Lib Filter

Contain functions to filter information from the DB.

idpconfgen.libs.libfilter.aligndb(db, exact=False)

Aligns IDPConfGen DB.

idpconfgen.libs.libfilter.make_any_overlap_regex(range_)

Make an overlap regex.

idpconfgen.libs.libfilter.make_helix_overlap_regex(range_)

Make an overlap regex.

idpconfgen.libs.libfilter.make_loop_overlap_regex(range_)

Make an overlap regex.

idpconfgen.libs.libfilter.make_overlap_regex(s, range_)

Make an overlap regex.

idpconfgen.libs.libfilter.make_ranges(regex_string, rang_rex=re.compile('(\\{\\d+\\,\\d+\\}|\\{\\d+\\}|\\{\\d+\\,\\}|\\{\\,\\d+\\})'), char_rex=re.compile('((\\w)\\{|\\[([\\w ]+)\\]\\{)'), max_range=30)

Define a set of ranges and characters from regex_string.

Examples

>>> make_range('L{1}H{1,2}')
[range(1, 2), range(1, 3)], ['L', 'H']

>>> make_range('L{1,}H{,2}')
[range(1, None), range(1, 3)], ['L', 'H']

idpconfgen.libs.libfilter.make_regex_combinations(ranges, chars, pre=None, suf=None)

Make combinations of regexes from ranges and chars.

This function is not a general abstraction. Is instead a partial abstraction within the problem of IDPConfGen.

Parameters:

• ranges (list of range objects) – Ranges where to start and stop searching in the regex. Ranges should follow regex conventions, usually 1-indexed and stop inclusive.

• chars (list of 1 letter chars) – The chars that will be searched in ranges.

• pre, suf (str) – Strings to add as prefix and suffix of the generates ranges.

idpconfgen.libs.libfilter.make_regex_combinations_from_ranges(regex_string, **kwargs)

.

idpconfgen.libs.libfilter.make_strand_overlap_regex(range_)

Make an overlap regex.

idpconfgen.libs.libfilter.regex_forward_no_overlap(sequence, regex)

Search for regex forward without overlap.

Examples

r’L’ r’L{2}’ r’L{1,3}’

In the first example, returns all indexes of single char L without

overlap.

On the second example, returns all indexes of entire ‘LL’ sequences

without overlap. So, ‘LLL’ returns only slice(0, 2).

3. returns all sequences with ‘LLL’ without overlap, if a terminal ‘LL’

   is found, returns that. Same for ‘L’ if found at the end.

Using expressions such as r’(?=(L))’ give not correct results. Use regex_forward_with_overlap instead.

idpconfgen.libs.libfilter.regex_forward_with_overlap(sequence, regex)

Find matches for regex in sequence of chars.

Considers regex defines overlap.

Accepts only regex expressions with overlap, for example:

r’(?=(L{3}))’

Returns:

list of slices – Where slice.start and slice.stop follow Python conventions.

idpconfgen.libs.libfilter.regex_has_overlap(regex_string, overlap_rex=re.compile('\\(\\?\\=\\(.+\\)'))

Find if a regex_string defines overlap.

Parameters:

• regex_string (str) – The regex string.

• overlap_fmt (str) – The regex to find overlap in regex_string.

Returns:

bool

idpconfgen.libs.libfilter.regex_range(sequence, regex_string, ncores=1)

Find slices of sequence where regex_string applies.

Searches forward and backwards by means of exploring ranges as individual regexes.

idpconfgen.libs.libfilter.regex_search(sequence, regex_string, rex_range=re.compile('(\\{\\d+\\,\\d+\\}|\\{\\d+\\}|\\{\\d+\\,\\}|\\{\\,\\d+\\})'), **kwargs)

Search for regex in sequence.

Parameters:

• sequence (str) – The sequence where to apply the regex.

• regex_string (str) – The regex to search for.

• regex_range (compiled regex) – A regex to apply in regex_string to identify if regex_string refers to a range.

Returns:

list of slices