minorg.functions module

minorg.functions.N_trailing_newlines(fname)

minorg.functions.adjusted_feature_ranges(seq, seq_range, feature_ranges, strand='+', sort=True, **kwargs)

returns feature ranges, adjusted for strand and gaps in alignment 0-indexed, start inclusive, end exclusive

minorg.functions.adjusted_pos(seq, pos, gap_char='-')

Return 0-indexed position adjusted for gaps in alignment

Parameters

• seq (str or Biopython Seq.Seq) – gapped sequence

• pos (int) – ungapped position

• gap_char (str) – gap character

Returns

pos adjusted for gaps in sequence

Return type

int

minorg.functions.adjusted_ranges(seq, *ranges, subtract_gaps=True, gap_char='-')

minorg.functions.append(fname, string, insert_newline_if_absent=True, insert_trailing_newline=True)

minorg.functions.assign_alias(val, mk_name=<function <lambda>>, start_index=1)

minorg.functions.cat_files(fnames, fout, remove=False)

minorg.functions.convert_range(ranges, index_in=0, index_out=1, start_incl_in=True, start_incl_out=True, end_incl_in=False, end_incl_out=True)

Convert range(s) from one indexing system to another.

Default values converts from 0-index [start, end) ranges to 1-index [start, end] ranges.

Parameters

• ranges (list or tuple) – range(s) to convert. Ranges may nested and discontiuous (e.g. [(1, 3), (5, 8)]) or single level (e.g. (1, 3)).

• index_in (int) – index of input range(s)

• index_out (int) – index of output range(s)

• start_incl_in (bool) – whether input range(s) is/are start-inclusive

• start_incl_out (bool) – whether output range(s) is/are start-inclusive

• end_incl_in (bool) – whether input range(s) is/are end_inclusive

• end_incl_out (bool) – whether output range(s) is/are end_inclusive

Returns

In same structure as input.

Return type

tuple or list

minorg.functions.empty_file(fname)

minorg.functions.file_ends_with_newline(fname)

minorg.functions.fill_template(template, **kwargs)

minorg.functions.gc_content(seq)

minorg.functions.get_count_dict(iterable)

minorg.functions.get_dat(fname)

minorg.functions.imap_progress(f, args, threads=1, overwrite=True, overwrite_last=True, return_output=True, msg=<function <lambda>>, lvl=0, quiet=False)

minorg.functions.is_empty_file(fname)

minorg.functions.is_range(r)

minorg.functions.last_line(fname)

minorg.functions.make_custom_get(header, parse_num=True)

minorg.functions.make_local_print(quiet, printf=<built-in function print>)

minorg.functions.non_string_iter(val)

minorg.functions.num_lines(fname)

minorg.functions.parse_get_data(fname, delim=None, detect=True)

minorg.functions.pos_to_ranges(pos) → list

Convert an iterable of integer positions to range(s). E.g. pos_to_range({1, 2, 6, 7, 8, 9}) –> [(1, 3), (6, 10)]

Parameters

pos (iterable) – iterable of integer positions

Returns

Of 0-index, start-inclusive, end-exclusive ranges

Return type

list

minorg.functions.prepend(fname, string, insert_newline=False)

minorg.functions.prepend_line(fname, string)

minorg.functions.ranges_intersect(r1, r2)

minorg.functions.ranges_subtract(r1, r2)

Subtract second range(s) from first range(s). Ranges should only be of integer values.

Ranges are converted to sets of integer values so set operations can be applied. Resultant set is then converted back to a list of range(s).

Parameters

• r1 (list) – range(s) to be subtracted from. Range(s) may nested and discontiuous (e.g. [(1, 3), (5, 8)]) or single level (e.g. (1, 3)).

• r2 (list) – range(s) to subtract from r1. Range(s) may nested and discontiuous (e.g. [(1, 3), (5, 8)]) or single level (e.g. (1, 3)).

Returns

Of range(s)

Return type

list

minorg.functions.ranges_to_pos(r)

Convert integer start-inclusive & end-exclusive range(s) to set of integer values in the range.

Parameters

r (tuple or list) – range(s) to convert. Ranges may nested and discontiuous (e.g. [(1, 3), (5, 8)]) or single level (e.g. (1, 3)).

Returns

Of integer values within range

Return type

set

minorg.functions.ranges_union(ranges)

minorg.functions.set_overlap(a, b)

minorg.functions.split_list(val)

minorg.functions.split_none(iterable)

minorg.functions.split_str(val)

minorg.functions.splitlines(fname, ignore_empty_lines=True)

minorg.functions.tsv_entries_as_dict(fname, header, f_filter=<function <lambda>>, fields=None)

minorg.functions.within(a, b) → bool

Return whether range a is within or equal to range b.

Parameters

• a (tuple or list) – single-level range (e.g. (4, 6))

• b (tuple or list) – single-level range (e.g. (2, 7))

Returns

Whether range a is within or equal to range b.

Return type

bool

minorg.functions.within_any(a, ranges) → bool

Return whether range a is within at least one range in ranges.

Parameters

• a (tuple or list) – single-level range (e.g (4, 6))

• ranges (tuple or list) – list of ranges (e.g. [(-1, 1), (2, 7), (5, 12)])

Returns

Whether range a is within any range in ranges

Return type

bool

minorg.functions.write_table(data, fout, header=[], sep='\t')

minorg.functions.write_tsv(fname, dat)