Package Bio :: Package SearchIO :: Package ExonerateIO :: Module exonerate_text

Module exonerate_text

Bio.SearchIO parser for Exonerate plain text output format.

Classes

ExonerateTextParser
Parser for Exonerate plain text output.

ExonerateTextIndexer
Indexer class for Exonerate plain text.

Functions

_flip_codons(codon_seq, target_seq)
Flips the codon characters from one seq to another.

source code

_get_block_coords(parsed_seq, row_dict, has_ner=False)
Returns a list of start, end coordinates for each given block in the sequence.

source code

_get_inter_coords(coords, strand=1)
From the given pairs of coordinates, returns a list of pairs covering the intervening ranges.

source code

_stitch_rows(raw_rows)
Stitches together the parsed alignment rows and returns them in a list.

source code

_get_row_dict(row_len)
Returns a dictionary of row indices for parsing alignment blocks.

source code

_get_blocks(rows, coords, idx)
Returns a list of dictionaries of sequences split by the coordinates.

source code

_get_scodon_moves(tmp_seq_blocks)
Returns a dictionary of split codon locations relative to each...

source code

_clean_blocks(tmp_seq_blocks)
Removes curly braces (split codon markers) from the given sequences.

source code

_comp_intron_lens(seq_type, inter_blocks, raw_inter_lens)
Returns the length of introns between fragments.

source code

_comp_coords(hsp, seq_type, inter_lens)
Fill the block coordinates of the given hsp dictionary.

source code

_comp_split_codons(hsp, seq_type, scodon_moves)
Computes the positions of split codons and puts the values in the given HSP dictionary.

source code

Variables

_RE_ALN_ROW = re.compile(r'\s*\d+\s+: (.*) :\s+\d+')

_RE_EXON = re.compile(r'[atgc ]{2,}?(?:(?:[<>]+ \w+ Intron \d+...

_RE_EXON_LEN = re.compile(r'(?:(\d+) bp // (\d+) bp)|(?:(\d+) ...

_RE_NER = re.compile(r'--<\s+\d+\s+>--')

_RE_NER_LEN = re.compile(r'--<\s+(\d+)\s+>--')

_RE_SCODON_START = re.compile(r'\{(\w{1,2})\}$')

_RE_SCODON_END = re.compile(r'^\{(\w{1,2})\}')

Function Details

Returns a dictionary of split codon locations relative to each
fragment's end

Variables Details

Value:

re.compile(r'[atgc ]{2,}?(?:(?:[<>]+ \w+ Intron \d+ [<>]+)|(?:\.+))[at
gc ]{2,}?')

Value:

re.compile(r'(?:(\d+) bp // (\d+) bp)|(?:(\d+) bp)')