Delete unneeded directory

[jabaws.git] / website / archive / binaries / mac / src / disembl / biopython-1.50 / Bio / Data / IUPACData.py

diff --git a/website/archive/binaries/mac/src/disembl/biopython-1.50/Bio/Data/IUPACData.py b/website/archive/binaries/mac/src/disembl/biopython-1.50/Bio/Data/IUPACData.py
deleted file mode 100644 (file)
index ebd5a12..0000000
--- a/website/archive/binaries/mac/src/disembl/biopython-1.50/Bio/Data/IUPACData.py
+++ /dev/null
@@ -1,209 +0,0 @@
-# Information about the IUPAC alphabets
-
-protein_letters = "ACDEFGHIKLMNPQRSTVWY"
-extended_protein_letters = "ACDEFGHIKLMNPQRSTVWYBXZJUO"
-#   B = "Asx";  aspartic acid or asparagine (D or N)
-#   X = "Xxx";  unknown or 'other' amino acid
-#   Z = "Glx";  glutamic acid or glutamine (E or Q)
-#   J = "Xle";  leucine or isoleucine (L or I, used in mass-spec)
-#   U = "Sec";  selenocysteine
-#   O = "Pyl";  pyrrolysine
-ambiguous_dna_letters = "GATCRYWSMKHBVDN"
-unambiguous_dna_letters = "GATC"
-ambiguous_rna_letters = "GAUCRYWSMKHBVDN"
-unambiguous_rna_letters = "GAUC"
-
-#   B == 5-bromouridine
-#   D == 5,6-dihydrouridine
-#   S == thiouridine
-#   W == wyosine
-extended_dna_letters = "GATCBDSW"
-
-# are there extended forms?
-#extended_rna_letters = "GAUCBDSW"
-
-ambiguous_dna_values = {
-    "A": "A",
-    "C": "C",
-    "G": "G",
-    "T": "T",
-    "M": "AC",
-    "R": "AG",
-    "W": "AT",
-    "S": "CG",
-    "Y": "CT",
-    "K": "GT",
-    "V": "ACG",
-    "H": "ACT",
-    "D": "AGT",
-    "B": "CGT",
-    "X": "GATC",
-    "N": "GATC",
-    }
-ambiguous_rna_values = {
-    "A": "A",
-    "C": "C",
-    "G": "G",
-    "U": "U",
-    "M": "AC",
-    "R": "AG",
-    "W": "AU",
-    "S": "CG",
-    "Y": "CU",
-    "K": "GU",
-    "V": "ACG",
-    "H": "ACU",
-    "D": "AGU",
-    "B": "CGU",
-    "X": "GAUC",
-    "N": "GAUC",
-    }
-
-ambiguous_dna_complement = {
-    "A": "T",
-    "C": "G",
-    "G": "C",
-    "T": "A",
-    "M": "K",
-    "R": "Y",
-    "W": "W",
-    "S": "S",
-    "Y": "R",
-    "K": "M",
-    "V": "B",
-    "H": "D",
-    "D": "H",
-    "B": "V",
-    "X": "X",
-    "N": "N",
-    }
-
-ambiguous_rna_complement = {
-    "A": "U",
-    "C": "G",
-    "G": "C",
-    "U": "A",
-    "M": "K",
-    "R": "Y",
-    "W": "W",
-    "S": "S",
-    "Y": "R",
-    "K": "M",
-    "V": "B",
-    "H": "D",
-    "D": "H",
-    "B": "V",
-    "X": "X",
-    "N": "N",
-    }
-
-
-def _make_ranges(dict):
-    d = {}
-    for key, value in dict.items():
-        d[key] = (value, value)
-    return d
-
-# From bioperl's SeqStats.pm
-unambiguous_dna_weights = {
-    "A": 347.,
-    "C": 323.,
-    "G": 363.,
-    "T": 322.,
-    }
-unambiguous_dna_weight_ranges = _make_ranges(unambiguous_dna_weights)
-
-unambiguous_rna_weights = {
-    "A": unambiguous_dna_weights["A"] + 16.,  # 16 for the oxygen
-    "C": unambiguous_dna_weights["C"] + 16.,
-    "G": unambiguous_dna_weights["G"] + 16.,
-    "U": 340.,
-}
-unambiguous_rna_weight_ranges = _make_ranges(unambiguous_rna_weights)
-
-def _make_ambiguous_ranges(dict, weight_table):
-    range_d = {}
-    avg_d = {}
-    for letter, values in dict.items():
-        #Following line is a quick hack to skip undefined weights for U and O
-        if len(values)==1 and values[0] not in weight_table : continue
-        weights = map(weight_table.get, values)
-        range_d[letter] = (min(weights), max(weights))
-        total_w = 0.0
-        for w in weights:
-            total_w = total_w + w
-        avg_d[letter] = total_w / len(weights)
-    return range_d, avg_d
-
-ambiguous_dna_weight_ranges, avg_ambiguous_dna_weights = \
-               _make_ambiguous_ranges(ambiguous_dna_values,
-                                      unambiguous_dna_weights)
-
-ambiguous_rna_weight_ranges, avg_ambiguous_rna_weights = \
-               _make_ambiguous_ranges(ambiguous_rna_values,
-                                      unambiguous_rna_weights)
-
-protein_weights = {
-    "A": 89.09,
-    "C": 121.16,
-    "D": 133.10,
-    "E": 147.13,
-    "F": 165.19,
-    "G": 75.07,
-    "H": 155.16,
-    "I": 131.18,
-    "K": 146.19,
-    "L": 131.18,
-    "M": 149.21,
-    "N": 132.12,
-    #"O": 0.0, # Needs to be recorded!
-    "P": 115.13,
-    "Q": 146.15,
-    "R": 174.20,
-    "S": 105.09,
-    "T": 119.12,
-    #"U": 168.05, # To be confirmed
-    "V": 117.15,
-    "W": 204.23,
-    "Y": 181.19
-    }
-
-extended_protein_values = {
-    "A": "A",
-    "B": "ND",
-    "C": "C",
-    "D": "D",
-    "E": "E",
-    "F": "F",
-    "G": "G",
-    "H": "H",
-    "I": "I",
-    "J": "IL",
-    "K": "K",
-    "L": "L",
-    "M": "M",
-    "N": "N",
-    "O": "O",
-    "P": "P",
-    "Q": "Q",
-    "R": "R",
-    "S": "S",
-    "T": "T",
-    "U": "U",
-    "V": "V",
-    "W": "W",
-    "X": "ACDEFGHIKLMNPQRSTVWY",
-    #TODO - Include U and O in the possible values of X?
-    #This could alter the extended_protein_weight_ranges ...
-    "Y": "Y",
-    "Z": "QE",
-}
-    
-protein_weight_ranges = _make_ranges(protein_weights)
-
-extended_protein_weight_ranges, avg_extended_protein_weights = \
-               _make_ambiguous_ranges(extended_protein_values,
-                                      protein_weights)
-
-
-