def is_this_name_OK_for_database(variable_name, content, allowed_chars = allowed_chars.replace('.', '')):
if content[0] in digits:
raise ConfigError, "Sorry, '%s' can't start with a digit. Long story. Please specify a sample name\
that starts with an ASCII letter." % variable_name
if len([c for c in content if c not in allowed_chars]):
raise ConfigError, "Well, '%s' parameter contains characters that anvi'o does not like. Please\
limit the characters to ASCII letters, digits, the underscore and dash\
characters ('_', '-')." % variable_name
def is_this_name_OK_for_database(variable_name, content, allowed_chars = allowed_chars.replace('.', '')):
if content[0] in digits:
raise ConfigError, "Sorry, '%s' can't start with a digit. Long story. Please specify a sample name\
that starts with an ASCII letter." % variable_name
if len([c for c in content if c not in allowed_chars]):
raise ConfigError, "Well, '%s' parameter contains characters that anvi'o does not like. Please\
limit the characters to ASCII letters, digits, the underscore and dash\
characters ('_', '-')." % variable_name
def get_HMM_sources_dictionary(source_dirs=[]):
if type(source_dirs) != type([]):
raise ConfigError, "source_dirs parameter must be a list (get_HMM_sources_dictionary)."
sources = {}
allowed_chars_for_proper_sources = allowed_chars.replace(".", "").replace("-", "")
PROPER = (
lambda w: not len([c for c in w if c not in allowed_chars_for_proper_sources])
and len(w) >= 3
and w[0] not in "_0123456789"
)
for source in source_dirs:
if source.endswith("/"):
source = source[:-1]
if not PROPER(os.path.basename(source)):
raise ConfigError, "One of the search database directories ('%s') contains characters in its name\
anvio does not like. Directory names should be at least three characters long\
and must not contain any characters but ASCII letters, digits and\
underscore" % os.path.basename(
source
)
for f in ["reference.txt", "kind.txt", "genes.txt", "genes.hmm.gz"]:
if not os.path.exists(os.path.join(source, f)):
raise ConfigError, "Each search database directory must contain following files:\
'kind.txt', 'reference.txt', 'genes.txt', and 'genes.hmm.gz'. %s does not seem\
to be a proper source." % os.path.basename(
source
)
ref = open(os.path.join(source, "reference.txt")).readlines()[0].strip()
kind = open(os.path.join(source, "kind.txt")).readlines()[0].strip()
if not PROPER(kind):
raise ConfigError, "'kind.txt' defines the kind of search this database offers. This file must contain a single\
word that is at least three characters long, and must not contain any characters but\
ASCII letters, digits, and underscore. Here are some nice examples: 'singlecopy',\
or 'pathogenicity', or 'noras_selection'. But yours is '%s'." % (
kind
)
genes = get_TAB_delimited_file_as_dictionary(
os.path.join(source, "genes.txt"), column_names=["gene", "accession", "hmmsource"]
)
sources[os.path.basename(source)] = {
"ref": ref,
"kind": kind,
"genes": genes.keys(),
"model": os.path.join(source, "genes.hmm.gz"),
}
return sources
def check_sample_id(sample_id):
if sample_id:
if sample_id[0] in digits:
raise ConfigError, "Sample names can't start with digits. Long story. Please specify a sample name\
that starts with an ASCII letter (you can use '-s' parameter for that)."
allowed_chars_for_samples = allowed_chars.replace('-', '').replace('.', '')
if len([c for c in sample_id if c not in allowed_chars_for_samples]):
raise ConfigError, "Sample name ('%s') contains characters that anvio does not like. Please\
limit the characters that make up the project name to ASCII letters,\
digits, and the underscore character ('_')." % sample_id
def check_sample_id(sample_id):
if sample_id:
if sample_id[0] in digits:
raise ConfigError, "Sample names can't start with digits. Long story. Please specify a sample name\
that starts with an ASCII letter (you may want to check '-s' parameter to set\
a sample name if your client permits (otherwise you are going to have to edit\
your input files))."
allowed_chars_for_samples = allowed_chars.replace('-', '').replace('.', '')
if len([c for c in sample_id if c not in allowed_chars_for_samples]):
raise ConfigError, "Sample name ('%s') contains characters that anvio does not like. Please\
limit the characters that make up the project name to ASCII letters,\
digits, and the underscore character ('_')." % sample_id
def check_sample_id(sample_id):
if sample_id:
if sample_id[0] in digits:
raise ConfigError, "Sample names can't start with digits. Long story. Please specify a sample name\
that starts with an ASCII letter (you may want to check '-s' parameter to set\
a sample name if your client permits (otherwise you are going to have to edit\
your input files))."
allowed_chars_for_samples = allowed_chars.replace('-', '').replace('.', '')
if len([c for c in sample_id if c not in allowed_chars_for_samples]):
raise ConfigError, "Sample name ('%s') contains characters that anvio does not like. Please\
limit the characters that make up the project name to ASCII letters,\
digits, and the underscore character ('_')." % sample_id
def get_HMM_sources_dictionary(source_dirs=[]):
if type(source_dirs) != type([]):
raise ConfigError, "source_dirs parameter must be a list (get_HMM_sources_dictionary)."
sources = {}
allowed_chars_for_proper_sources = allowed_chars.replace('.', '').replace(
'-', '')
PROPER = lambda w: not len([c for c in w if c not in allowed_chars_for_proper_sources]) \
and len(w) >= 3 \
and w[0] not in '_0123456789'
for source in source_dirs:
if source.endswith('/'):
source = source[:-1]
if not PROPER(os.path.basename(source)):
raise ConfigError, "One of the search database directories ('%s') contains characters in its name\
anvio does not like. Directory names should be at least three characters long\
and must not contain any characters but ASCII letters, digits and\
underscore" % os.path.basename(source)
for f in ['reference.txt', 'kind.txt', 'genes.txt', 'genes.hmm.gz']:
if not os.path.exists(os.path.join(source, f)):
raise ConfigError, "Each search database directory must contain following files:\
'kind.txt', 'reference.txt', 'genes.txt', and 'genes.hmm.gz'. %s does not seem\
to be a proper source." % os.path.basename(
source)
ref = open(os.path.join(source,
'reference.txt')).readlines()[0].strip()
kind = open(os.path.join(source, 'kind.txt')).readlines()[0].strip()
if not PROPER(kind):
raise ConfigError, "'kind.txt' defines the kind of search this database offers. This file must contain a single\
word that is at least three characters long, and must not contain any characters but\
ASCII letters, digits, and underscore. Here are some nice examples: 'singlecopy',\
or 'pathogenicity', or 'noras_selection'. But yours is '%s'." % (
kind)
genes = get_TAB_delimited_file_as_dictionary(
os.path.join(source, 'genes.txt'),
column_names=['gene', 'accession', 'hmmsource'])
sources[os.path.basename(source)] = {
'ref': ref,
'kind': kind,
'genes': genes.keys(),
'model': os.path.join(source, 'genes.hmm.gz')
}
return sources
