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comparison tools/rgenetics/rgTDT.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 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 """
9 Parameters for wiggle track definition lines
10 All 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
21 import sys,math,shutil,subprocess,os,time,tempfile,shutil,string
22 from os.path import abspath
23 from optparse import OptionParser
24 from rgutils import timenow, plinke
25 myversion = 'v0.003 January 2010'
26 verbose = False
27
28
29
30 def makeGFF(resf='',outfname='',logf=None,twd='.',name='track name',description='track description',topn=1000):
31 """
32 score must be scaled to 0-1000
33
34 Want to make some wig tracks from each analysis
35 Best n -log10(p). Make top hit the window.
36 we use our tab output which has
37 rs chrom offset ADD_stat ADD_p ADD_log10p
38 rs3094315 1 792429 1.151 0.2528 0.597223
39
40 """
41
42 def is_number(s):
43 try:
44 float(s)
45 return True
46 except ValueError:
47 return False
48 header = 'track name=%s description="%s" visibility=2 useScore=1 color=0,60,120\n' % (name,description)
49 column_names = [ 'Seqname', 'Source', 'Feature', 'Start', 'End', 'Score', 'Strand', 'Frame', 'Group' ]
50 halfwidth=100
51 resfpath = os.path.join(twd,resf)
52 resf = open(resfpath,'r')
53 resfl = resf.readlines() # dumb but convenient for millions of rows
54 resfl = [x.split() for x in resfl]
55 headl = resfl[0]
56 resfl = resfl[1:]
57 headl = [x.strip().upper() for x in headl]
58 headIndex = dict(zip(headl,range(0,len(headl))))
59 # s = 'rs\tchrom\toffset\ta1\ta2\ttransmitted\tuntransmitted\tTDTChiSq\tTDTp\t-log10TDTp\tAbsTDTOR\tTDTOR'
60 chrpos = headIndex.get('CHROM',None)
61 rspos = headIndex.get('RS',None)
62 offspos = headIndex.get('OFFSET',None)
63 ppos = headIndex.get('-LOG10TDTP',None)
64 wewant = [chrpos,rspos,offspos,ppos]
65 if None in wewant: # missing something
66 logf.write('### Error missing a required header in makeGFF - headIndex=%s\n' % headIndex)
67 return
68 resfl = [x for x in resfl if x[ppos] > '']
69 resfl = [(float(x[ppos]),x) for x in resfl] # decorate
70 resfl.sort()
71 resfl.reverse() # using -log10 so larger is better
72 resfl = resfl[:topn] # truncate
73 pvals = [x[0] for x in resfl] # need to scale
74 resfl = [x[1] for x in resfl] # drop decoration
75 maxp = max(pvals) # need to scale
76 minp = min(pvals)
77 prange = abs(maxp-minp) + 0.5 # fudge
78 scalefact = 1000.0/prange
79 logf.write('###maxp=%f,minp=%f,prange=%f,scalefact=%f\n' % (maxp,minp,prange,scalefact))
80 for i,row in enumerate(resfl):
81 row[ppos] = '%d' % (int(scalefact*pvals[i]))
82 resfl[i] = row # replace
83 outf = file(outfname,'w')
84 outf.write(header)
85 outres = [] # need to resort into chrom offset order
86 for i,lrow in enumerate(resfl):
87 chrom,snp,offset,p, = [lrow[x] for x in wewant]
88 gff = ('chr%s' % chrom,'rgTDT','variation','%d' % (int(offset)-halfwidth),
89 '%d' % (int(offset)+halfwidth),p,'.','.','%s logp=%1.2f' % (snp,pvals[i]))
90 outres.append(gff)
91 outres = [(x[0],int(x[3]),x) for x in outres] # decorate
92 outres.sort() # into chrom offset
93 outres=[x[2] for x in outres] # undecorate
94 outres = ['\t'.join(x) for x in outres]
95 outf.write('\n'.join(outres))
96 outf.write('\n')
97 outf.close()
98
99
100
101 def xformTDT(infname='',resf='',outfname='',name='foo',mapf='/usr/local/galaxy/data/rg/lped/x.bim'):
102 """munge a plink .tdt file into either a ucsc track or an xls file
103 CHR SNP A1:A2 T:U_TDT OR_TDT CHISQ_TDT P_TDT
104 0 MitoT217C 2:3 0:0 NA NA NA
105 0 MitoG228A 1:4 0:0 NA NA NA
106 0 MitoT250C 2:3 0:0 NA NA NA
107 map file has
108 1 rs4378174 0 003980745
109 1 rs10796404 0 005465256
110 1 rs2697965 0 014023092
111
112 grrr!
