--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/rgenetics/rgTDT.py	Fri Mar 09 19:37:19 2012 -0500
@@ -0,0 +1,264 @@
+#!/usr/local/bin/python
+# hack to run and process a plink tdt
+# expects args as
+# bfilepath outname jobname outformat (wig,xls)
+# ross lazarus
+# for wig files, we need annotation so look for map file or complain
+
+"""
+Parameters for wiggle track definition lines
+All options are placed in a single line separated by spaces:
+
+  track type=wiggle_0 name=track_label description=center_label \
+        visibility=display_mode color=r,g,b altColor=r,g,b \
+        priority=priority autoScale=on|off \
+        gridDefault=on|off maxHeightPixels=max:default:min \
+        graphType=bar|points viewLimits=lower:upper \
+        yLineMark=real-value yLineOnOff=on|off \
+        windowingFunction=maximum|mean|minimum smoothingWindow=off|2-16
+"""
+
+import sys,math,shutil,subprocess,os,time,tempfile,shutil,string
+from os.path import abspath
+from optparse import OptionParser
+from rgutils import timenow, plinke
+myversion = 'v0.003 January 2010'
+verbose = False
+
+
+
+def makeGFF(resf='',outfname='',logf=None,twd='.',name='track name',description='track description',topn=1000):
+    """
+    score must be scaled to 0-1000
+
+    Want to make some wig tracks from each analysis
+    Best n -log10(p). Make top hit the window.
+    we use our tab output which has
+    rs	chrom	offset	ADD_stat	ADD_p	ADD_log10p
+    rs3094315	1	792429	1.151	0.2528	0.597223
+
+    """
+
+    def is_number(s):
+        try:
+            float(s)
+            return True
+        except ValueError:
+            return False
+    header = 'track name=%s description="%s" visibility=2 useScore=1 color=0,60,120\n' % (name,description)
+    column_names = [ 'Seqname', 'Source', 'Feature', 'Start', 'End', 'Score', 'Strand', 'Frame', 'Group' ]
+    halfwidth=100
+    resfpath = os.path.join(twd,resf)
+    resf = open(resfpath,'r')
+    resfl = resf.readlines() # dumb but convenient for millions of rows
+    resfl = [x.split() for x in resfl]
+    headl = resfl[0]
+    resfl = resfl[1:]
+    headl = [x.strip().upper() for x in headl]
+    headIndex = dict(zip(headl,range(0,len(headl))))
+    # s = 'rs\tchrom\toffset\ta1\ta2\ttransmitted\tuntransmitted\tTDTChiSq\tTDTp\t-log10TDTp\tAbsTDTOR\tTDTOR'
+    chrpos = headIndex.get('CHROM',None)
+    rspos = headIndex.get('RS',None)
+    offspos = headIndex.get('OFFSET',None)
+    ppos = headIndex.get('-LOG10TDTP',None)
+    wewant = [chrpos,rspos,offspos,ppos]
+    if None in wewant: # missing something
+       logf.write('### Error missing a required header in makeGFF - headIndex=%s\n' % headIndex)
+       return
+    resfl = [x for x in resfl if x[ppos] > '']
+    resfl = [(float(x[ppos]),x) for x in resfl] # decorate
+    resfl.sort()
+    resfl.reverse() # using -log10 so larger is better
+    resfl = resfl[:topn] # truncate
+    pvals = [x[0] for x in resfl] # need to scale
+    resfl = [x[1] for x in resfl] # drop decoration
+    maxp = max(pvals) # need to scale
+    minp = min(pvals)
+    prange = abs(maxp-minp) + 0.5 # fudge
+    scalefact = 1000.0/prange
+    logf.write('###maxp=%f,minp=%f,prange=%f,scalefact=%f\n' % (maxp,minp,prange,scalefact))
+    for i,row in enumerate(resfl):
+        row[ppos] = '%d' % (int(scalefact*pvals[i]))
+        resfl[i] = row # replace
+    outf = file(outfname,'w')
+    outf.write(header)
