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comparison tools/rgenetics/rgCaCo.py @ 0:9071e359b9a3

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author xuebing
date Fri, 09 Mar 2012 19:37:19 -0500
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1 #!/usr/local/bin/python
2 # hack to run and process a plink case control association
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 Parameters for wiggle track definition lines
9 All options are placed in a single line separated by spaces:
10
11 track type=wiggle_0 name=track_label description=center_label \
12 visibility=display_mode color=r,g,b altColor=r,g,b \
13 priority=priority autoScale=on|off \
14 gridDefault=on|off maxHeightPixels=max:default:min \
15 graphType=bar|points viewLimits=lower:upper \
16 yLineMark=real-value yLineOnOff=on|off \
17 windowingFunction=maximum|mean|minimum smoothingWindow=off|2-16
18 """
19
20 import sys,math,shutil,subprocess,os,time,tempfile,string
21 from os.path import abspath
22 from rgutils import timenow, plinke
23 imagedir = '/static/rg' # if needed for images
24 myversion = 'V000.1 April 2007'
25 verbose = False
26
27 def makeGFF(resf='',outfname='',logf=None,twd='.',name='track name',description='track description',topn=1000):
28 """
29 score must be scaled to 0-1000
30
31 Want to make some wig tracks from each analysis
32 Best n -log10(p). Make top hit the window.
33 we use our tab output which has
34 rs chrom offset ADD_stat ADD_p ADD_log10p
35 rs3094315 1 792429 1.151 0.2528 0.597223
36
37 """
38
39 def is_number(s):
40 try:
41 float(s)
42 return True
43 except ValueError:
44 return False
45 header = 'track name=%s description="%s" visibility=2 useScore=1 color=0,60,120\n' % (name,description)
46 column_names = [ 'Seqname', 'Source', 'Feature', 'Start', 'End', 'Score', 'Strand', 'Frame', 'Group' ]
47 halfwidth=100
48 resfpath = os.path.join(twd,resf)
49 resf = open(resfpath,'r')
50 resfl = resf.readlines() # dumb but convenient for millions of rows
51 resfl = [x.split() for x in resfl]
52 headl = resfl[0]
53 resfl = resfl[1:]
54 headl = [x.strip().upper() for x in headl]
55 headIndex = dict(zip(headl,range(0,len(headl))))
56 whatwewant = ['CHR','RS','OFFSET','LOG10ARMITAGEP']
57 wewant = [headIndex.get(x,None) for x in whatwewant]
58 if None in wewant: # missing something
59 logf.write('### Error missing a required header from %s in makeGFF - headIndex=%s\n' % (whatwewant,headIndex))
60 return
61 ppos = wewant[3] # last in list
62 resfl = [x for x in resfl if x[ppos] > '' and x[ppos] <> 'NA']
63 resfl = [(float(x[ppos]),x) for x in resfl] # decorate
64 resfl.sort()
65 resfl.reverse() # using -log10 so larger is better
66 pvals = [x[0] for x in resfl] # need to scale
67 resfl = [x[1] for x in resfl] # drop decoration
68 resfl = resfl[:topn] # truncate
69 maxp = max(pvals) # need to scale
70 minp = min(pvals)
71 prange = abs(maxp-minp) + 0.5 # fudge
72 scalefact = 1000.0/prange
73 logf.write('###maxp=%f,minp=%f,prange=%f,scalefact=%f\n' % (maxp,minp,prange,scalefact))
74 for i,row in enumerate(resfl):
75 row[ppos] = '%d' % (int(scalefact*pvals[i]))
76 resfl[i] = row # replace
77 outf = file(outfname,'w')
78 outf.write(header)
79 outres = [] # need to resort into chrom offset order
80 for i,lrow in enumerate(resfl):
81 chrom,snp,offset,p, = [lrow[x] for x in wewant]
82 gff = ('chr%s' % chrom,'rgCaCo','variation','%d' % (int(offset)-halfwidth),
83 '%d' % (int(offset)+halfwidth),p,'.','.','%s logp=%1.2f' % (snp,pvals[i]))
84 outres.append(gff)
85 outres = [(x[0],int(x[3]),x) for x in outres] # decorate
86 outres.sort() # into chrom offset
87 outres=[x[2] for x in outres] # undecorate
88 outres = ['\t'.join(x) for x in outres]
