", default=False, action="store_true", \
help="Primers with same sequence and tag")
parser_dump.add_argument("--table", dest="table", default=False, action="store_true", \
help="Primer pair table with locations")
parser_dump.add_argument("--outfile", dest="outfile", default='', type=str, \
help="Output file name")
parser_dump.set_defaults(which='dump')
options = parser.parse_args()
# read config and open database
with open(options.config) as conf:
config = json.load(conf, object_hook=ascii_encode_dict)
here = config['primerbed'] if 'primerbed' in config.keys(
) and config['primerbed'] else None
db = PrimerDB(config['database'], dump=here)
if options.which == 'add': # read primers and add to database
# import primer pairs
if options.primers.split('.')[-1].startswith('fa'):
pairs = importPrimerPairs(
options.primers, config,
primer3=False) # import and locate primer pairs
print >> sys.stderr, "Storing Primers..."
db.addPair(
*pairs
) # store pairs in database (assume they are correctly designed as mispriming is ignored and capped at 1000)
sys.stderr.write('Added {} primer pairs to database\n'.format(
len(pairs)))
# store locations if table
if not options.primers.split('.')[-1].startswith(
'fa'): # assume table format
locations = importPrimerLocations(options.primers)
print >> sys.stderr, "Setting Primer locations..."
db.addLocations(*locations.items())
sys.stderr.write(
'Added {} locations for imported primers\n'.format(
len(locations)))
elif options.which == 'dump': # data dump fucntions (`for bulk downloads`)
if options.amplicons:
try:
l = options.amplicons.split('-')
assert len(l) == 2
amplen = map(int, l)
except (AssertionError, ValueError):
raise ConfigError('must give amplicon size to retrieve')
except:
raise
else:
# get amplicons amplen
data, colnames = db.dump('amplicons', size=amplen)
elif options.ordersheet:
data, colnames = db.dump('ordersheet', **config['ordersheet'])
elif options.locations:
data, colnames = db.dump('locations')
elif options.table:
data, colnames = db.dump('table')
elif options.redundancies:
data, colnames = db.getRedundantPrimers()
else:
print >> sys.stderr, "What to dump stranger?"
sys.exit(1)
# format data output
if options.outfile:
dump = Data(data, colnames)
dump.writefile(options.outfile) # sets format by file extension
else:
print '\t'.join(colnames)
for row in data:
print '\t'.join(map(str, row))
elif options.which == 'update': #update location primer pairs are stored
if options.location:
primer, vessel, well = options.location
updateLocation(primer, Location(vessel, well), db, options.force)
if options.locationtable:
updateList = readprimerlocations(options.locationtable)
for item in updateList: # [ Primer, Location ]
updateLocation(item[0], item[1], db, options.force)
if options.blacklist:
print >> sys.stderr, 'BLACKLISTED PAIRS: {}'.format(','.join(
db.blacklist(options.blacklist)))
print >> sys.stderr, 'REMOVED ORPHANS: {}'.format(','.join(
db.removeOrphans()))
elif options.which == 'get': # get primers for targets (BED/VCF or interval)
zippyPrimerQuery(config, options.targets, options.design, options.outfile, \
db, options.store, map(int,options.tiers.split(',')), options.gap)
elif options.which == 'batch':
zippyBatchQuery(config, options.targets.split(','), options.design, options.outfile, \
db, options.predesign, map(int,options.tiers.split(',')))
elif options.which == 'query':
searchByName(options.subString, db)
# dump amplicons fo given size to stdout
try:
l = options.amplicons.split('-')
assert len(l) == 2
amplen = map(int, l)
except (AssertionError, ValueError):
raise ConfigError('must give amplicon size to retrieve')
except:
raise
else:
# get amplicons amplen
data, colnames = db.dump('amplicons', size=amplen)
# format data output
if options.outfile:
dump = Data(data, colnames)
dump.writefile(
options.outfile) # sets format by file extension
else:
print '\t'.join(colnames)
for row in data:
print '\t'.join(map(str, row))
elif options.which == 'get': # get primers for targets (BED/VCF or interval)
intervals = readTargets(
options.targets) # get intervals from file or commandline
ivpairs = {} # found/designed primer pairs (from database or design)
# primer searching
for iv in intervals:
if options.database: # check if inteval covered by primer pair
ivpairs[iv] = db.query(iv, config['tiling']['flank'])
def main():
from zippylib import ascii_encode_dict
from zippylib import banner
print >> sys.stderr, banner(__version__)
parser = ArgumentParser(prog="zippy.py", description="Zippy - Primer design and database")
parser.add_argument(
"--version",
action="version",
version="%(prog)s " + __version__ + "(" + __status__ + ")",
help="Displays version",
)
