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

リビジョン 2, 11.2 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central
行番号 
1# utilities for rgenetics
2#
3# copyright 2009 ross lazarus
4# released under the LGPL
5#
6
7import subprocess, os, sys, time, tempfile,string,plinkbinJZ
8
9galhtmlprefix = """<?xml version="1.0" encoding="utf-8" ?>
10<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
11<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
12<head>
13<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
14<meta name="generator" content="Galaxy %s tool output - see http://g2.trac.bx.psu.edu/" />
15<title></title>
16<link rel="stylesheet" href="/static/style/base.css" type="text/css" />
17</head>
18<body>
19<div class="document">
20"""
21galhtmlattr = """<h3><a href="http://rgenetics.org">Rgenetics</a> tool %s run at %s</h3>"""
22galhtmlpostfix = """</div></body></html>\n"""
23
24plinke = 'plink' # changed jan 2010 - all exes must be on path
25rexe = 'R'       # to avoid cluster/platform dependencies
26smartpca = 'smartpca.perl'
27
28def timenow():
29    """return current time as a string
30    """
31    return time.strftime('%d/%m/%Y %H:%M:%S', time.localtime(time.time()))
32
33def fail( message ):
34    print >> sys.stderr, message
35    return -1
36
37def whereis(program):
38    for path in os.environ.get('PATH', '').split(':'):
39        if os.path.exists(os.path.join(path, program)) and \
40           not os.path.isdir(os.path.join(path, program)):
41            return os.path.join(path, program)
42    return None
43
44
45def oRRun(rcmd=[],outdir=None,title='myR',rexe='R'):
46    """
47    run an r script, lines in rcmd,
48    in a temporary directory
49    move everything, r script and all back to outdir which will be an html file
50
51
52      # test
53      RRun(rcmd=['print("hello cruel world")','q()'],title='test')
54    """
55    rlog = []
56    print '### rexe = %s' % rexe
57    assert os.path.isfile(rexe)
58    rname = '%s.R' % title
59    stoname = '%s.R.log' % title
60    rfname = rname
61    stofname = stoname
62    if outdir: # want a specific path
63        rfname = os.path.join(outdir,rname)
64        stofname = os.path.join(outdir,stoname)
65        try:
66                os.makedirs(outdir) # might not be there yet...
67        except:
68            pass
69    else:
70        outdir = tempfile.mkdtemp(prefix=title)
71        rfname = os.path.join(outdir,rname)
72        stofname = os.path.join(outdir,stoname)
73        rmoutdir = True
74    f = open(rfname,'w')
75    if type(rcmd) == type([]):
76        f.write('\n'.join(rcmd))
77    else: # string
78        f.write(rcmd)
79    f.write('\n')
80    f.close()
81    sto = file(stofname,'w')
82    vcl = [rexe,"--vanilla --slave", '<', rfname ]
83    x = subprocess.Popen(' '.join(vcl),shell=True,stderr=sto,stdout=sto,cwd=outdir)
84    retval = x.wait()
85    sto.close()
86    rlog = file(stofname,'r').readlines()
87    rlog.insert(0,'## found R at %s' % rexe)
88    if outdir <> None:
89        flist = os.listdir(outdir)
90    else:
91        flist = os.listdir('.')
92    flist.sort
93    flist = [(x,x) for x in flist]
94    for i,x in enumerate(flist):
95        if x == rname:
96            flist[i] = (x,'R script for %s' % title)
97        elif x == stoname:
98            flist[i] = (x,'R log for %s' % title)
99    if False and rmoutdir:
100        os.removedirs(outdir)
101    return rlog,flist # for html layout
102
103
104
105
106def RRun(rcmd=[],outdir=None,title='myR',tidy=True):
107    """
108    run an r script, lines in rcmd,
109    in a temporary directory
110    move everything, r script and all back to outdir which will be an html file
111
112
113      # test
114      RRun(rcmd=['print("hello cruel world")','q()'],title='test')
115    echo "a <- c(5, 5); b <- c(0.5, 0.5)" | cat - RScript.R | R --slave \ --vanilla
116    suggested by http://tolstoy.newcastle.edu.au/R/devel/05/09/2448.html
117    """
118    killme = string.punctuation + string.whitespace
119    trantab = string.maketrans(killme,'_'*len(killme))
120    title = title.translate(trantab)
121    rlog = []
122    tempout=False
123    rname = '%s.R' % title
124    stoname = '%s.R.log' % title
125    cwd = os.getcwd()
126    if outdir: # want a specific path
127        try:
128            os.makedirs(outdir) # might not be there yet...
