Changes to use of constant namedb and seq files#7
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…ia command line to annotate-seqs.py mouse.namedb, mouse.namedb.fullname and mouse.protein.faa were hardcoded into namedb.py. Now, it picks up from sys.argv[4] and sys.argv[5], where sys.argv is supplied to annotate-seqs.py Possible regression bugs if namedb.py is used by scripts other than annotate-seqs.py that use a different command line argument pattern
file and constant namedb files make-namedb changed to pickle into constant names.db and fullnames.db files, and pickle sequence filename into names.db. namedb.py modified to unpickle correspondingly. Lines expecting extra CMD line args in annotate-seqs removed.
make-namedb.py
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Two comments --
since sys.argv[1] is now used twice in the script (and in any case I wrote it badly in the first place), please set a variable to the value at the top, and then reuse the variable down here. I guess something like 'seqfile = sys.argv[1]'.
second, you don't need to create a dict and then populate it and then dump it. Just do
dump(seqfile, fp)
dump(names, fp)
following which you can do
seqfile = load(fp)
names = load(fp)
This also eliminates the use of 'get' below...
dict() used in previous commit has been removed, sequential calls to dump() and load() are used instead. A variable 'seqFile' id used to store sequence file name from CMD line args.
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These are changes that override the changes from the previous commit/pull-request. Changes have been made in the way objects are pickled and unpickled, and also in the use of CMD line args.
Ram