iotbx.bioinformatics
index
/net/chevy/raid1/nat/src/cctbx_project/iotbx/bioinformatics/__init__.py

 
Package Contents
       
alignment_as_hsearch
ebi_wu_blast_xml
ncbi_blast_xml
pubmed
structure
xmlbuild

 
Classes
       
__builtin__.object
SequenceFormat
alignment
clustal_alignment
fasta_alignment
pir_alignment
ebi_pdb_header
generic_alignment_parser
sequential_alignment_parser
generic_sequence
generic_sequence_parser
hhpred_parser
hhalign_parser
hhsearch_parser
homology_search_hit
midline
sequence
fasta_sequence
pdb_sequence
pir_sequence

 
class SequenceFormat(__builtin__.object)
    Bundle of independent parsing data
 
  Methods defined here:
__init__(self, regex, expected, create)

Data descriptors defined here:
__dict__
dictionary for instance variables (if defined)
__weakref__
list of weak references to the object (if defined)

 
class alignment(__builtin__.object)
    Alignment
 
  Methods defined here:
__init__(self, alignments, names, gap='-')
__str__(self)
aligned_positions_count(self)
assign_as_target(self, index)
copy(self, **kwd)
extend(self, sequences)
extra(self)
format(self, width)
identity_count(self)
identity_fraction(self)
length(self)
multiplicity(self)
sequence_strings(self)
shortest_seqlen(self)

Data descriptors defined here:
__dict__
dictionary for instance variables (if defined)
__weakref__
list of weak references to the object (if defined)

 
class clustal_alignment(alignment)
    Clustal alignment
 
 
Method resolution order:
clustal_alignment
alignment
__builtin__.object

Methods defined here:
__init__(self, alignments, names, program='CLUSTAL 2.0.9', gap='-')
__str__(self)
extra(self)
format(self, aln_width, caption_width, middle_line=None)
make_aln_info(self, caption, alignment, aln_width)

Methods inherited from alignment:
aligned_positions_count(self)
assign_as_target(self, index)
copy(self, **kwd)
extend(self, sequences)
identity_count(self)
identity_fraction(self)
length(self)
multiplicity(self)
sequence_strings(self)
shortest_seqlen(self)

Data descriptors inherited from alignment:
__dict__
dictionary for instance variables (if defined)
__weakref__
list of weak references to the object (if defined)

 
class ebi_pdb_header(__builtin__.object)
    EBI-style parsed header
 
  Methods defined here:
__init__(self, identifier, chain)
__str__(self)

Class methods defined here:
parse(cls, data) from __builtin__.type

Data descriptors defined here:
__dict__
dictionary for instance variables (if defined)
__weakref__
list of weak references to the object (if defined)

Data and other attributes defined here:
format = '>PDB:XXXX_X'
regex = <_sre.SRE_Pattern object>

 
class fasta_alignment(alignment)
    Fasta alignment
 
 
Method resolution order:
fasta_alignment
alignment
__builtin__.object

Methods defined here:
__init__(self, alignments, names, descriptions, gap='-')
__str__(self)
extra(self)
format(self, width)

Methods inherited from alignment:
aligned_positions_count(self)
assign_as_target(self, index)
copy(self, **kwd)
extend(self, sequences)
identity_count(self)
identity_fraction(self)
length(self)
multiplicity(self)
sequence_strings(self)
shortest_seqlen(self)

Data descriptors inherited from alignment:
__dict__
dictionary for instance variables (if defined)
__weakref__
list of weak references to the object (if defined)

 
class fasta_sequence(sequence)
    Fasta sequence
 
 
Method resolution order:
fasta_sequence
sequence
__builtin__.object

Methods defined here:
__init__(self, sequence, name='', description='')
format(self, width)

Methods inherited from sequence:
__eq__(self, other)
__len__(self)
__ne__(self, other)
__str__(self)

Data descriptors inherited from sequence:
__dict__
dictionary for instance variables (if defined)
__weakref__
list of weak references to the object (if defined)

 
class generic_alignment_parser(__builtin__.object)
    General purpose alignment parser
 
  Methods defined here:
__call__(self, text)
assess_parsing_results(self, data_dict, text)
extract(self, text)
fail(self, text)