89 outf.write('\n'.join(outres))
90 outf.write('\n')
91 outf.close()
92
93
94 def plink_assocToGG(plinkout="hm",tag='test'):
95 """ plink --assoc output looks like this
96 # CHR SNP A1 F_A F_U A2 CHISQ P OR
97 # 1 rs3094315 G 0.6685 0.1364 A 104.1 1.929e-24 12.77
98 # write as a genegraph input file
99 """
100 inf = file('%s.assoc' % plinkout,'r')
101 outf = file('%sassoc.xls' % plinkout,'w')
102 res = ['rs\tlog10p%s\tFakeInvOR%s\tRealOR%s' % (tag,tag,tag),] # output header for ucsc genome graphs
103 head = inf.next()
104 for l in inf:
105 ll = l.split()
106 if len(ll) >= 8:
107 p = float(ll[7])
108 if p <> 'NA': # eesh
109 logp = '%9.9f' % -math.log10(p)
110 else:
111 logp = 'NA'
112 try:
113 orat = ll[8]
114 except:
115 orat = 'NA'
116 orat2 = orat
117 # invert large negative odds ratios
118 if float(orat) < 1 and float(orat) > 0.0:
119 orat2 = '%9.9f' % (1.0/float(orat))
120 outl = [ll[1],logp, orat2, orat]
121 res.append('\t'.join(outl))
122 outf.write('\n'.join(res))
123 outf.write('\n')
124 outf.close()
125 inf.close()
126
127 def xformModel(infname='',resf='',outfname='',
128 name='foo',mapf='/usr/local/galaxy/data/rg/ped/x.bim',flog=None):
129 """munge a plink .model file into either a ucsc track or an xls file
130 rerla@meme ~/plink]$ head hmYRI_CEU.model
131 CHR SNP TEST AFF UNAFF CHISQ DF P
132 1 rs3094315 GENO 41/37/11 0/24/64 NA NA NA
133 1 rs3094315 TREND 119/59 24/152 81.05 1 2.201e-19
134 1 rs3094315 ALLELIC 119/59 24/152 104.1 1 1.929e-24
135 1 rs3094315 DOM 78/11 24/64 NA NA NA
136
137 bim file has
138 [rerla@beast pbed]$ head plink_wgas1_example.bim
139 1 rs3094315 0.792429 792429 G A
140 1 rs6672353 0.817376 817376 A G
141 """
142 if verbose:
143 print 'Rgenetics rgCaCo.xformModel got resf=%s, outfname=%s' % (resf,outfname)
144 res = []
145 rsdict = {}
146 map = file(mapf,'r')
147 for l in map: # plink map
148 ll = l.strip().split()
149 if len(ll) >= 3:
150 rs=ll[1].strip()
151 chrom = ll[0]
152 if chrom.lower() == 'x':
153 chrom='23'
154 elif chrom.lower() == 'y':
155 chrom = 24
156 elif chrom.lower() == 'mito':
157 chrom = 25
158 offset = ll[3]
159 rsdict[rs] = (chrom,offset)
160 res.append('rs\tChr\tOffset\tGenop\tlog10Genop\tArmitagep\tlog10Armitagep\tAllelep\tlog10Allelep\tDomp\tlog10Domp')
161 f = open(resf,'r')
162 headl = f.readline()
163 if headl.find('\t') <> -1:
164 headl = headl.split('\t')
165 delim = '\t'
166 else:
167 headl = headl.split()
168 delim = None
169 whatwewant = ['CHR','SNP','TEST','AFF','UNAFF','CHISQ','P']
170 wewant = [headl.index(x) for x in whatwewant]
171 llen = len(headl)
172 lnum = anum = 0
173 lastsnp = None # so we know when to write out a gg line
174 outl = {}
175 f.seek(0)
176 for lnum,l in enumerate(f):
177 if lnum == 0:
178 continue
179 ll = l.split()
180 if delim:
181 ll = l.split(delim)
182 if len(ll) >= llen: # valid line
183 chr,snp,test,naff,nuaff,chi,p = [ll[x] for x in wewant]
184 snp = snp.strip()
185 chrom,offset = rsdict.get(snp,(None,None))
186 anum += 1
187 fp = 1.0 # if NA
188 lp = 0.0
189 try:
190 fp = float(p)
191 if fp > 0:
192 lp = -math.log10(fp)
193 else:
194 fp = 9e-100
195 flog.write('### WARNING - Plink calculated %s for %s p value!!! 9e-100 substituted!\n' % (p,test))
196 flog.write('### offending line #%d in %s = %s' % (lnum,l))
197 except:
198 pass
199 if snp <> lastsnp:
200 if len(outl.keys()) > 3:
201 sl = [outl.get(x,'?') for x in ('snp','chrom','offset','GENO','TREND','ALLELIC','DOM')]
202 res.append('\t'.join(sl)) # last snp line
203 outl = {'snp':snp,'chrom':chrom,'offset':offset} # first 3 cols for gg line
204 lastsnp = snp # reset for next marker
205 #if p == 'NA':
206 # p = 1.0
207 # let's pass downstream for handling R is fine?
