root/galaxy-central/tools/rgenetics/rgGLM.py

リビジョン 2, 10.3 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central
行番号 
1#!/usr/local/bin/python
2"""
3# added most of the available options for linear models
4# june 2009 rml
5# hack to run and process a plink quantitative trait
6#
7
8This is a wrapper for Shaun Purcell's Plink linear/logistic models for
9traits, covariates and genotypes.
10
11It requires some judgement to interpret the findings
12We need some better visualizations - manhattan plots are good.
13svg with rs numbers for top 1%?
14
15toptable tools - truncate a gg file down to some low percentile
16
17intersect with other tables - eg gene expression regressions on snps
18
19
20
21"""
22
23import sys,math,shutil,subprocess,os,string,tempfile,shutil,commands
24from rgutils import plinke
25
26def makeGFF(resf='',outfname='',logf=None,twd='.',name='track name',description='track description',topn=1000):
27    """
28    score must be scaled to 0-1000
29   
30    Want to make some wig tracks from each analysis
31    Best n -log10(p). Make top hit the window.
32    we use our tab output which has
33    rs  chrom   offset  ADD_stat        ADD_p   ADD_log10p
34    rs3094315   1       792429  1.151   0.2528  0.597223
35
36    """
37
38    def is_number(s):
39        try:
40            float(s)
41            return True
42        except ValueError:
43            return False
44    header = 'track name=%s description="%s" visibility=2 useScore=1 color=0,60,120\n' % (name,description)         
45    column_names = [ 'Seqname', 'Source', 'Feature', 'Start', 'End', 'Score', 'Strand', 'Frame', 'Group' ]
46    halfwidth=100
47    resfpath = os.path.join(twd,resf)
48    resf = open(resfpath,'r')
49    resfl = resf.readlines() # dumb but convenient for millions of rows
50    resfl = [x.split() for x in resfl]
51    headl = resfl[0]
52    resfl = resfl[1:]
53    headl = [x.strip().upper() for x in headl]
54    headIndex = dict(zip(headl,range(0,len(headl))))
55    chrpos = headIndex.get('CHROM',None)
56    rspos = headIndex.get('RS',None)
57    offspos = headIndex.get('OFFSET',None)
58    ppos = headIndex.get('ADD_LOG10P',None)
59    wewant = [chrpos,rspos,offspos,ppos]
60    if None in wewant: # missing something
61       logf.write('### Error missing a required header in makeGFF - headIndex=%s\n' % headIndex)
62       return
63    resfl = [x for x in resfl if x[ppos] > '']
64    resfl = [(float(x[ppos]),x) for x in resfl] # decorate
65    resfl.sort()
66    resfl.reverse() # using -log10 so larger is better
67    resfl = resfl[:topn] # truncate
68    pvals = [x[0] for x in resfl] # need to scale
69    resfl = [x[1] for x in resfl] # drop decoration
70    if len(pvals) == 0:
71        logf.write('### no pvalues found in resfl - %s' % (resfl[:3]))
72        sys.exit(1)
73    maxp = max(pvals) # need to scale
74    minp = min(pvals)
75    prange = abs(maxp-minp) + 0.5 # fudge
76    scalefact = 1000.0/prange
77    logf.write('###maxp=%f,minp=%f,prange=%f,scalefact=%f\n' % (maxp,minp,prange,scalefact))
78    for i,row in enumerate(resfl):
79        row[ppos] = '%d' % (int(scalefact*pvals[i]))
80        resfl[i] = row # replace
81    outf = file(outfname,'w')
82    outf.write(header)
83    outres = [] # need to resort into chrom offset order
84    for i,lrow in enumerate(resfl):
85        chrom,snp,offset,p, = [lrow[x] for x in wewant]
86        gff = ('chr%s' % chrom,'rgGLM','variation','%d' % (int(offset)-halfwidth),
87               '%d' % (int(offset)+halfwidth),p,'.','.','%s logp=%1.2f' % (snp,pvals[i]))
88        outres.append(gff)
89    outres = [(x[0],int(x[3]),x) for x in outres] # decorate
90    outres.sort() # into chrom offset
91    outres=[x[2] for x in outres] # undecorate
92    outres = ['\t'.join(x) for x in outres]   
93    outf.write('\n'.join(outres))
94    outf.write('\n')
95    outf.close()
96
97
98def xformQassoc(resf='',outfname='',logf=None,twd='.'):
99    """ plink.assoc.linear to gg file
100from the docs
101The output per each SNP might look something like:
102
103    CHR        SNP      BP  A1       TEST   NMISS       OR      STAT         P
104      5   rs000001   10001   A        ADD     664   0.7806    -1.942   0.05216
105      5   rs000001   10001   A     DOMDEV     664   0.9395   -0.3562    0.7217
106      5   rs000001   10001   A       COV1     664   0.9723   -0.7894    0.4299
107      5   rs000001   10001   A       COV2     664    1.159    0.5132    0.6078
108      5   rs000001   10001   A   GENO_2DF     664       NA     5.059    0.0797   
109    need to transform into gg columns for each distinct test
110    or bed for tracks?
