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| Clone Mass | Clones in CloneSet | Parameter Count | Clone Similarity | Syntax Category [Sequence Length] |
|---|---|---|---|---|
| 89 | 2 | 0 | 1.000 | compound_stmt |
| Clone Abstraction | Parameter Bindings |
| Clone Instance (Click to see clone) | Line Count | Source Line | Source File |
|---|---|---|---|
| 1 | 89 | 53 | Bio/ExPASy/Prosite.py |
| 2 | 89 | 98 | Bio/Prosite/__init__.py |
| ||||
class Record:
"""Holds information from a Prosite record.
Members:
name ID of the record. e.g. ADH_ZINC
type Type of entry. e.g. PATTERN, MATRIX, or RULE
accession e.g. PS00387
created Date the entry was created. (MMM-YYYY)
data_update Date the 'primary' data was last updated.
info_update Date data other than 'primary' data was last updated.
pdoc ID of the PROSITE DOCumentation.
description Free-format description.
pattern The PROSITE pattern. See docs.
matrix List of strings that describes a matrix entry.
rules List of rule definitions (from RU lines). (strings)
prorules List of prorules (from PR lines). (strings)
NUMERICAL RESULTS
nr_sp_release SwissProt release.
nr_sp_seqs Number of seqs in that release of Swiss-Prot. (int)
nr_total Number of hits in Swiss-Prot. tuple of (hits, seqs)
nr_positive True positives. tuple of (hits, seqs)
nr_unknown Could be positives. tuple of (hits, seqs)
nr_false_pos False positives. tuple of (hits, seqs)
nr_false_neg False negatives. (int)
nr_partial False negatives, because they are fragments. (int)
COMMENTS
cc_taxo_range Taxonomic range. See docs for format
cc_max_repeat Maximum number of repetitions in a protein
cc_site Interesting site. list of tuples (pattern pos, desc.)
cc_skip_flag Can this entry be ignored?
cc_matrix_type
cc_scaling_db
cc_author
cc_ft_key
cc_ft_desc
cc_version version number (introduced in release 19.0)
DATA BANK REFERENCES - The following are all
lists of tuples (swiss-prot accession,
swiss-prot name)
dr_positive
dr_false_neg
dr_false_pos
dr_potential Potential hits, but fingerprint region not yet available.
dr_unknown Could possibly belong
pdb_structs List of PDB entries.
"""
def __init__(self):
self.name = ""
self.type = ""
self.accession = ""
self.created = ""
self.data_update = ""
self.info_update = ""
self.pdoc = ""
self.description = ""
self.pattern = ""
self.matrix = [ ]
self.rules = [ ]
self.prorules = [ ]
self.postprocessing = [ ]
self.nr_sp_release = ""
self.nr_sp_seqs = ""
self.nr_total = (None,None)
self.nr_positive = (None,None)
self.nr_unknown = (None,None)
self.nr_false_pos = (None,None)
self.nr_false_neg = None
self.nr_partial = None
self.cc_taxo_range = ""
self.cc_max_repeat = ""
self.cc_site = [ ]
self.cc_skip_flag = ""
self.dr_positive = [ ]
self.dr_false_neg = [ ]
self.dr_false_pos = [ ]
self.dr_potential = [ ]
self.dr_unknown = [ ]
self.pdb_structs = [ ]
# Everything below are private functions
|
| ||||
class Record:
"""Holds information from a Prosite record.
Members:
name ID of the record. e.g. ADH_ZINC
type Type of entry. e.g. PATTERN, MATRIX, or RULE
accession e.g. PS00387
created Date the entry was created. (MMM-YYYY)
data_update Date the 'primary' data was last updated.
info_update Date data other than 'primary' data was last updated.
pdoc ID of the PROSITE DOCumentation.
description Free-format description.
pattern The PROSITE pattern. See docs.
matrix List of strings that describes a matrix entry.
rules List of rule definitions (from RU lines). (strings)
prorules List of prorules (from PR lines). (strings)
NUMERICAL RESULTS
nr_sp_release SwissProt release.
nr_sp_seqs Number of seqs in that release of Swiss-Prot. (int)
nr_total Number of hits in Swiss-Prot. tuple of (hits, seqs)
nr_positive True positives. tuple of (hits, seqs)
nr_unknown Could be positives. tuple of (hits, seqs)
nr_false_pos False positives. tuple of (hits, seqs)
nr_false_neg False negatives. (int)
nr_partial False negatives, because they are fragments. (int)
COMMENTS
cc_taxo_range Taxonomic range. See docs for format
cc_max_repeat Maximum number of repetitions in a protein
cc_site Interesting site. list of tuples (pattern pos, desc.)
cc_skip_flag Can this entry be ignored?
cc_matrix_type
cc_scaling_db
cc_author
cc_ft_key
cc_ft_desc
cc_version version number (introduced in release 19.0)
DATA BANK REFERENCES - The following are all
lists of tuples (swiss-prot accession,
swiss-prot name)
dr_positive
dr_false_neg
dr_false_pos
dr_potential Potential hits, but fingerprint region not yet available.
dr_unknown Could possibly belong
pdb_structs List of PDB entries.