129        except:
130            pass
131        os.chdir(outdir)
132    if type(rcmd) == type([]):
133        script = '\n'.join(rcmd)
134    else: # string
135        script = rcmd
136    sto = file(stoname,'w')
137    rscript = file(rname,'w')
138    rscript.write(script)
139    rscript.write('\n#R script autogenerated by rgenetics/rgutils.py on %s\n' % timenow())
140    rscript.close()
141    vcl = '%s --slave --vanilla < %s' %  (rexe,rname)
142    if outdir:
143        x = subprocess.Popen(vcl,shell=True,stderr=sto,stdout=sto,cwd=outdir)
144    else:
145        x = subprocess.Popen(vcl,shell=True,stderr=sto,stdout=sto)
146    retval = x.wait()
147    sto.close()
148    rlog = file(stoname,'r').readlines()
149    if retval <> 0:
150        rlog.insert(0,'Nonzero exit code = %d' % retval) # indicate failure
151    if outdir:
152        flist = os.listdir(outdir)
153    else:
154        flist = os.listdir(os.getcwd())
155    flist.sort
156    flist = [(x,x) for x in flist]
157    for i,x in enumerate(flist):
158        if x == rname:
159            flist[i] = (x,'R script for %s' % title)
160        elif x == stoname:
161            flist[i] = (x,'R log for %s' % title)
162    if outdir:
163        os.chdir(cwd)
164    return rlog,flist # for html layout
165
166def runPlink(bfn='bar',ofn='foo',logf=None,plinktasks=[],cd='./',vclbase = []):
167    """run a series of plink tasks and append log results to stdout
168    vcl has a list of parameters for the spawnv
169    common settings can all go in the vclbase list and are added to each plinktask
170    """
171    # root for all
172    fplog,plog = tempfile.mkstemp()
173    if type(logf) == type('  '): # open otherwise assume is file - ugh I'm in a hurry
174        mylog = file(logf,'a+')
175    else:
176        mylog = logf
177    mylog.write('## Rgenetics: http://rgenetics.org Galaxy Tools rgQC.py Plink runner\n')
178    for task in plinktasks: # each is a list
179        vcl = vclbase + task
180        sto = file(plog,'w')
181        x = subprocess.Popen(' '.join(vcl),shell=True,stdout=sto,stderr=sto,cwd=cd)
182        retval = x.wait()
183        sto.close()
184        try:
185            lplog = file(plog,'r').read()
186            mylog.write(lplog)
187            os.unlink(plog) # no longer needed
188        except:
189            mylog.write('### %s Strange - no std out from plink when running command line\n%s' % (timenow(),' '.join(vcl)))
190
191def pruneLD(plinktasks=[],cd='./',vclbase = []):
192    """
193    plink blathers when doing pruning - ignore
194    Linkage disequilibrium based SNP pruning
195    if a million snps in 3 billion base pairs, have mean 3k spacing
196    assume 40-60k of ld in ceu, a window of 120k width is about 40 snps
197    so lots more is perhaps less efficient - each window computational cost is
198    ON^2 unless the code is smart enough to avoid unecessary computation where
199    allele frequencies make it impossible to see ld > the r^2 cutoff threshold
200    So, do a window and move forward 20?
201    The fine Plink docs at http://pngu.mgh.harvard.edu/~purcell/plink/summary.shtml#prune
202    reproduced below
203
204Sometimes it is useful to generate a pruned subset of SNPs that are in approximate linkage equilibrium with each other. This can be achieved via two commands: --indep which prunes based on the variance inflation factor (VIF), which recursively removes SNPs within a sliding window; second, --indep-pairwise which is similar, except it is based only on pairwise genotypic correlation.