111   
112    """
113    logf.write('xformQassoc got resf=%s, outfname=%s\n' % (resf,outfname))
114    resdict = {}
115    rsdict = {}
116    markerlist = []
117    # plink is "clever" - will run logistic if only 2 categories such as gender
118    resfs = resf.split('.')
119    if resfs[-1] == 'logistic':
120        resfs[-1] = 'linear'
121    else:
122        resfs[-1] = 'logistic'
123    altresf = '.'.join(resfs)
124
125    altresfpath = os.path.join(twd,altresf)
126    resfpath = os.path.join(twd,resf)
127    try:
128        resf = open(resfpath,'r')
129    except:
130        try:
131            resf = open(altresfpath,'r')
132        except:
133            print >> sys.stderr, '## error - no file plink output %s or %s found - cannot continue' % (resfpath, altresfpath)
134            sys.exit(1)
135    for lnum,row in enumerate(resf):
136        if lnum == 0:
137            headl = row.split()
138            headl = [x.strip().upper() for x in headl]
139            headIndex = dict(zip(headl,range(0,len(headl))))
140            chrpos = headIndex.get('CHR',None)
141            rspos = headIndex.get('SNP',None)
142            offspos = headIndex.get('BP',None)
143            nmisspos = headIndex.get('NMISS',None)
144            testpos = headIndex.get('TEST',None)
145            ppos = headIndex.get('P',None)
146            coeffpos = headIndex.get('OR',None)
147            if not coeffpos:
148                coeffpos = headIndex.get('BETA',None)
149            apos = headIndex.get('A1',None)
150            statpos = headIndex.get('STAT',None)
151            wewant = [chrpos,rspos,offspos,testpos,statpos,ppos,coeffpos,apos]
152            if None in wewant: # missing something
153               logf.write('missing a required header in xformQassoc - headIndex=%s\n' % headIndex)
154               return
155            llen = len(headl)       
156        else: # no Nones!
157            ll = row.split()
158            if len(ll) >= llen: # valid line
159                chrom,snp,offset,test,stat,p,coeff,allele = [ll[x] for x in wewant]
160                snp = snp.strip()
161                if p <> 'NA' :
162                  try:
163                    ffp = float(p)
164                    if ffp <> 0:
165                       lp =  -math.log10(ffp)
166                  except:
167                    lp = 0.0
168                  resdict.setdefault(test,{})
169                  resdict[test][snp] = (stat,p,'%f' % lp)
170                  if rsdict.get(snp,None) == None:
171                      rsdict[snp] = (chrom,offset)
172                      markerlist.append(snp)
173    # now have various tests indexed by rs
174    tk = resdict.keys()
175    tk.sort() # tests
176    ohead = ['rs','chrom','offset']
177    for t in tk: # add headers
178        ohead.append('%s_stat' % t)
179        ohead.append('%s_p' % t)
180        ohead.append('%s_log10p' % t)
181    oheads = '\t'.join(ohead)
182    res = [oheads,]
183    for snp in markerlist: # retain original order
184        chrom,offset = rsdict[snp]
185        outl = [snp,chrom,offset]
186        for t in tk:
187            outl += resdict[t][snp] # add stat,p for this test
188        outs = '\t'.join(outl)
189        res.append(outs)
190    f = file(outfname,'w')
191    res.append('')
192    f.write('\n'.join(res))
193    f.close()
194
195               
196if __name__ == "__main__":
197    """
198
199    <command interpreter="python">   
200        rgGLM.py '$i.extra_files_path/$i.metadata.base_name' '$phef.extra_files_path/$phef.metadata.base_name'
201        "$title1" '$predvar' '$covar' '$out_file1' '$logf' '$i.metadata.base_name'
202        '$inter' '$cond' '$gender' '$mind' '$geno' '$maf' '$logistic' '$wigout'
203    </command>
204    """
205    topn = 1000
206    killme = string.punctuation+string.whitespace
207    trantab = string.maketrans(killme,'_'*len(killme))
208    if len(sys.argv) < 17:
209       s = 'rgGLM.py needs 17 params - got %s \n' % (sys.argv)
210       sys.stderr.write(s) # print >>,s would probably also work?