"""
def __init__(self):
self.name = ""
self.type = ""
self.accession = ""
self.created = ""
self.data_update = ""
self.info_update = ""
self.pdoc = ""
self.description = ""
self.pattern = ""
self.matrix = [ ]
self.rules = [ ]
self.prorules = [ ]
self.postprocessing = [ ]
self.nr_sp_release = ""
self.nr_sp_seqs = ""
self.nr_total = (None,None)
self.nr_positive = (None,None)
self.nr_unknown = (None,None)
self.nr_false_pos = (None,None)
self.nr_false_neg = None
self.nr_partial = None
self.cc_taxo_range = ""
self.cc_max_repeat = ""
self.cc_site = [ ]
self.cc_skip_flag = ""
self.dr_positive = [ ]
self.dr_false_neg = [ ]
self.dr_false_pos = [ ]
self.dr_potential = [ ]
self.dr_unknown = [ ]
self.pdb_structs = [ ]
|
| |||
class Record:
"""Holds information from a Prosite record.
Members:
name ID of the record. e.g. ADH_ZINC
type Type of entry. e.g. PATTERN, MATRIX, or RULE
accession e.g. PS00387
created Date the entry was created. (MMM-YYYY)
data_update Date the 'primary' data was last updated.
info_update Date data other than 'primary' data was last updated.
pdoc ID of the PROSITE DOCumentation.
description Free-format description.
pattern The PROSITE pattern. See docs.
matrix List of strings that describes a matrix entry.
rules List of rule definitions (from RU lines). (strings)
prorules List of prorules (from PR lines). (strings)
NUMERICAL RESULTS
nr_sp_release SwissProt release.
nr_sp_seqs Number of seqs in that release of Swiss-Prot. (int)
nr_total Number of hits in Swiss-Prot. tuple of (hits, seqs)
nr_positive True positives. tuple of (hits, seqs)
nr_unknown Could be positives. tuple of (hits, seqs)
nr_false_pos False positives. tuple of (hits, seqs)
nr_false_neg False negatives. (int)
nr_partial False negatives, because they are fragments. (int)
COMMENTS
cc_taxo_range Taxonomic range. See docs for format
cc_max_repeat Maximum number of repetitions in a protein
cc_site Interesting site. list of tuples (pattern pos, desc.)
cc_skip_flag Can this entry be ignored?
cc_matrix_type
cc_scaling_db
cc_author
cc_ft_key
cc_ft_desc
cc_version version number (introduced in release 19.0)
DATA BANK REFERENCES - The following are all
lists of tuples (swiss-prot accession,
swiss-prot name)
dr_positive
dr_false_neg
dr_false_pos
dr_potential Potential hits, but fingerprint region not yet available.
dr_unknown Could possibly belong
pdb_structs List of PDB entries.
"""
def __init__(self):
self.name = ""
self.type = ""
self.accession = ""
self.created = ""
self.data_update = ""
self.info_update = ""
self.pdoc = ""
self.description = ""
self.pattern = ""
self.matrix = [ ]
self.rules = [ ]
self.prorules = [ ]
self.postprocessing = [ ]
self.nr_sp_release = ""
self.nr_sp_seqs = ""
self.nr_total = (None,None)
self.nr_positive = (None,None)
self.nr_unknown = (None,None)
self.nr_false_pos = (None,None)
self.nr_false_neg = None
self.nr_partial = None
self.cc_taxo_range = ""
self.cc_max_repeat = ""
self.cc_site = [ ]
self.cc_skip_flag = ""
self.dr_positive = [ ]
self.dr_false_neg = [ ]
self.dr_false_pos = [ ]
self.dr_potential = [ ]
self.dr_unknown = [ ]
self.pdb_structs = [ ]
# Everything below are private functions
|
| CloneAbstraction |
| Parameter Index | Clone Instance | Parameter Name | Value |
|---|---|---|---|
| None | |||