+    outres = [] # need to resort into chrom offset order
+    for i,lrow in enumerate(resfl):
+        chrom,snp,offset,p, = [lrow[x] for x in wewant]
+        gff = ('chr%s' % chrom,'rgTDT','variation','%d' % (int(offset)-halfwidth),
+               '%d' % (int(offset)+halfwidth),p,'.','.','%s logp=%1.2f' % (snp,pvals[i]))
+        outres.append(gff)
+    outres = [(x[0],int(x[3]),x) for x in outres] # decorate
+    outres.sort() # into chrom offset
+    outres=[x[2] for x in outres] # undecorate
+    outres = ['\t'.join(x) for x in outres]
+    outf.write('\n'.join(outres))
+    outf.write('\n')
+    outf.close()
+
+
+
+def xformTDT(infname='',resf='',outfname='',name='foo',mapf='/usr/local/galaxy/data/rg/lped/x.bim'):
+    """munge a plink .tdt file into either a ucsc track or an xls file
+  CHR         SNP  A1:A2      T:U_TDT       OR_TDT    CHISQ_TDT        P_TDT
+   0   MitoT217C    2:3          0:0           NA           NA           NA
+   0   MitoG228A    1:4          0:0           NA           NA           NA
+   0   MitoT250C    2:3          0:0           NA           NA           NA
+    map file has
+    1       rs4378174       0       003980745
+    1       rs10796404      0       005465256
+    1       rs2697965       0       014023092
+
+   grrr!
+   Changed in 1.01 to
+   [rerla@hg fresh]$ head database/job_working_directory/445/rgTDT.tdt
+     CHR         SNP           BP  A1  A2      T      U           OR        CHISQ            P
+   1  rs12562034       758311   1   3     71     79       0.8987       0.4267       0.5136
+   1   rs3934834       995669   4   2     98    129       0.7597        4.233      0.03963
+
+
+    """
+    if verbose:
+        print 'Rgenetics Galaxy Tools, rgTDT.py.xformTDT got resf=%s, outtype=%s, outfname=%s' % (resf,outtype,outfname)
+    wewantcols = ['SNP','CHR','BP','A1','A2','T','U','OR','CHISQ','P']
+    res = []
+    s = 'rs\tchrom\toffset\ta1\ta2\ttransmitted\tuntransmitted\tTDTChiSq\tTDTp\t-log10TDTp\tAbsTDTOR\tTDTOR' # header
+    res.append(s)
+    rsdict = {}
+    if not mapf:
+        sys.stderr.write('rgTDT called but no map file provided - cannot determine locations')
+        sys.exit(1)
+    map = file(mapf,'r')
+    for l in map: # plink map
+        ll = l.strip().split()
+        if len(ll) >= 3:
+            rs=ll[1].strip()
+            chrom = ll[0]
+            if chrom.lower() == 'x':
+               chrom = '23'
+            if chrom.lower() == 'y':
+               chrom = '24'
+            if chrom.lower() == 'mito':
+               chrom = '25'
+            offset = ll[3]
+            rsdict[rs] = (chrom,offset)
+    f = open(resf,'r')
+    headl = f.next().strip()
+    headl = headl.split()
+    wewant = [headl.index(x) for x in wewantcols]
+    llen = len(headl)
+    lnum = anum = 0
+    for l in f:
+        lnum += 1
+        ll = l.strip().split()
+        if len(ll) >= llen: # valid line
+            snp,chrom,offset,a1,a2,t,u,orat,chisq,p = [ll[x] for x in wewant]
+            if chisq == 'NA' or p == 'NA' or orat == 'NA':
+                continue # can't use these lines - gg gets unhappy
+            snp = snp.strip()
+            lp = '0.0'
+            fp = '1.0'
+            fakeorat = '1.0'
+            if p.upper().strip() <> 'NA':
+                try:
+                   fp = float(p)
+                   if fp <> 0:
+                       lp = '%6f' % -math.log10(fp)
+                       fp = '%6f' % fp
+                except:
+                  pass
+            else:
+                p = '1.0'
+            if orat.upper().strip() <> 'NA':
+                try:
+                   fakeorat = orat
+                   if float(orat) < 1.0:
+                      fakeorat = '%6f' % (1.0/float(orat)) # invert so large values big
+                except:
+                   pass
+            else:
+                orat = '1.0'
+            outl = '\t'.join([snp,chrom,offset,a1,a2,t,u,chisq,p,lp,fakeorat,orat])
+            res.append(outl)
+    f = file(outfname,'w')
+    res.append('')
+    f.write('\n'.join(res))
+    f.close()
+
+
+if __name__ == "__main__":
+    """ called as
+    <command interpreter="python">
+        rgTDT.py -i '$infile.extra_files_path/$infile.metadata.base_name' -o '$title' -f '$outformat' -r '$out_file1' -l '$logf' -x '${GALAXY_DATA_INDEX_DIR}/rg/bin/pl$
+
+    </command>
+
+    """
+    u = """ called in xml as
+        <command interpreter="python2.4">
+        rgTDT.py -i $i -o $out_prefix -f $outformat -r $out_file1 -l $logf
+    </command>
+    """
+    if len(sys.argv) < 6:
+       s = '## Error rgTDT.py needs 5 command line params - got %s \n' % (sys.argv)
+       if verbose:
+            print >> sys.stdout, s
+       sys.exit(0)
+    parser = OptionParser(usage=u, version="%prog 0.01")
+    a = parser.add_option
+    a("-i","--infile",dest="bfname")
+    a("-o","--oprefix",dest="oprefix")
+    a("-f","--formatOut",dest="outformat")
+    a("-r","--results",dest="outfname")
+    a("-l","--logfile",dest="logf")
+    a("-d","--du",dest="uId")
+    a("-e","--email",dest="uEmail")
+    a("-g","--gff",dest="gffout",default="")
+    (options,args) = parser.parse_args()
+    killme = string.punctuation + string.whitespace
+    trantab = string.maketrans(killme,'_'*len(killme))
+    title = options.oprefix
+    title = title.translate(trantab)
+    map_file = '%s.bim' % (options.bfname) #
+    me = sys.argv[0]
+    alogf = options.logf # absolute paths
+    od = os.path.split(alogf)[0]
+    try:
+      os.path.makedirs(od)
+    except:
+      pass
+    aoutf = options.outfname # absolute paths
+    od = os.path.split(aoutf)[0]
+    try:
+      os.path.makedirs(od)
+    except:
+      pass
+    vcl = [plinke,'--noweb', '--bfile',options.bfname,'--out',title,'--mind','0.5','--tdt']
+    logme = []
+    if verbose:
+        s = 'Rgenetics %s http://rgenetics.org Galaxy Tools rgTDT.py started %s\n' % (myversion,timenow())
+        print >> sys.stdout,s
+        logme.append(s)
+        s ='rgTDT.py: bfname=%s, logf=%s, argv = %s\n' % (options.bfname,alogf, sys.argv)
+        print >> sys.stdout,s
+        logme.append(s)
+        s = 'rgTDT.py: vcl=%s\n' % (' '.join(vcl))
+        print >> sys.stdout,s
+        logme.append(s)
+    twd = tempfile.mkdtemp(suffix='rgTDT') # make sure plink doesn't spew log file into the root!
+    tname = os.path.join(twd,title)
+    p=subprocess.Popen(' '.join(vcl),shell=True,cwd=twd)
+    retval = p.wait()
+    shutil.copy('%s.log' % tname,alogf)
+    sto = file(alogf,'a')
+    sto.write('\n'.join(logme))
+    resf = '%s.tdt' % tname # plink output is here we hope
+    xformTDT(options.bfname,resf,aoutf,title,map_file) # leaves the desired summary file
+    gffout = options.gffout
+    if gffout > '':
+        makeGFF(resf=aoutf,outfname=gffout,logf=sto,twd='.',name='rgTDT_Top_Table',description=title,topn=1000)
+    shutil.rmtree(twd)
+    sto.close()
+
+
+