root/galaxy-central/tools/rgenetics/rgTDT.py @ 2

リビジョン 2, 9.7 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central
行番号 
1#!/usr/local/bin/python
2# hack to run and process a plink tdt
3# expects args as
4# bfilepath outname jobname outformat (wig,xls)
5# ross lazarus
6# for wig files, we need annotation so look for map file or complain
7
8"""
9Parameters for wiggle track definition lines
10All options are placed in a single line separated by spaces:
11
12  track type=wiggle_0 name=track_label description=center_label \
13        visibility=display_mode color=r,g,b altColor=r,g,b \
14        priority=priority autoScale=on|off \
15        gridDefault=on|off maxHeightPixels=max:default:min \
16        graphType=bar|points viewLimits=lower:upper \
17        yLineMark=real-value yLineOnOff=on|off \
18        windowingFunction=maximum|mean|minimum smoothingWindow=off|2-16
19"""
20
21import sys,math,shutil,subprocess,os,time,tempfile,shutil,string
22from os.path import abspath
23from optparse import OptionParser
24from rgutils import timenow, plinke
25myversion = 'v0.003 January 2010'
26verbose = False
27
28
29def makeGFF(resf='',outfname='',logf=None,twd='.',name='track name',description='track description',topn=1000):
30    """
31    score must be scaled to 0-1000
32
33    Want to make some wig tracks from each analysis
34    Best n -log10(p). Make top hit the window.
35    we use our tab output which has
36    rs  chrom   offset  ADD_stat        ADD_p   ADD_log10p
37    rs3094315   1       792429  1.151   0.2528  0.597223
38
39    """
40
41    def is_number(s):
42        try:
43            float(s)
44            return True
45        except ValueError:
46            return False
47    header = 'track name=%s description="%s" visibility=2 useScore=1 color=0,60,120\n' % (name,description)
48    column_names = [ 'Seqname', 'Source', 'Feature', 'Start', 'End', 'Score', 'Strand', 'Frame', 'Group' ]
49    halfwidth=100
50    resfpath = os.path.join(twd,resf)
51    resf = open(resfpath,'r')
52    resfl = resf.readlines() # dumb but convenient for millions of rows
53    resfl = [x.split() for x in resfl]
54    headl = resfl[0]
55    resfl = resfl[1:]
56    headl = [x.strip().upper() for x in headl]
57    headIndex = dict(zip(headl,range(0,len(headl))))
58    # s = 'rs\tchrom\toffset\ta1\ta2\ttransmitted\tuntransmitted\tTDTChiSq\tTDTp\t-log10TDTp\tAbsTDTOR\tTDTOR'
59    chrpos = headIndex.get('CHROM',None)
60    rspos = headIndex.get('RS',None)
61    offspos = headIndex.get('OFFSET',None)
62    ppos = headIndex.get('-LOG10TDTP',None)
63    wewant = [chrpos,rspos,offspos,ppos]
64    if None in wewant: # missing something
65       logf.write('### Error missing a required header in makeGFF - headIndex=%s\n' % headIndex)
66       return
67    resfl = [x for x in resfl if x[ppos] > '']
68    resfl = [(float(x[ppos]),x) for x in resfl] # decorate
69    resfl.sort()
70    resfl.reverse() # using -log10 so larger is better
71    resfl = resfl[:topn] # truncate
72    pvals = [x[0] for x in resfl] # need to scale
73    resfl = [x[1] for x in resfl] # drop decoration
74    maxp = max(pvals) # need to scale
75    minp = min(pvals)
76    prange = abs(maxp-minp) + 0.5 # fudge
77    scalefact = 1000.0/prange
78    logf.write('###maxp=%f,minp=%f,prange=%f,scalefact=%f\n' % (maxp,minp,prange,scalefact))
79    for i,row in enumerate(resfl):
80        row[ppos] = '%d' % (int(scalefact*pvals[i]))
81        resfl[i] = row # replace
82    outf = file(outfname,'w')
83    outf.write(header)
84    outres = [] # need to resort into chrom offset order
85    for i,lrow in enumerate(resfl):