Data descriptors defined here:
__dict__
dictionary for instance variables (if defined)
__weakref__
list of weak references to the object (if defined)

 
class generic_sequence(__builtin__.object)
    Sequence
 
  Methods defined here:
__init__(self, header, body)
__len__(self)
__str__(self)
format(self, width)
reinterpret_header(self, header)

Data descriptors defined here:
__dict__
dictionary for instance variables (if defined)
__weakref__
list of weak references to the object (if defined)

 
class generic_sequence_parser(__builtin__.object)
    General-purpose sequence parser
 
  Methods defined here:
__call__(self, text, **kwargs)
__init__(self, regex, type)
parse(self, text, **kwargs)

Data descriptors defined here:
__dict__
dictionary for instance variables (if defined)
__weakref__
list of weak references to the object (if defined)

 
class hhalign_parser(hhpred_parser)
    Specific for hhalign output
 
 
Method resolution order:
hhalign_parser
hhpred_parser
__builtin__.object

Methods defined here:
add_match_to_hit_header_results(self, match)
alignment(self)
merge_and_process_block_hits(self, matches)
setup_data_arrays(self)

Data and other attributes defined here:
BLOCKS = <_sre.SRE_Pattern object>
HITS = <_sre.SRE_Pattern object>

Methods inherited from hhpred_parser:
__init__(self, output)
merge_sequence_numbers(self, starts, ends, others)
process_blocks(self, blocks)
process_header(self, header)
process_hits(self, hits)

Data descriptors inherited from hhpred_parser:
__dict__
dictionary for instance variables (if defined)
__weakref__
list of weak references to the object (if defined)

Data and other attributes inherited from hhpred_parser:
HEADER = <_sre.SRE_Pattern object>
SPLIT = <_sre.SRE_Pattern object>

 
class hhpred_parser(__builtin__.object)
    Parses .hhr files from HHPred
 
  Methods defined here:
__init__(self, output)
merge_sequence_numbers(self, starts, ends, others)
process_blocks(self, blocks)
process_header(self, header)
process_hits(self, hits)

Data descriptors defined here:
__dict__
dictionary for instance variables (if defined)
__weakref__
list of weak references to the object (if defined)

Data and other attributes defined here:
HEADER = <_sre.SRE_Pattern object>
SPLIT = <_sre.SRE_Pattern object>

 
class hhsearch_parser(hhpred_parser)
    Specific for hhsearch output
 
 
Method resolution order:
hhsearch_parser
hhpred_parser
__builtin__.object

Methods defined here:
add_match_to_hit_header_results(self, match)
hits(self)
merge_and_process_block_hits(self, matches)
restrict(self, max_count)
setup_data_arrays(self)

Data and other attributes defined here:
BLOCKS = <_sre.SRE_Pattern object>
HITS = <_sre.SRE_Pattern object>

Methods inherited from hhpred_parser:
__init__(self, output)
merge_sequence_numbers(self, starts, ends, others)
process_blocks(self, blocks)
process_header(self, header)
process_hits(self, hits)

Data descriptors inherited from hhpred_parser:
__dict__
dictionary for instance variables (if defined)
__weakref__
list of weak references to the object (if defined)

Data and other attributes inherited from hhpred_parser:
HEADER = <_sre.SRE_Pattern object>
SPLIT = <_sre.SRE_Pattern object>

 
class homology_search_hit(__builtin__.object)
    A hit from a homology search
 
  Methods defined here:
__init__(self, identifier, chain, annotation, alignment)

Data descriptors defined here:
__dict__
dictionary for instance variables (if defined)
__weakref__
list of weak references to the object (if defined)

 
class midline(__builtin__.object)
    Alignment midline
 
  Methods defined here:
__init__(self, identical='*', conserved=':', semi='.', differ=' ')
compare(self, alignments, gap='-')
conservation_code(self, residues)

Data descriptors defined here:
__dict__
dictionary for instance variables (if defined)
__weakref__
list of weak references to the object (if defined)

 
class pdb_sequence(sequence)
    PDB sequence
 
 
Method resolution order:
pdb_sequence
sequence
__builtin__.object

Methods defined here:
__init__(self, sequence, name='', chain='')
format(self, width)

Methods inherited from sequence:
__eq__(self, other)
__len__(self)
__ne__(self, other)
__str__(self)