205
206Hint The output of either of these commands is two lists of SNPs: those that are pruned out and those that are not. A separate command using the --extract or --exclude option is necessary to actually perform the pruning.
207
208The VIF pruning routine is performed:
209plink --file data --indep 50 5 2
210
211will create files
212
213     plink.prune.in
214     plink.prune.out
215
216Each is a simlpe list of SNP IDs; both these files can subsequently be specified as the argument for
217a --extract or --exclude command.
218
219The parameters for --indep are: window size in SNPs (e.g. 50), the number of SNPs to shift the
220window at each step (e.g. 5), the VIF threshold. The VIF is 1/(1-R^2) where R^2 is the multiple correlation coefficient for a SNP being regressed on all other SNPs simultaneously. That is, this considers the correlations between SNPs but also between linear combinations of SNPs. A VIF of 10 is often taken to represent near collinearity problems in standard multiple regression analyses (i.e. implies R^2 of 0.9). A VIF of 1 would imply that the SNP is completely independent of all other SNPs. Practically, values between 1.5 and 2 should probably be used; particularly in small samples, if this threshold is too low and/or the window size is too large, too many SNPs may be removed.
221
222The second procedure is performed:
223plink --file data --indep-pairwise 50 5 0.5
224
225This generates the same output files as the first version; the only difference is that a
226simple pairwise threshold is used. The first two parameters (50 and 5) are the same as above (window size and step); the third parameter represents the r^2 threshold. Note: this represents the pairwise SNP-SNP metric now, not the multiple correlation coefficient; also note, this is based on the genotypic correlation, i.e. it does not involve phasing.
227
228To give a concrete example: the command above that specifies 50 5 0.5 would a) consider a
229window of 50 SNPs, b) calculate LD between each pair of SNPs in the window, b) remove one of a pair of SNPs if the LD is greater than 0.5, c) shift the window 5 SNPs forward and repeat the procedure.
230
231To make a new, pruned file, then use something like (in this example, we also convert the
232standard PED fileset to a binary one):
233plink --file data --extract plink.prune.in --make-bed --out pruneddata
234    """
235    fplog,plog = tempfile.mkstemp()
236    alog = []
237    alog.append('## Rgenetics: http://rgenetics.org Galaxy Tools rgQC.py Plink pruneLD runner\n')
238    for task in plinktasks: # each is a list
239        vcl = vclbase + task
240        sto = file(plog,'w')
241        x = subprocess.Popen(' '.join(vcl),shell=True,stdout=sto,stderr=sto,cwd=cd)
242        retval = x.wait()
243        sto.close()
244        try:
245            lplog = file(plog,'r').readlines()
246            lplog = [x for x in lplog if x.find('Pruning SNP') == -1]
247            alog += lplog
248            alog.append('\n')
249            os.unlink(plog) # no longer needed
250        except:
251            alog.append('### %s Strange - no std out from plink when running command line\n%s\n' % (timenow(),' '.join(vcl)))
252    return alog
253
254def readMap(mapfile=None,allmarkers=False,rsdict={},c=None,spos=None,epos=None):
255    """abstract out - keeps reappearing
256    """
257    mfile = open(mapfile, 'r')
258    markers = []
259    snpcols = {}
260    snpIndex = 0 # in case empty or comment lines
261    for rownum,row in enumerate(mfile):
262        line = row.strip()
263        if not line or line[0]=='#': continue
264        chrom, snp, genpos, abspos = line.split()[:4] # just in case more cols
265        try:
266            abspos = int(abspos)
267        except:
268            abspos = 0 # stupid framingham data grumble grumble
269        if allmarkers or rsdict.get(snp,None) or (chrom == c and (spos <= abspos <= epos)):
270            markers.append((chrom,abspos,snp)) # decorate for sort into genomic
271            snpcols[snp] = snpIndex # so we know which col to find genos for this marker
272            snpIndex += 1
273    markers.sort()
274    rslist = [x[2] for x in markers] # drop decoration
275    rsdict = dict(zip(rslist,rslist))
276    mfile.close()
277    return markers,snpcols,rslist,rsdict
278
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