[Biopython-dev] [Bug 2688] New: Removal of depreciated string functions

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2688

           Summary: Removal of depreciated string functions
           Product: Biopython
           Version: Not Applicable
          Platform: PC
        OS/Version: Linux
            Status: NEW
          Severity: minor
          Priority: P5
         Component: Main Distribution
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: bsouthey at gmail.com


This is a general bug to remove any depreciated string functions from Biopython
modules. I apologize in advance for the noise this creates especially due to my
mistakes.

I have tested and validated the subsequent patches on my Linux system with
Python versions 2.3, 2.4, 2.5 and 2.6. However, I do recognize that patches may
be in code not used by the tests. 


The following files require importing the string module and are thus excluded
(although depreciated functions may still be used):
Bio/Decode.py - maketrans()
Bio/EUtils/POM.py - maketrans()
Bio/Prosite/Pattern.py - maketrans()
Bio/Seq.py - maketrans()
triefind.py - defines string.punctuation + string.whitespace

The following files have alternative reports
GenBank/__init__.py
HotRand.py


The following files are depreciated and are excluded:
Emboss/Primer.py
stringfns.py
MetaTool/__init__.py
MetaTool/metatool_format.py
MetaTool/Record.py
NBRF/__init__.py
Ndb/__init__.py
Transcribe.py


The following files import but do not use the string module 
AlignAce/AlignAceStandalone.py (fixed)
AlignAce/CompareAceStandalone.py (fixed)
Crystal/__init__.py
IntelliGenetics/__init__.py
IntelliGenetics/intelligenetics_format.py
IntelliGenetics/Record.py
NetCatch.py
SCOP/__init__.py


The following files are known to use string module and have patches:
Align/AlignInfo.py
Blast/ParseBlastTable.py
FSSP/__init__.py
NMR/NOEtools.py
NMR/xpktools.py
PDB/MMCIFParser.py
SubsMat/__init__.py
Blast/Record.py
Compass/__init__.py
Data/CodonTable.py
Eutils/sourcegen.py
Eutils/tests/unittest.py
Fasta/FastaAlign.py
FilteredReader.py
GFF/easy.py
HMM/Utilities.py
Index.py
MEME/Parser.py
NeuralNetwork/Gene/Pattern.py
NeuralNetwork/Gene/Schema.py
Parsers/spark.py
PDB/parse_pdb_header.py
PDB/PDBList.py
PDB/PDBParser.py
PDB/PSEA.py
SCOP/__init__.py
utils.py

I did not see an trivial resolution for the functions in:
SubsMat/FreqTable.py
So I rewrote the functions to avoid using map.


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