86        chrom,snp,offset,p, = [lrow[x] for x in wewant]
87        gff = ('chr%s' % chrom,'rgGLM','variation','%d' % (int(offset)-halfwidth),
88               '%d' % (int(offset)+halfwidth),p,'.','.','%s logp=%1.2f' % (snp,pvals[i]))
89        outres.append(gff)
90    outres = [(x[0],int(x[3]),x) for x in outres] # decorate
91    outres.sort() # into chrom offset
92    outres=[x[2] for x in outres] # undecorate
93    outres = ['\t'.join(x) for x in outres]
94    outf.write('\n'.join(outres))
95    outf.write('\n')
96    outf.close()
97
98
99
100def xformTDT(infname='',resf='',outfname='',name='foo',mapf='/usr/local/galaxy/data/rg/lped/x.bim'):
101    """munge a plink .tdt file into either a ucsc track or an xls file
102  CHR         SNP  A1:A2      T:U_TDT       OR_TDT    CHISQ_TDT        P_TDT
103   0   MitoT217C    2:3          0:0           NA           NA           NA
104   0   MitoG228A    1:4          0:0           NA           NA           NA
105   0   MitoT250C    2:3          0:0           NA           NA           NA
106    map file has
107    1       rs4378174       0       003980745
108    1       rs10796404      0       005465256
109    1       rs2697965       0       014023092
110
111   grrr!
112   Changed in 1.01 to
113   [rerla@hg fresh]$ head database/job_working_directory/445/rgTDT.tdt
114     CHR         SNP           BP  A1  A2      T      U           OR        CHISQ            P
115   1  rs12562034       758311   1   3     71     79       0.8987       0.4267       0.5136
116   1   rs3934834       995669   4   2     98    129       0.7597        4.233      0.03963
117
118
119    """
120    if verbose:
121        print 'Rgenetics Galaxy Tools, rgTDT.py.xformTDT got resf=%s, outtype=%s, outfname=%s' % (resf,outtype,outfname)
122    wewantcols = ['SNP','CHR','BP','A1','A2','T','U','OR','CHISQ','P']
123    res = []
124    s = 'rs\tchrom\toffset\ta1\ta2\ttransmitted\tuntransmitted\tTDTChiSq\tTDTp\t-log10TDTp\tAbsTDTOR\tTDTOR' # header
125    res.append(s)
126    rsdict = {}
127    if not mapf:
128        sys.stderr.write('rgTDT called but no map file provided - cannot determine locations')
129        sys.exit(1)
130    map = file(mapf,'r')
131    for l in map: # plink map
132        ll = l.strip().split()
133        if len(ll) >= 3:
134            rs=ll[1].strip()
135            chrom = ll[0]
136            if chrom.lower() == 'x':
137               chrom = '23'
138            if chrom.lower() == 'y':
139               chrom = '24'
140            if chrom.lower() == 'mito':
141               chrom = '25'
142            offset = ll[3]
143            rsdict[rs] = (chrom,offset)
144    f = open(resf,'r')
145    headl = f.next().strip()
146    headl = headl.split()
147    wewant = [headl.index(x) for x in wewantcols]
148    llen = len(headl)
149    lnum = anum = 0
150    for l in f:
151        lnum += 1
152        ll = l.strip().split()
153        if len(ll) >= llen: # valid line
154            snp,chrom,offset,a1,a2,t,u,orat,chisq,p = [ll[x] for x in wewant]
155            if chisq == 'NA' or p == 'NA' or orat == 'NA':
156                continue # can't use these lines - gg gets unhappy
157            snp = snp.strip()
158            lp = '0.0'
159            fp = '1.0'
160            fakeorat = '1.0'
161            if p.upper().strip() <> 'NA':
162                try:
163                   fp = float(p)
164                   if fp <> 0:
165                       lp = '%6f' % -math.log10(fp)
166                       fp = '%6f' % fp
167                except:
168                  pass
169            else:
170                p = '1.0'
