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

source code

Bio.SearchIO parser for Exonerate plain text output format.

Classes [hide private]
  ExonerateTextParser
Parser for Exonerate plain text output.
  ExonerateTextIndexer
Indexer class for Exonerate plain text.
Functions [hide private]
 
_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.
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_get_row_dict(row_len)
Returns a dictionary of row indices for parsing alignment blocks.
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_get_blocks(rows, coords, idx)
Returns a list of dictionaries of sequences split by the coordinates.
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_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.
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_comp_intron_lens(seq_type, inter_blocks, raw_inter_lens)
Returns the length of introns between fragments.
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_comp_coords(hsp, seq_type, inter_lens)
Fill the block coordinates of the given hsp dictionary.
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_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 [hide private]
  _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})\}')
  __package__ = 'Bio.SearchIO.ExonerateIO'
Function Details [hide private]

_get_scodon_moves(tmp_seq_blocks)

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


Variables Details [hide private]

_RE_EXON

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

_RE_EXON_LEN

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