113 Changed in 1.01 to
114 [rerla@hg fresh]$ head database/job_working_directory/445/rgTDT.tdt
115 CHR SNP BP A1 A2 T U OR CHISQ P
116 1 rs12562034 758311 1 3 71 79 0.8987 0.4267 0.5136
117 1 rs3934834 995669 4 2 98 129 0.7597 4.233 0.03963
118
119
120 """
121 if verbose:
122 print 'Rgenetics Galaxy Tools, rgTDT.py.xformTDT got resf=%s, outtype=%s, outfname=%s' % (resf,outtype,outfname)
123 wewantcols = ['SNP','CHR','BP','A1','A2','T','U','OR','CHISQ','P']
124 res = []
125 s = 'rs\tchrom\toffset\ta1\ta2\ttransmitted\tuntransmitted\tTDTChiSq\tTDTp\t-log10TDTp\tAbsTDTOR\tTDTOR' # header
126 res.append(s)
127 rsdict = {}
128 if not mapf:
129 sys.stderr.write('rgTDT called but no map file provided - cannot determine locations')
130 sys.exit(1)
131 map = file(mapf,'r')
132 for l in map: # plink map
133 ll = l.strip().split()
134 if len(ll) >= 3:
135 rs=ll[1].strip()
136 chrom = ll[0]
137 if chrom.lower() == 'x':
138 chrom = '23'
139 if chrom.lower() == 'y':
140 chrom = '24'
141 if chrom.lower() == 'mito':
142 chrom = '25'
143 offset = ll[3]
144 rsdict[rs] = (chrom,offset)
145 f = open(resf,'r')
146 headl = f.next().strip()
147 headl = headl.split()
148 wewant = [headl.index(x) for x in wewantcols]
149 llen = len(headl)
150 lnum = anum = 0
151 for l in f:
152 lnum += 1
153 ll = l.strip().split()
154 if len(ll) >= llen: # valid line
155 snp,chrom,offset,a1,a2,t,u,orat,chisq,p = [ll[x] for x in wewant]
156 if chisq == 'NA' or p == 'NA' or orat == 'NA':
157 continue # can't use these lines - gg gets unhappy
158 snp = snp.strip()
159 lp = '0.0'
160 fp = '1.0'
161 fakeorat = '1.0'
162 if p.upper().strip() <> 'NA':
163 try:
164 fp = float(p)
165 if fp <> 0:
166 lp = '%6f' % -math.log10(fp)
167 fp = '%6f' % fp
168 except:
169 pass
170 else:
171 p = '1.0'
172 if orat.upper().strip() <> 'NA':
173 try:
174 fakeorat = orat
175 if float(orat) < 1.0:
176 fakeorat = '%6f' % (1.0/float(orat)) # invert so large values big
177 except:
178 pass
179 else:
180 orat = '1.0'
181 outl = '\t'.join([snp,chrom,offset,a1,a2,t,u,chisq,p,lp,fakeorat,orat])
182 res.append(outl)
183 f = file(outfname,'w')
184 res.append('')
185 f.write('\n'.join(res))
186 f.close()
187
188
189 if __name__ == "__main__":
190 """ called as
191 <command interpreter="python">
192 rgTDT.py -i '$infile.extra_files_path/$infile.metadata.base_name' -o '$title' -f '$outformat' -r '$out_file1' -l '$logf' -x '${GALAXY_DATA_INDEX_DIR}/rg/bin/pl$
193
194 </command>
195
196 """
197 u = """ called in xml as
198 <command interpreter="python2.4">
199 rgTDT.py -i $i -o $out_prefix -f $outformat -r $out_file1 -l $logf
200 </command>
201 """
202 if len(sys.argv) < 6:
203 s = '## Error rgTDT.py needs 5 command line params - got %s \n' % (sys.argv)
204 if verbose:
205 print >> sys.stdout, s
206 sys.exit(0)
207 parser = OptionParser(usage=u, version="%prog 0.01")
208 a = parser.add_option
209 a("-i","--infile",dest="bfname")
210 a("-o","--oprefix",dest="oprefix")
211 a("-f","--formatOut",dest="outformat")
212 a("-r","--results",dest="outfname")
213 a("-l","--logfile",dest="logf")
214 a("-d","--du",dest="uId")
215 a("-e","--email",dest="uEmail")
216 a("-g","--gff",dest="gffout",default="")
217 (options,args) = parser.parse_args()
218 killme = string.punctuation + string.whitespace
219 trantab = string.maketrans(killme,'_'*len(killme))
220 title = options.oprefix
221 title = title.translate(trantab)
222 map_file = '%s.bim' % (options.bfname) #
223 me = sys.argv[0]
224 alogf = options.logf # absolute paths
225 od = os.path.split(alogf)[0]
226 try:
227 os.path.makedirs(od)
228 except:
229 pass
230 aoutf = options.outfname # absolute paths
231 od = os.path.split(aoutf)[0]
232 try:
233 os.path.makedirs(od)
234 except:
235 pass
236 vcl = [plinke,'--noweb', '--bfile',options.bfname,'--out',title,'--mind','0.5','--tdt']
237 logme = []
238 if verbose:
239 s = 'Rgenetics %s http://rgenetics.org Galaxy Tools rgTDT.py started %s\n' % (myversion,timenow())
240 print >> sys.stdout,s
241 logme.append(s)
242 s ='rgTDT.py: bfname=%s, logf=%s, argv = %s\n' % (options.bfname,alogf, sys.argv)
243 print >> sys.stdout,s
244 logme.append(s)
245 s = 'rgTDT.py: vcl=%s\n' % (' '.join(vcl))
246 print >> sys.stdout,s
247 logme.append(s)
248 twd = tempfile.mkdtemp(suffix='rgTDT') # make sure plink doesn't spew log file into the root!
249 tname = os.path.join(twd,title)
250 p=subprocess.Popen(' '.join(vcl),shell=True,cwd=twd)
251 retval = p.wait()
252 shutil.copy('%s.log' % tname,alogf)
253 sto = file(alogf,'a')
254 sto.write('\n'.join(logme))
255 resf = '%s.tdt' % tname # plink output is here we hope
256 xformTDT(options.bfname,resf,aoutf,title,map_file) # leaves the desired summary file
257 gffout = options.gffout
258 if gffout > '':
259 makeGFF(resf=aoutf,outfname=gffout,logf=sto,twd='.',name='rgTDT_Top_Table',description=title,topn=1000)
260 shutil.rmtree(twd)
261 sto.close()
262
263
264