208 outl[test] = '%s\t%f' % (p,lp)
209 if len(outl.keys()) > 3:
210 l = [outl.get(x,'?') for x in ('snp','chrom','offset','GENO','TREND','ALLELIC','DOM')]
211 res.append('\t'.join(l)) # last snp line
212 f = file(outfname,'w')
213 res.append('')
214 f.write('\n'.join(res))
215 f.close()
216
217
218
219
220 if __name__ == "__main__":
221 """
222 # called as
223 <command interpreter="python">
224 rgCaCo.py '$i.extra_files_path/$i.metadata.base_name' "$name"
225 '$out_file1' '$logf' '$logf.files_path' '$gffout'
226 </command> </command>
227 """
228 if len(sys.argv) < 7:
229 s = 'rgCaCo.py needs 6 params - got %s \n' % (sys.argv)
230 print >> sys.stdout, s
231 sys.exit(0)
232 bfname = sys.argv[1]
233 name = sys.argv[2]
234 killme = string.punctuation + string.whitespace
235 trantab = string.maketrans(killme,'_'*len(killme))
236 name = name.translate(trantab)
237 outfname = sys.argv[3]
238 logf = sys.argv[4]
239 logoutdir = sys.argv[5]
240 gffout = sys.argv[6]
241 topn = 1000
242 try:
243 os.makedirs(logoutdir)
244 except:
245 pass
246 map_file = None
247 me = sys.argv[0]
248 amapf = '%s.bim' % bfname # to decode map in xformModel
249 flog = file(logf,'w')
250 logme = []
251 cdir = os.getcwd()
252 s = 'Rgenetics %s http://rgenetics.org Galaxy Tools, rgCaCo.py started %s\n' % (myversion,timenow())
253 print >> sys.stdout, s # so will appear as blurb for file
254 logme.append(s)
255 if verbose:
256 s = 'rgCaCo.py: bfname=%s, logf=%s, argv = %s\n' % (bfname, logf, sys.argv)
257 print >> sys.stdout, s # so will appear as blurb for file
258 logme.append(s)
259 twd = tempfile.mkdtemp(suffix='rgCaCo') # make sure plink doesn't spew log file into the root!
260 tname = os.path.join(twd,name)
261 vcl = [plinke,'--noweb','--bfile',bfname,'--out',name,'--model']
262 p=subprocess.Popen(' '.join(vcl),shell=True,stdout=flog,cwd=twd)
263 retval = p.wait()
264 resf = '%s.model' % tname # plink output is here we hope
265 xformModel(bfname,resf,outfname,name,amapf,flog) # leaves the desired summary file
266 makeGFF(resf=outfname,outfname=gffout,logf=flog,twd=twd,name='rgCaCo_TopTable',description=name,topn=topn)
267 flog.write('\n'.join(logme))
268 flog.close() # close the log used
269 #shutil.copytree(twd,logoutdir)
270 shutil.rmtree(twd) # clean up
271