171            if orat.upper().strip() <> 'NA':
172                try:
173                   fakeorat = orat
174                   if float(orat) < 1.0:
175                      fakeorat = '%6f' % (1.0/float(orat)) # invert so large values big
176                except:
177                   pass
178            else:
179                orat = '1.0'
180            outl = '\t'.join([snp,chrom,offset,a1,a2,t,u,chisq,p,lp,fakeorat,orat])
181            res.append(outl)
182    f = file(outfname,'w')
183    res.append('')
184    f.write('\n'.join(res))
185    f.close()
186
187
188if __name__ == "__main__":
189    """ called as
190    <command interpreter="python">
191        rgTDT.py -i '$infile.extra_files_path/$infile.metadata.base_name' -o '$title' -f '$outformat' -r '$out_file1' -l '$logf' -x '${GALAXY_DATA_INDEX_DIR}/rg/bin/pl$
192
193    </command>
194
195    """
196    u = """ called in xml as
197        <command interpreter="python2.4">
198        rgTDT.py -i $i -o $out_prefix -f $outformat -r $out_file1 -l $logf
199    </command>
200    """
201    if len(sys.argv) < 6:
202       s = '## Error rgTDT.py needs 5 command line params - got %s \n' % (sys.argv)
203       if verbose:
204            print >> sys.stdout, s
205       sys.exit(0)
206    parser = OptionParser(usage=u, version="%prog 0.01")
207    a = parser.add_option
208    a("-i","--infile",dest="bfname")
209    a("-o","--oprefix",dest="oprefix")
210    a("-f","--formatOut",dest="outformat")
211    a("-r","--results",dest="outfname")
212    a("-l","--logfile",dest="logf")
213    a("-d","--du",dest="uId")
214    a("-e","--email",dest="uEmail")
215    a("-g","--gff",dest="gffout",default="")
216    (options,args) = parser.parse_args()
217    killme = string.punctuation + string.whitespace
218    trantab = string.maketrans(killme,'_'*len(killme))
219    title = options.oprefix
220    title = title.translate(trantab)
221    map_file = '%s.bim' % (options.bfname) #
222    me = sys.argv[0]
223    alogf = options.logf # absolute paths
224    od = os.path.split(alogf)[0]
225    try:
226      os.path.makedirs(od)
227    except:
228      pass
229    aoutf = options.outfname # absolute paths
230    od = os.path.split(aoutf)[0]
231    try:
232      os.path.makedirs(od)
233    except:
234      pass
235    vcl = [plinke,'--noweb', '--bfile',options.bfname,'--out',title,'--mind','0.5','--tdt']
236    logme = []
237    if verbose:
238        s = 'Rgenetics %s http://rgenetics.org Galaxy Tools rgTDT.py started %s\n' % (myversion,timenow())
239        print >> sys.stdout,s
240        logme.append(s)
241        s ='rgTDT.py: bfname=%s, logf=%s, argv = %s\n' % (options.bfname,alogf, sys.argv)
242        print >> sys.stdout,s
243        logme.append(s)
244        s = 'rgTDT.py: vcl=%s\n' % (' '.join(vcl))
245        print >> sys.stdout,s
246        logme.append(s)
247    twd = tempfile.mkdtemp(suffix='rgTDT') # make sure plink doesn't spew log file into the root!
248    tname = os.path.join(twd,title)
249    p=subprocess.Popen(' '.join(vcl),shell=True,cwd=twd)
250    retval = p.wait()
251    shutil.copy('%s.log' % tname,alogf)
252    sto = file(alogf,'a')
253    sto.write('\n'.join(logme))
254    resf = '%s.tdt' % tname # plink output is here we hope
255    xformTDT(options.bfname,resf,aoutf,title,map_file) # leaves the desired summary file
256    gffout = options.gffout
257    if gffout > '':
258        makeGFF(resf=aoutf,outfname=gffout,logf=sto,twd='.',name='rgTDT_Top_Table',description=title,topn=1000)
259    shutil.rmtree(twd)
260    sto.close()
261
262
263
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