"""
gs.py

A reusable program to fetch gene symbols using probe set IDs
"""
import sys, string, os, subprocess, tempfile

rprog="""getGeneSymbol=function(probesetIds, database)
{
    library(annaffy)

    gene <- aaf.handler(probesetIds, database, "Symbol")
    #geneSymbol <- getText(gene)
    #geneSymbol <- paste("###geneSymbol", geneSymbol, sep='=')
    #geneSymbol
    return (getText(gene))
}
"""

rcall="""
  symbols = getGeneSymbol(c(%s), "%s")
  for (i in 1:length(symbols)) {
    s = paste("CISTROME_SYM:", symbols[i], "\\n")
    cat(s)
  }
"""

def main():
    """called as 
getGeneSymbol.py database probesetId1 [probesetId2, ..., probesetIdn]

eg
getGeneSymbol.py hgu133a.db 1053_at 1007_s_at
    """
    nparm = len(sys.argv) - 1
    appname = sys.argv[0]
    if (3 > len(sys.argv)):
        print '%s needs at least 2 parameters' % (appname)
        print 'usage: %s database probesetId1 [probesetId2, ..., probesetIdn]' % (appname)
        print 'eg: %s hgu133a.db 1053_at 1007_s_at' % (appname)
        sys.exit(1)
        # short command line error
    database = sys.argv[1].strip()
    probesetIds = sys.argv[2:]
    print getGeneSymbols(database, probesetIds)

def getGeneSymbols(database, probesetIds):
    ids = ""
    for (id) in probesetIds:
        ids += '"' + id + '",'
    ids = ids.rstrip(',')

    r = rprog + (rcall % (ids, database))

    tempdir = tempfile.mkdtemp()
    tmpfilename = os.path.join(tempdir, "stdout.txt")
    tmpfile = open(tmpfilename, "w+b")
    p = subprocess.Popen("R --vanilla", shell=True, executable="/bin/bash", stdin=subprocess.PIPE, stdout=tmpfile)
    p.communicate(r)
    tmpfile.close()
    tmpfile = open(tmpfilename, "r")
    symbols = tmpfile.readlines()
    tmpfile.close()
    os.unlink(tmpfilename)
    os.removedirs(tempdir)

    symbols = [x for x in symbols if x.startswith("CISTROME_SYM:")]
    symbols = [x.split("CISTROME_SYM:")[1].strip() for x in symbols]
    mappings = {}
    for i in range(0, len(probesetIds)):
        symbol = symbols[i]
        if (symbol == ''):
            symbol = probesetIds[i]
        mappings[probesetIds[i]] = symbol

    return mappings

if __name__ == "__main__":
    main()