# configuration files
global_group = parser.add_argument_group("Global options")
global_group.add_argument(
"-c", dest="config", default="zippy.json", metavar="JSON_FILE", help="configuration file [zippy.json]"
)
# run modes
subparsers = parser.add_subparsers(help="Help for subcommand")
## add primers
parser_add = subparsers.add_parser("add", help="Add previously designed primers to database")
parser_add.add_argument(
"primers", default=None, metavar="FASTA/TAB", help="Primers or locations to add to database"
)
parser_add.set_defaults(which="add")
## retrieve
parser_retrieve = subparsers.add_parser("get", help="Get/design primers")
parser_retrieve.add_argument(
"targets",
default=None,
metavar="VCF/BED/Interval/GenePred",
help="File with intervals of interest or CHR:START-END (mandatory for gap-PCR)",
)
parser_retrieve.add_argument(
"--design", dest="design", default=False, action="store_true", help="Design primers if not in database"
)
parser_retrieve.add_argument(
"--gap", dest="gap", default=None, metavar="CHR:START-END", help="Second break point for gap-PCR"
)
parser_retrieve.add_argument(
"--nodeep", dest="deep", default=True, action="store_false", help="Skip deep search for primers"
)
parser_retrieve.add_argument(
"--nostore", dest="store", default=True, action="store_false", help="Do not store result in database"
)
parser_retrieve.add_argument("--outfile", dest="outfile", default="", type=str, help="Output file name")
parser_retrieve.set_defaults(which="get")
## query database for primers by name
parser_query = subparsers.add_parser("query", help="Query database for primers with specified sub-string in name")
parser_query.add_argument(
"subString", default=None, metavar="Sub-string within name", help="String found within primer name"
)
parser_query.set_defaults(which="query")
## batch
parser_batch = subparsers.add_parser("batch", help="Batch design primers for sample list")
parser_batch.add_argument("targets", default=None, metavar="SNPpy result table", help="SNPpy result table")
parser_batch.add_argument(
"--predesign",
dest="predesign",
default=False,
action="store_true",
help="Design primers for all genes in batch",
)
parser_batch.add_argument(
"--nodesign", dest="design", default=True, action="store_false", help="Skip primer design if not in database"
)
parser_batch.add_argument(
"--nodeep", dest="deep", default=True, action="store_false", help="Skip deep search for primers"
)
parser_batch.add_argument(
"--outfile", dest="outfile", default="", type=str, help="Create worksheet PDF, order and robot CSV"
)
parser_batch.set_defaults(which="batch")
## update
parser_update = subparsers.add_parser("update", help="Update status and location of primers")
parser_update.add_argument(
"-l", dest="location", nargs=3, help="Update storage location of primer pair (primerid vessel well)"
)
parser_update.add_argument(
"-t", dest="locationtable", help="Batch update storage locations from TSV (primerid vessel well)"
)
parser_update.add_argument(
"--force", dest="force", default=False, action="store_true", help="Force Location update (resets existing)"
)
parser_update.add_argument("-b", dest="blacklist", type=str, help="Blacklist primer")
parser_update.set_defaults(which="update")
## dump specific datasets from database
parser_dump = subparsers.add_parser("dump", help="Data dump")
parser_dump.add_argument(
"--amplicons", dest="amplicons", default="", type=str, help="Retrieve amplicons of given size (eg. 10-1000)"
)
parser_dump.add_argument(
"--ordersheet",
dest="ordersheet",
default=False,
action="store_true",
help="IDT order sheet (primer pairs with no status marker)",
)
parser_dump.add_argument(
"--locations", dest="locations", default=False, action="store_true", help="Primer locations"
)
parser_dump.add_argument(
"--redundancies",
dest="redundancies",
default=False,
action="store_true",
help="Primers with same sequence and tag",
)
parser_dump.add_argument(
"--table", dest="table", default=False, action="store_true", help="Primer pair table with locations"
)
parser_dump.add_argument("--outfile", dest="outfile", default="", type=str, help="Output file name")
parser_dump.set_defaults(which="dump")
options = parser.parse_args()
# read config and open database
with open(options.config) as conf:
config = json.load(conf, object_hook=ascii_encode_dict)
here = config["primerbed"] if "primerbed" in config.keys() and config["primerbed"] else None
db = PrimerDB(config["database"], dump=here)
if options.which == "add": # read primers and add to database
# import primer pairs
if options.primers.split(".")[-1].startswith("fa"):
pairs = importPrimerPairs(options.primers, config, primer3=False) # import and locate primer pairs
print >> sys.stderr, "Storing Primers..."
