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ecopcr: fixed and improved the options to keep nuclotides around the

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This commit is contained in:
Celine Mercier
2019-12-26 20:45:54 +01:00
parent 694d1934a8
commit 6c018b403c
5 changed files with 28 additions and 16 deletions
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14
python/obitools3/commands/ecopcr.pyx
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@@ -107,14 +107,20 @@ def addOptions(parser):
help="Defines the method used for estimating the Tm (melting temperature) between the primers and their corresponding "
"target sequences. SANTALUCIA: 1, or OWCZARZY: 2. Default: 1.")
group.add_argument('--keep-primers', '-p',
action="store_true",
dest="ecopcr:keep-primers",
default=False,
help="Whether to keep the primers attached to the output sequences (default: the primers are cut out).")
group.add_argument('--keep-nucs', '-D',
action="store",
dest="ecopcr:keep-nucs",
metavar="<INTEGER>",
metavar="<N>",
type=int,
default=0,
help="Keeps the specified number of nucleotides on each side of the in silico amplified sequences, "
"(already including the amplified DNA fragment plus the two target sequences of the primers).")
help="Keeps N nucleotides on each side of the in silico amplified sequences, "
"not including the primers (implying that primers are automatically kept if N > 0).")
group.add_argument('--kingdom-mode', '-k',
action="store_true",
@@ -185,7 +191,7 @@ def run(config):
config['ecopcr']['min-length'], config['ecopcr']['max-length'], \
restrict_to_taxids_p, ignore_taxids_p, \
config['ecopcr']['circular'], config['ecopcr']['salt-concentration'], config['ecopcr']['salt-correction-method'], \
config['ecopcr']['keep-nucs'], config['ecopcr']['kingdom-mode']) < 0:
config['ecopcr']['keep-nucs'], config['ecopcr']['keep-primers'], config['ecopcr']['kingdom-mode']) < 0:
raise Exception("Error running ecopcr")
# Save command config in DMS comments