Data descriptors inherited from sequence:
__dict__
dictionary for instance variables (if defined)
__weakref__
list of weak references to the object (if defined)

 
class pir_alignment(alignment)
    Pir alignment
 
 
Method resolution order:
pir_alignment
alignment
__builtin__.object

Methods defined here:
__init__(self, alignments, names, types, descriptions, gap='-')
__str__(self)
extra(self)
format(self, width)

Methods inherited from alignment:
aligned_positions_count(self)
assign_as_target(self, index)
copy(self, **kwd)
extend(self, sequences)
identity_count(self)
identity_fraction(self)
length(self)
multiplicity(self)
sequence_strings(self)
shortest_seqlen(self)

Data descriptors inherited from alignment:
__dict__
dictionary for instance variables (if defined)
__weakref__
list of weak references to the object (if defined)

 
class pir_sequence(sequence)
    Pir sequence
 
 
Method resolution order:
pir_sequence
sequence
__builtin__.object

Methods defined here:
__init__(self, sequence, name='', type='P1', description='')
format(self, width)

Methods inherited from sequence:
__eq__(self, other)
__len__(self)
__ne__(self, other)
__str__(self)

Data descriptors inherited from sequence:
__dict__
dictionary for instance variables (if defined)
__weakref__
list of weak references to the object (if defined)

 
class sequence(__builtin__.object)
    Sequence
 
  Methods defined here:
__eq__(self, other)
__init__(self, sequence, name='')
__len__(self)
__ne__(self, other)
__str__(self)
format(self, width)

Data descriptors defined here:
__dict__
dictionary for instance variables (if defined)
__weakref__
list of weak references to the object (if defined)

 
class sequential_alignment_parser(generic_alignment_parser)
    Specific for sequential format alignments
 
 
Method resolution order:
sequential_alignment_parser
generic_alignment_parser
__builtin__.object

Methods defined here:
__init__(self, regex, type)
parse(self, text)

Methods inherited from generic_alignment_parser:
__call__(self, text)
assess_parsing_results(self, data_dict, text)
extract(self, text)
fail(self, text)

Data descriptors inherited from generic_alignment_parser:
__dict__
dictionary for instance variables (if defined)
__weakref__
list of weak references to the object (if defined)

 
Functions
       
alignment_parser_for(file_name)
alignment_parser_for_extension(extension)
any_alignment_file(file_name)
any_alignment_string(data, extension=None)
any_hh_file(file_name)
any_sequence_format(file_name, assign_name_if_not_defined=False)
# XXX test needed
check_alignments_are_valid(alignments)
clustal_alignment_parse(text)
Specific for Clustal alignments
composition_from_sequence(sequence)
composition_from_sequence_file(file_name, log=None)
hhalign_alignment_parse(text)
known_alignment_formats()
known_sequence_formats()
merge_sequence_files(file_names, output_file, sequences=(), include_non_compliant=False, call_back_on_error=None, force_new_file=False)
parse_sequence(data)
parse_sequence_str(data, format)
Generic purpose sequence header parser
partition_string(data, regex)
Partition sequence files
sequence_parser_for(file_name)
sequence_parser_for_extension(extension)
tf_sequence_parse(text)
Tom's format sequence parser
wrap(text, width)
# Wrap lines that are longer than 'width'

 
Data
        CLUSTAL_BODY = <_sre.SRE_Pattern object>
CLUSTAL_HEADER = <_sre.SRE_Pattern object>
CLUSTAL_MIDLINE = <_sre.SRE_Pattern object>
ali_alignment_parse = <iotbx.bioinformatics.sequential_alignment_parser object>
dbfetch_sequence_parse = <iotbx.bioinformatics.generic_sequence_parser object>
division = _Feature((2, 2, 0, 'alpha', 2), (3, 0, 0, 'alpha', 0), 8192)
fasta_alignment_parse = <iotbx.bioinformatics.sequential_alignment_parser object>
fasta_sequence_parse = <iotbx.bioinformatics.generic_sequence_parser object>
lineseparated_sequence_parse = <iotbx.bioinformatics.generic_sequence_parser object>
pir_alignment_parse = <iotbx.bioinformatics.sequential_alignment_parser object>
pir_sequence_parse = <iotbx.bioinformatics.generic_sequence_parser object>
seq_sequence_parse = <iotbx.bioinformatics.generic_sequence_parser object>
st_separated_fasta = <iotbx.bioinformatics.SequenceFormat object>
tolerant_pir_sequence_parse = <iotbx.bioinformatics.generic_sequence_parser object>