211       sys.exit(0)
212    blurb = 'rgGLM.py called with %s' % sys.argv
213    print >> sys.stdout,blurb
214    bfname = sys.argv[1]
215    phename = sys.argv[2]
216    title = sys.argv[3]
217    title.translate(trantab)
218    predvar = sys.argv[4]
219    covar = sys.argv[5].strip()
220    outfname = sys.argv[6]
221    logfname = sys.argv[7]
222    op = os.path.split(logfname)[0]
223    try: # for test - needs this done
224        os.makedirs(op)
225    except:
226        pass   
227    basename = sys.argv[8].translate(trantab)
228    inter = sys.argv[9] == '1'
229    cond = sys.argv[10].strip()
230    if cond == 'None':
231        cond = ''
232    gender = sys.argv[11] == '1'
233    mind = sys.argv[12]
234    geno = sys.argv[13]
235    maf = sys.argv[14]
236    logistic = sys.argv[15].strip()=='1'
237    gffout = sys.argv[16]
238    me = sys.argv[0]
239    phepath = '%s.pphe' % phename
240    twd = tempfile.mkdtemp(suffix='rgGLM') # make sure plink doesn't spew log file into the root!
241    tplog = os.path.join(twd,'%s.log' % basename) # should be path to plink log
242    vcl = [plinke,'--noweb','--bfile',bfname,'--pheno-name','"%s"' % predvar,'--pheno',
243           phepath,'--out',basename,'--mind %s' % mind, '--geno %s' % geno,
244           '--maf %s' % maf]
245    if logistic:
246        vcl.append('--logistic')
247        resf = '%s.assoc.logistic' % basename # plink output is here we hope
248    else:
249        vcl.append('--linear')
250        resf = '%s.assoc.linear' % basename # plink output is here we hope
251    resf = os.path.join(twd,resf)
252    if gender:
253        vcl.append('--sex')
254    if inter:
255        vcl.append('--interaction')
256    if covar > 'None':
257        vcl += ['--covar',phepath,'--covar-name',covar] # comma sep list of covariates
258    tcfile = None
259    if len(cond) > 0: # plink wants these in a file..
260        dummy,tcfile = tempfile.mkstemp(suffix='condlist') #
261        f = open(tcfile,'w')
262        cl = cond.split()
263        f.write('\n'.join(cl))
264        f.write('\n')
265        f.close()
266        vcl.append('--condition-list %s' % tcfile)
267    p=subprocess.Popen(' '.join(vcl),shell=True,cwd=twd)
268    retval = p.wait()
269    if tcfile:
270        os.unlink(tcfile)
271    plinklog = file(tplog,'r').read()
272    logf = file(logfname,'w')
273    logf.write(blurb)
274    logf.write('\n')
275    logf.write('vcl=%s\n' % vcl)
276    xformQassoc(resf=resf,outfname=outfname,logf=logf,twd=twd) # leaves the desired summary file
277    makeGFF(resf=outfname,outfname=gffout,logf=logf,twd=twd,name='rgGLM_TopTable',description=title,topn=topn)
278    logf.write('\n')
279    logf.write(plinklog)
280    logf.close()
281    #shutil.rmtree(twd) # clean up
282
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