corebio.data

Package corebio :: Module data

Module corebio.data

Standard information used in computational biology.


To convert a property dictionary to a list :
>>> comp = [ amino_acid_composition[k] for k in amino_acid_letters]


Resources: (Various standard data files.)
 

BLOSUM Scoring Matrices
    Source: ftp://ftp.ncbi.nih.gov/repository/blocks/unix/blosum
    These are all new blast style with 1/3 bit scaling
    - blosum35
    - blosum45    
    - blosum62    
    - blosum40    
    - blosum50    
    - blosum80    
    - blosum100   

Other subsitution scoring matrices:
    - dist20_comp 
    - pam250
    - pam120
    
    
Status: Beta (Data needs to be proof checked.)

Function Summary
	`data_filename(name)`
	`data_object(name, parser)`
	`data_stream(name)`
	`data_string(name)`

Variable Summary
`str`	`amino_acid_alternative_letters` = `'ARNDCQEGHILKMFPSTWYV'`
`dict`	`amino_acid_ambiguity` = `{'A': 'A', 'C': 'C', 'B': 'ND', '...`
`dict`	`amino_acid_composition` = `{'A': 0.082000000000000003, 'C'...`
`str`	`amino_acid_extended_letters` = `'ACDEFGHIKLMNOPQRSTUVWYBJZ...`
`str`	`amino_acid_letters` = `'ACDEFGHIKLMNPQRSTVWY'`
`dict`	`amino_acid_mass` = `{'A': 89.090000000000003, 'C': 121.16,...`
`dict`	`amino_acid_names` = `{'*': 'translation stop', '-': 'gap',...`
`dict`	`dna_ambiguity` = `{'A': 'A', 'C': 'C', 'B': 'CGT', 'D': 'A...`
`str`	`dna_extended_letters` = `'GATCRYWSMKHBVDN'`
`str`	`dna_letters` = `'GATC'`
`dict`	`dna_mass` = `{'A': 347.0, 'C': 323.0, 'T': 322.0, 'G': 363...`
`dict`	`extended_three_to_one` = `{'Val': 'V', 'Chg': 'A', 'Hac': ...`
`dict`	`kyte_doolittle_hydrophobicity` = `{'A': 1.8, 'C': 2.5, 'E'...`
`dict`	`nucleotide_names` = `{'A': 'Adenosine', 'C': 'Cytidine', '...`
`dict`	`one_to_three` = `{'A': 'Ala', 'C': 'Cys', 'B': 'Asx', 'E':...`
`list`	`resource_names` = `['blosum35', 'blosum45', 'blosum62', 'b...`
`dict`	`rna_ambiguity` = `{'A': 'A', 'C': 'C', 'B': 'CGU', 'D': 'A...`
`str`	`rna_extended_letters` = `'GAUCRYWSMKHBVDN'`
`str`	`rna_letters` = `'GAUC'`
`dict`	`rna_mass` = `{'A': 363.0, 'C': 319.0, 'U': 340.0, 'G': 379...`
`dict`	`standard_three_to_one` = `{'Val': 'V', 'Xaa': 'X', 'Cys': ...`

Variable Details

amino_acid_alternative_letters

Type:: str
Value:: 'ARNDCQEGHILKMFPSTWYV'

amino_acid_ambiguity

Type:: dict
Value:: {'A': 'A', 'B': 'ND', 'C': 'C', 'D': 'D', 'E': 'E', 'F': 'F', 'G': 'G', 'H': 'H', ...

amino_acid_composition

Type:: dict
Value:: {'A': 0.082000000000000003, 'C': 0.017000000000000001, 'D': 0.052999999999999999, 'E': 0.062, 'F': 0.039, 'G': 0.071999999999999995, 'H': 0.021999999999999999, 'I': 0.051999999999999998, ...

amino_acid_extended_letters

Type:: str
Value:: 'ACDEFGHIKLMNOPQRSTUVWYBJZX*-'

amino_acid_letters

Type:: str
Value:: 'ACDEFGHIKLMNPQRSTVWY'

amino_acid_mass

Type:: dict
Value:: {'A': 89.090000000000003, 'B': 132.66, 'C': 121.16, 'D': 133.09999999999999, 'E': 147.13, 'F': 165.19, 'G': 75.069999999999993, 'H': 155.16, ...

amino_acid_names

Type:: dict
Value:: {'*': 'translation stop', '-': 'gap', 'A': 'alanine', 'B': 'aspartic acid or asparagine', 'C': 'cysteine', 'D': 'aspartic acid', 'E': 'glutamic acid', 'F': 'phenylalanine', ...

dna_ambiguity

Type:: dict
Value:: {'A': 'A', 'B': 'CGT', 'C': 'C', 'D': 'AGT', 'G': 'G', 'H': 'ACT', 'K': 'GT', 'M': 'AC', ...

dna_extended_letters

Type:: str
Value:: 'GATCRYWSMKHBVDN'

dna_letters

Type:: str
Value:: 'GATC'

dna_mass

Type:: dict
Value:: {'A': 347.0, 'C': 323.0, 'T': 322.0, 'G': 363.0}

extended_three_to_one

Type:: dict
Value:: {'5hp': 'E', 'Aya': 'A', 'Bnn': 'A', 'Chg': 'A', 'Hac': 'A', 'Har': 'R', 'Trp': 'W', 'Val': 'V', ...

kyte_doolittle_hydrophobicity

Type:: dict
Value:: {'A': 1.8, 'C': 2.5, 'D': -3.5, 'E': -3.5, 'F': 2.7999999999999998, 'G': -0.40000000000000002, 'H': -3.2000000000000002, 'I': 4.5, ...

nucleotide_names

Type:: dict
Value:: {'-': 'gap', 'A': 'Adenosine', 'B': 'G T C (not A) (B comes after A)', 'C': 'Cytidine', 'D': 'G A T (not C) (D comes after C)', 'G': 'Guanine', 'H': 'A C T (not G) (H comes after G)', 'K': 'G T (Ketone)', ...

one_to_three

Type:: dict
Value:: {'A': 'Ala', 'B': 'Asx', 'C': 'Cys', 'D': 'Asp', 'E': 'Glu', 'F': 'Phe', 'G': 'Gly', 'H': 'His', ...

resource_names

Type:: list
Value:: ['blosum35', 'blosum45', 'blosum62', 'blosum40', 'blosum50', 'blosum80', 'blosum100', 'dist20_comp', ...

rna_ambiguity

Type:: dict
Value:: {'A': 'A', 'B': 'CGU', 'C': 'C', 'D': 'AGU', 'G': 'G', 'H': 'ACU', 'K': 'GU', 'M': 'AC', ...

rna_extended_letters

Type:: str
Value:: 'GAUCRYWSMKHBVDN'

rna_letters

Type:: str
Value:: 'GAUC'

rna_mass

Type:: dict
Value:: {'A': 363.0, 'C': 319.0, 'U': 340.0, 'G': 379.0}

standard_three_to_one

Type:: dict
Value:: {'Ala': 'A', 'Arg': 'R', 'Asn': 'N', 'Asp': 'D', 'Asx': 'B', 'Cys': 'C', 'Gln': 'Q', 'Glu': 'E', ...

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