def test_init_raise(self):
tests = [('a', check_choice(['b', 'c'])),
(9, check_choice(range(8))),
(1, check_range(2, 6))]
for v, f in tests:
with self.assertRaises(ValueError):
OptionParam('-i', value=v, action=f)
def test_check_choice(self):
checker = check_choice(range(3))
val = 1
self.assertEqual(val, checker(val))
val = 5
with self.assertRaises(ValueError):
checker(val)
OptionParam('-i',
'query',
help='FASTA/Genbank input file (default reads from stdin).'),
OptionParam('-a', help='File to store protein translations.'),
OptionParam('-d', help='File to store nuc sequence of predicted gene.'),
OptionParam(
'-s',
help='Write all potential genes (with scores) to the selected file.'),
OptionParam('-t',
help=('Write a training file (if none exists); '
'otherwise, read and use the specified training file.')),
OptionParam('-o', 'output',
help='output file (default writes to stdout).'),
OptionParam('-f',
'fmt',
action=check_choice(('gbk', 'gff', 'sco')),
help='output format (gbk, gff, or sco). Default is gbk.'),
OptionParam('-g', help='translation table to use (default 11).'),
OptionParam(
'-m',
help=
'Treat runs of N as masked sequence; do not build genes across them.'),
OptionParam('-p',
'mode',
action=check_choice(('single', 'meta')),
help='Select procedure (single or meta). Default is single.'),
OptionParam('-c',
help='Closed ends. Do not allow genes to run off edges.'),
OptionParam('-v', help='Print version number and exit.'),
OptionParam('-q', help='Run quietly (suppress normal stderr output).'),
OptionParam('-h', help='Print help menu and exit.'),
help=('Path to query input file in FASTA or FASTQ format '
'(may be gzip compressed).'))]
makedb_params = [
OptionParam('--threads', '-p', name='cpus'),
OptionParam('--in', name='fasta',
help='protein reference database file in FASTA format (may be gzip compressed)'),
OptionParam('--db', '-d',
help='DIAMOND database file.'),
OptionParam('--block-size',
help='Block size in billions of sequence letters to be processed at a time.')]
view_params = [
OptionParam('--outfmt', name='fmt', action=check_choice(('tab', 'sam')),
help=('Format of output file. (tab = BLAST tabular format;'
'sam = SAM format)')),
OptionParam('--daa', '-a',
help='Path to DAA file.'),
OptionParam('--out', '-o',
help='Path to output file.'),
OptionParam('--compress', action=check_choice((0, 1)),
help='Compression for output file (0=none, 1=gzip).')]
def run_blast(query, daa, aligner='blastp', **kwargs):
'''Search query sequences against the database.
Parameters
----------
from ..parsers.embl import _parse_records
params = [
OptionParam("-i", "query", help="FASTA/Genbank input file (default reads from stdin)."),
OptionParam("-a", help="File to store protein translations."),
OptionParam("-d", help="File to store nuc sequence of predicted gene."),
OptionParam("-s", help="Write all potential genes (with scores) to the selected file."),
OptionParam(
"-t", help=("Write a training file (if none exists); " "otherwise, read and use the specified training file.")
),
OptionParam("-o", "output", help="output file (default writes to stdout)."),
OptionParam(
"-f",
"fmt",
action=check_choice(("gbk", "gff", "sco")),
help="output format (gbk, gff, or sco). Default is gbk.",
),
OptionParam("-g", help="translation table to use (default 11)."),
OptionParam("-m", help="Treat runs of N as masked sequence; do not build genes across them."),
OptionParam(
"-p",
"mode",
action=check_choice(("single", "meta")),
help="Select procedure (single or meta). Default is single.",
),
OptionParam("-c", help="Closed ends. Do not allow genes to run off edges."),
OptionParam("-v", help="Print version number and exit."),
OptionParam("-q", help="Run quietly (suppress normal stderr output)."),
OptionParam("-h", help="Print help menu and exit."),
OptionParam("-n", help="Bypass Shine-Dalgarno trainer and force a full motif scan."),
def test_check_choice_iter(self):
checker = check_choice((i for i in 'a'))
val = 'a'
self.assertEqual(val, checker(val))
val = 'a'
self.assertEqual(val, checker(val))
name='fasta',
help=
'protein reference database file in FASTA format (may be gzip compressed)'
),
OptionParam('--db', '-d', help='DIAMOND database file.'),
OptionParam(
'--block-size',
help=
'Block size in billions of sequence letters to be processed at a time.'
)
]
view_params = [
OptionParam('--outfmt',
name='fmt',
action=check_choice(('tab', 'sam')),
help=('Format of output file. (tab = BLAST tabular format;'
'sam = SAM format)')),
OptionParam('--daa', '-a', help='Path to DAA file.'),
OptionParam('--out', '-o', help='Path to output file.'),
OptionParam('--compress',
action=check_choice((0, 1)),
help='Compression for output file (0=none, 1=gzip).')
]
def run_blast(query, daa, aligner='blastp', **kwargs):
'''Search query sequences against the database.
Parameters
----------