db.addPair(
*pairs
) # store pairs in database (assume they are correctly designed as mispriming is ignored and capped at 1000)
sys.stderr.write("Added {} primer pairs to database\n".format(len(pairs)))
# store locations if table
if not options.primers.split(".")[-1].startswith("fa"): # assume table format
locations = importPrimerLocations(options.primers)
print >> sys.stderr, "Setting Primer locations..."
db.addLocations(*locations.items())
sys.stderr.write("Added {} locations for imported primers\n".format(len(locations)))
elif options.which == "dump": # data dump fucntions (`for bulk downloads`)
if options.amplicons:
try:
l = options.amplicons.split("-")
assert len(l) == 2
amplen = map(int, l)
except (AssertionError, ValueError):
raise ConfigError("must give amplicon size to retrieve")
except:
raise
else:
# get amplicons amplen
data, colnames = db.dump("amplicons", size=amplen)
elif options.ordersheet:
data, colnames = db.dump("ordersheet", **config["ordersheet"])
elif options.locations:
data, colnames = db.dump("locations")
elif options.table:
data, colnames = db.dump("table")
elif options.redundancies:
data, colnames = db.getRedundantPrimers()
else:
print >> sys.stderr, "What to dump stranger?"
sys.exit(1)
# format data output
if options.outfile:
dump = Data(data, colnames)
dump.writefile(options.outfile) # sets format by file extension
else:
print "\t".join(colnames)
for row in data:
print "\t".join(map(str, row))
elif options.which == "update": # update location primer pairs are stored
if options.location:
primer, vessel, well = options.location
updateLocation(primer, Location(vessel, well), db, options.force)
if options.locationtable:
updateList = readprimerlocations(options.locationtable)
for item in updateList: # [ Primer, Location ]
updateLocation(item[0], item[1], db, options.force)
if options.blacklist:
print >> sys.stderr, "BLACKLISTED PAIRS: {}".format(",".join(db.blacklist(options.blacklist)))
print >> sys.stderr, "REMOVED ORPHANS: {}".format(",".join(db.removeOrphans()))
elif options.which == "get": # get primers for targets (BED/VCF or interval)
zippyPrimerQuery(
config, options.targets, options.design, options.outfile, db, options.store, options.deep, options.gap
)
elif options.which == "batch":
zippyBatchQuery(config, options.targets, options.design, options.outfile, db, options.predesign, options.deep)
elif options.which == "query":
searchByName(options.subString, db)
# dump amplicons fo given size to stdout
try:
l = options.amplicons.split('-')
assert len(l)==2
amplen = map(int,l)
except (AssertionError, ValueError):
raise ConfigError('must give amplicon size to retrieve')
except:
raise
else:
# get amplicons amplen
data,colnames = db.dump('amplicons',size=amplen)
# format data output
if options.outfile:
dump = Data(data,colnames)
dump.writefile(options.outfile) # sets format by file extension
else:
print '\t'.join(colnames)
for row in data:
print '\t'.join(map(str,row))
elif options.which=='get': # get primers for targets (BED/VCF or interval)
intervals = readTargets(options.targets) # get intervals from file or commandline
ivpairs = {} # found/designed primer pairs (from database or design)
# primer searching
for iv in intervals:
if options.database: # check if inteval covered by primer pair
ivpairs[iv] = db.query(iv, config['tiling']['flank'])
print ivpairs[iv]
if ivpairs[iv]:
