Files
galaxy/tools/rgenetics/rgutils.py
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Python

# utilities for rgenetics
#
# copyright 2009 ross lazarus
# released under the LGPL
#
import subprocess, os, sys, time, tempfile,string,plinkbinJZ
import datetime
galhtmlprefix = """<?xml version="1.0" encoding="utf-8" ?>
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
<meta name="generator" content="Galaxy %s tool output - see http://g2.trac.bx.psu.edu/" />
<title></title>
<link rel="stylesheet" href="/static/style/base.css" type="text/css" />
</head>
<body>
<div class="document">
"""
galhtmlattr = """<h3><a href="http://rgenetics.org">Rgenetics</a> tool %s run at %s</h3>"""
galhtmlpostfix = """</div></body></html>\n"""
plinke = 'plink' # changed jan 2010 - all exes must be on path
rexe = 'R' # to avoid cluster/platform dependencies
smartpca = 'smartpca.perl'
def timenow():
"""return current time as a string
"""
return time.strftime('%d/%m/%Y %H:%M:%S', time.localtime(time.time()))
def timestamp():
return datetime.datetime.now().strftime('%Y%m%d%H%M%S')
def fail( message ):
print >> sys.stderr, message
return -1
def whereis(program):
for path in os.environ.get('PATH', '').split(':'):
if os.path.exists(os.path.join(path, program)) and \
not os.path.isdir(os.path.join(path, program)):
return os.path.join(path, program)
return None
def bedToPicInterval(infile=None):
"""
Picard tools requiring targets want
a sam style header which incidentally, MUST be sorted in natural order - not lexicographic order:
@SQ SN:chrM LN:16571
@SQ SN:chr1 LN:247249719
@SQ SN:chr2 LN:242951149
@SQ SN:chr3 LN:199501827
@SQ SN:chr4 LN:191273063
added to the start of what looks like a bed style file
chr1 67052400 67052451 - CCDS635.1_cds_0_0_chr1_67052401_r
chr1 67060631 67060788 - CCDS635.1_cds_1_0_chr1_67060632_r
chr1 67065090 67065317 - CCDS635.1_cds_2_0_chr1_67065091_r
chr1 67066082 67066181 - CCDS635.1_cds_3_0_chr1_67066083_r
see http://genome.ucsc.edu/FAQ/FAQtracks.html#tracks1
we need to add 1 to start coordinates on the way through - but length calculations are easier
"""
# bedToPicard.py
# ross lazarus October 2010
# LGPL
# for Rgenetics
def getFlen(bedfname=None):
"""
find all features in a BED file and sum their lengths
"""
features = {}
try:
infile = open(bedfname,'r')
except:
print '###ERROR: getFlen unable to open bedfile %s' % bedfname
sys.exit(1)
for i,row in enumerate(infile):
if row[0] == '@': # shouldn't happen given a bed file!
print 'row %d=%s - should NOT start with @!' % (i,row)
sys.exit(1)
row = row.strip()
if len(row) > 0:
srow = row.split('\t')
f = srow[0]
spos = srow[1] # zero based from UCSC so no need to add 1 - eg 0-100 is 100 bases numbered 0-99 (!)
epos = srow[2] # see http://genome.ucsc.edu/FAQ/FAQtracks.html#tracks1
flen = int(epos) - int(spos)
features.setdefault(f,0)
features[f] += flen
infile.close()
return features
def keynat(string):
'''
borrowed from http://code.activestate.com/recipes/285264-natural-string-sorting/
A natural sort helper function for sort() and sorted()
without using regular expressions or exceptions.
>>> items = ('Z', 'a', '10th', '1st', '9')
>>> sorted(items)
['10th', '1st', '9', 'Z', 'a']
>>> sorted(items, key=keynat)
['1st', '9', '10th', 'a', 'Z']
'''
it = type(1)
r = []
for c in string:
if c.isdigit():
d = int(c)
if r and type( r[-1] ) == it:
r[-1] = r[-1] * 10 + d
else:
r.append(d)
else:
r.append(c.lower())
return r
def writePic(outfname=None,bedfname=None):
"""
collect header info and rewrite bed with header for picard
"""
featlen = getFlen(bedfname=bedfname)
try:
outf = open(outfname,'w')
except:
print '###ERROR: writePic unable to open output picard file %s' % outfname
sys.exit(1)
infile = open(bedfname,'r') # already tested in getFlen
k = featlen.keys()
fk = sorted(k, key=keynat)
header = ['@SQ\tSN:%s\tLN:%d' % (x,featlen[x]) for x in fk]
outf.write('\n'.join(header))
outf.write('\n')
for row in infile:
row = row.strip()
if len(row) > 0: # convert zero based start coordinate to 1 based
srow = row.split('\t')
srow[1] = '%d' % (int(srow[1])+1) # see http://genome.ucsc.edu/FAQ/FAQtracks.html#tracks1
outf.write('\t'.join(srow))
outf.write('\n')
outf.close()
infile.close()
# bedToPicInterval starts here
fd,outf = tempfile.mkstemp(prefix='rgPicardHsMetrics')
writePic(outfname=outf,bedfname=infile)
return outf
def getFileString(fpath, outpath):
"""
format a nice file size string
"""
size = ''
fp = os.path.join(outpath, fpath)
s = '? ?'
if os.path.isfile(fp):
n = float(os.path.getsize(fp))
if n > 2**20:
size = ' (%1.1f MB)' % (n/2**20)
elif n > 2**10:
size = ' (%1.1f KB)' % (n/2**10)
elif n > 0:
size = ' (%d B)' % (int(n))
s = '%s %s' % (fpath, size)
return s
def fixPicardOutputs(tempout=None,output_dir=None,log_file=None,html_output=None,progname=None,cl=[],transpose=True):
"""
picard produces long hard to read tab header files
make them available but present them transposed for readability
"""
rstyle="""<style type="text/css">
tr.d0 td {background-color: oldlace; color: black;}
tr.d1 td {background-color: aliceblue; color: black;}
</style>"""
cruft = []
dat = []
try:
r = open(tempout,'r').readlines()
except:
r = []
for row in r:
if row.strip() > '':
srow = row.split('\t')
if row[0] == '#':
cruft.append(row.strip()) # want strings
else:
dat.append(srow) # want lists
res = [rstyle,]
res.append(galhtmlprefix % progname)
res.append(galhtmlattr % (progname,timenow()))
flist = os.listdir(output_dir)
pdflist = [x for x in flist if os.path.splitext(x)[-1].lower() == '.pdf']
if len(pdflist) > 0: # assumes all pdfs come with thumbnail .jpgs
for p in pdflist:
imghref = '%s.jpg' % os.path.splitext(p)[0] # removes .pdf
res.append('<table cellpadding="10"><tr><td>\n')
res.append('<a href="%s"><img src="%s" alt="Click thumbnail to download %s" hspace="10" align="middle"></a>\n' % (p,imghref,p))
res.append('</tr></td></table>\n')
res.append('<b>Your job produced the following output files.</b><hr/>\n')
res.append('<table>\n')
for i,f in enumerate(flist):
fn = os.path.split(f)[-1]
res.append('<tr><td><a href="%s">%s</a></td></tr>\n' % (fn,fn))
res.append('</table><p/>\n')
if len(cruft) + len(dat) > 0:
res.append('<b>Picard on line resources</b><ul>\n')
res.append('<li><a href="http://picard.sourceforge.net/index.shtml">Click here for Picard Documentation</a></li>\n')
res.append('<li><a href="http://picard.sourceforge.net/picard-metric-definitions.shtml">Click here for Picard Metrics definitions</a></li></ul><hr/>\n')
if transpose:
res.append('<b>Picard output (transposed for readability)</b><hr/>\n')
else:
res.append('<b>Picard output</b><hr/>\n')
res.append('<table cellpadding="3" >\n')
if len(cruft) > 0:
cres = ['<tr class="d%d"><td>%s</td></tr>' % (i % 2,x) for i,x in enumerate(cruft)]
res += cres
if len(dat) > 0:
maxrows = 100
if transpose:
tdat = map(None,*dat) # transpose an arbitrary list of lists
missing = len(tdat) - maxrows
tdat = ['<tr class="d%d"><td>%s</td><td>%s</td></tr>\n' % ((i+len(cruft)) % 2,x[0],x[1]) for i,x in enumerate(tdat) if i < maxrows]
if len(tdat) > maxrows:
tdat.append('<tr><td colspan="2">...WARNING: %d rows deleted for sanity...see raw files for all rows</td></tr>' % missing)
else:
tdat = ['<tr class="d%d"><td>%s</td></tr>\n' % ((i+len(cruft)) % 2,x) for i,x in enumerate(dat) if i < maxrows]
if len(dat) > maxrows:
missing = len(dat) - maxrows
tdat.append('<tr><td>...WARNING: %d rows deleted for sanity...see raw files for all rows</td></tr>' % missing)
res += tdat
res.append('</table>\n')
else:
res.append('<b>No Picard output found - please consult the Picard log above for an explanation</b>')
l = open(log_file,'r').readlines()
if len(l) > 0:
res.append('<b>Picard log</b><hr/>\n')
rlog = ['<pre>',]
rlog += l
rlog.append('</pre>')
res += rlog
else:
res.append("Odd, Picard left no log file %s - must have really barfed badly?" % log_file)
res.append('<hr/>The freely available <a href="http://picard.sourceforge.net/command-line-overview.shtml">Picard software</a> \n')
res.append( 'generated all outputs reported here, using this command line:<br/>\n<pre>%s</pre>\n' % ''.join(cl))
res.append(galhtmlpostfix)
outf = open(html_output,'w')
outf.write(''.join(res))
outf.write('\n')
outf.close()
def keynat(string):
'''
borrowed from http://code.activestate.com/recipes/285264-natural-string-sorting/
A natural sort helper function for sort() and sorted()
without using regular expressions or exceptions.
>>> items = ('Z', 'a', '10th', '1st', '9')
>>> sorted(items)
['10th', '1st', '9', 'Z', 'a']
>>> sorted(items, key=keynat)
['1st', '9', '10th', 'a', 'Z']
'''
it = type(1)
r = []
for c in string:
if c.isdigit():
d = int(c)
if r and type( r[-1] ) == it:
r[-1] = r[-1] * 10 + d
else:
r.append(d)
else:
r.append(c.lower())
return r
def getFlen(bedfname=None):
"""
find all features in a BED file and sum their lengths
"""
features = {}
otherHeaders = []
try:
infile = open(bedfname,'r')
except:
print '###ERROR: getFlen unable to open bedfile %s' % bedfname
sys.exit(1)
for i,row in enumerate(infile):
if row.startswith('@'): # add to headers if not @SQ
if not row.startswith('@SQ'):
otherHeaders.append(row)
else:
row = row.strip()
if row.startswith('#') or row.lower().startswith('browser') or row.lower().startswith('track'):
continue # ignore headers
srow = row.split('\t')
if len(srow) > 3:
srow = row.split('\t')
f = srow[0]
spos = srow[1] # zero based from UCSC so no need to add 1 - eg 0-100 is 100 bases numbered 0-99 (!)
epos = srow[2] # see http://genome.ucsc.edu/FAQ/FAQtracks.html#tracks1
flen = int(epos) - int(spos)
features.setdefault(f,0)
features[f] += flen
infile.close()
fk = features.keys()
fk = sorted(fk, key=keynat)
return features,fk,otherHeaders
def bedToPicInterval(infile=None,outfile=None):
"""
Picard tools requiring targets want
a sam style header which incidentally, MUST be sorted in natural order - not lexicographic order:
@SQ SN:chrM LN:16571
@SQ SN:chr1 LN:247249719
@SQ SN:chr2 LN:242951149
@SQ SN:chr3 LN:199501827
@SQ SN:chr4 LN:191273063
added to the start of what looks like a bed style file
chr1 67052400 67052451 - CCDS635.1_cds_0_0_chr1_67052401_r
chr1 67060631 67060788 - CCDS635.1_cds_1_0_chr1_67060632_r
chr1 67065090 67065317 - CCDS635.1_cds_2_0_chr1_67065091_r
chr1 67066082 67066181 - CCDS635.1_cds_3_0_chr1_67066083_r
see http://genome.ucsc.edu/FAQ/FAQtracks.html#tracks1
we need to add 1 to start coordinates on the way through - but length calculations are easier
"""
# bedToPicard.py
# ross lazarus October 2010
# LGPL
# for Rgenetics
"""
collect header info and rewrite bed with header for picard
"""
featlen,fk,otherHeaders = getFlen(bedfname=infile)
try:
outf = open(outfile,'w')
except:
print '###ERROR: writePic unable to open output picard file %s' % outfile
sys.exit(1)
inf = open(infile,'r') # already tested in getFlen
header = ['@SQ\tSN:%s\tLN:%d' % (x,featlen[x]) for x in fk]
if len(otherHeaders) > 0:
header += otherHeaders
outf.write('\n'.join(header))
outf.write('\n')
for row in inf:
row = row.strip()
if len(row) > 0: # convert zero based start coordinate to 1 based
if row.startswith('@'):
continue
else:
srow = row.split('\t')
srow[1] = '%d' % (int(srow[1])+1) # see http://genome.ucsc.edu/FAQ/FAQtracks.html#tracks1
outf.write('\t'.join(srow))
outf.write('\n')
outf.close()
inf.close()
def oRRun(rcmd=[],outdir=None,title='myR',rexe='R'):
"""
run an r script, lines in rcmd,
in a temporary directory
move everything, r script and all back to outdir which will be an html file
# test
RRun(rcmd=['print("hello cruel world")','q()'],title='test')
"""
rlog = []
print '### rexe = %s' % rexe
assert os.path.isfile(rexe)
rname = '%s.R' % title
stoname = '%s.R.log' % title
rfname = rname
stofname = stoname
if outdir: # want a specific path
rfname = os.path.join(outdir,rname)
stofname = os.path.join(outdir,stoname)
try:
os.makedirs(outdir) # might not be there yet...
except:
pass
else:
outdir = tempfile.mkdtemp(prefix=title)
rfname = os.path.join(outdir,rname)
stofname = os.path.join(outdir,stoname)
rmoutdir = True
f = open(rfname,'w')
if type(rcmd) == type([]):
f.write('\n'.join(rcmd))
else: # string
f.write(rcmd)
f.write('\n')
f.close()
sto = file(stofname,'w')
vcl = [rexe,"--vanilla --slave", '<', rfname ]
x = subprocess.Popen(' '.join(vcl),shell=True,stderr=sto,stdout=sto,cwd=outdir)
retval = x.wait()
sto.close()
rlog = file(stofname,'r').readlines()
rlog.insert(0,'## found R at %s' % rexe)
if outdir <> None:
flist = os.listdir(outdir)
else:
flist = os.listdir('.')
flist.sort
flist = [(x,x) for x in flist]
for i,x in enumerate(flist):
if x == rname:
flist[i] = (x,'R script for %s' % title)
elif x == stoname:
flist[i] = (x,'R log for %s' % title)
if False and rmoutdir:
os.removedirs(outdir)
return rlog,flist # for html layout
def RRun(rcmd=[],outdir=None,title='myR',tidy=True):
"""
run an r script, lines in rcmd,
in a temporary directory
move everything, r script and all back to outdir which will be an html file
# test
RRun(rcmd=['print("hello cruel world")','q()'],title='test')
echo "a <- c(5, 5); b <- c(0.5, 0.5)" | cat - RScript.R | R --slave \ --vanilla
suggested by http://tolstoy.newcastle.edu.au/R/devel/05/09/2448.html
"""
killme = string.punctuation + string.whitespace
trantab = string.maketrans(killme,'_'*len(killme))
title = title.translate(trantab)
rlog = []
tempout=False
rname = '%s.R' % title
stoname = '%s.R.log' % title
cwd = os.getcwd()
if outdir: # want a specific path
try:
os.makedirs(outdir) # might not be there yet...
except:
pass
os.chdir(outdir)
if type(rcmd) == type([]):
script = '\n'.join(rcmd)
else: # string
script = rcmd
sto = file(stoname,'w')
rscript = file(rname,'w')
rscript.write(script)
rscript.write('\n#R script autogenerated by rgenetics/rgutils.py on %s\n' % timenow())
rscript.close()
vcl = '%s --slave --vanilla < %s' % (rexe,rname)
if outdir:
x = subprocess.Popen(vcl,shell=True,stderr=sto,stdout=sto,cwd=outdir)
else:
x = subprocess.Popen(vcl,shell=True,stderr=sto,stdout=sto)
retval = x.wait()
sto.close()
rlog = file(stoname,'r').readlines()
if retval <> 0:
rlog.insert(0,'Nonzero exit code = %d' % retval) # indicate failure
if outdir:
flist = os.listdir(outdir)
else:
flist = os.listdir(os.getcwd())
flist.sort
flist = [(x,x) for x in flist]
for i,x in enumerate(flist):
if x == rname:
flist[i] = (x,'R script for %s' % title)
elif x == stoname:
flist[i] = (x,'R log for %s' % title)
if outdir:
os.chdir(cwd)
return rlog,flist # for html layout
def runPlink(bfn='bar',ofn='foo',logf=None,plinktasks=[],cd='./',vclbase = []):
"""run a series of plink tasks and append log results to stdout
vcl has a list of parameters for the spawnv
common settings can all go in the vclbase list and are added to each plinktask
"""
# root for all
fplog,plog = tempfile.mkstemp()
if type(logf) == type(' '): # open otherwise assume is file - ugh I'm in a hurry
mylog = file(logf,'a+')
else:
mylog = logf
mylog.write('## Rgenetics: http://rgenetics.org Galaxy Tools rgQC.py Plink runner\n')
for task in plinktasks: # each is a list
vcl = vclbase + task
sto = file(plog,'w')
x = subprocess.Popen(' '.join(vcl),shell=True,stdout=sto,stderr=sto,cwd=cd)
retval = x.wait()
sto.close()
try:
lplog = file(plog,'r').read()
mylog.write(lplog)
os.unlink(plog) # no longer needed
except:
mylog.write('### %s Strange - no std out from plink when running command line\n%s' % (timenow(),' '.join(vcl)))
def pruneLD(plinktasks=[],cd='./',vclbase = []):
"""
plink blathers when doing pruning - ignore
Linkage disequilibrium based SNP pruning
if a million snps in 3 billion base pairs, have mean 3k spacing
assume 40-60k of ld in ceu, a window of 120k width is about 40 snps
so lots more is perhaps less efficient - each window computational cost is
ON^2 unless the code is smart enough to avoid unecessary computation where
allele frequencies make it impossible to see ld > the r^2 cutoff threshold
So, do a window and move forward 20?
The fine Plink docs at http://pngu.mgh.harvard.edu/~purcell/plink/summary.shtml#prune
reproduced below
Sometimes 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.
Hint 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.
The VIF pruning routine is performed:
plink --file data --indep 50 5 2
will create files
plink.prune.in
plink.prune.out
Each is a simlpe list of SNP IDs; both these files can subsequently be specified as the argument for
a --extract or --exclude command.
The parameters for --indep are: window size in SNPs (e.g. 50), the number of SNPs to shift the
window 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.
The second procedure is performed:
plink --file data --indep-pairwise 50 5 0.5
This generates the same output files as the first version; the only difference is that a
simple 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.
To give a concrete example: the command above that specifies 50 5 0.5 would a) consider a
window 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.
To make a new, pruned file, then use something like (in this example, we also convert the
standard PED fileset to a binary one):
plink --file data --extract plink.prune.in --make-bed --out pruneddata
"""
fplog,plog = tempfile.mkstemp()
alog = []
alog.append('## Rgenetics: http://rgenetics.org Galaxy Tools rgQC.py Plink pruneLD runner\n')
for task in plinktasks: # each is a list
vcl = vclbase + task
sto = file(plog,'w')
x = subprocess.Popen(' '.join(vcl),shell=True,stdout=sto,stderr=sto,cwd=cd)
retval = x.wait()
sto.close()
try:
lplog = file(plog,'r').readlines()
lplog = [x for x in lplog if x.find('Pruning SNP') == -1]
alog += lplog
alog.append('\n')
os.unlink(plog) # no longer needed
except:
alog.append('### %s Strange - no std out from plink when running command line\n%s\n' % (timenow(),' '.join(vcl)))
return alog
def readMap(mapfile=None,allmarkers=False,rsdict={},c=None,spos=None,epos=None):
"""abstract out - keeps reappearing
"""
mfile = open(mapfile, 'r')
markers = []
snpcols = {}
snpIndex = 0 # in case empty or comment lines
for rownum,row in enumerate(mfile):
line = row.strip()
if not line or line[0]=='#': continue
chrom, snp, genpos, abspos = line.split()[:4] # just in case more cols
try:
abspos = int(abspos)
except:
abspos = 0 # stupid framingham data grumble grumble
if allmarkers or rsdict.get(snp,None) or (chrom == c and (spos <= abspos <= epos)):
markers.append((chrom,abspos,snp)) # decorate for sort into genomic
snpcols[snp] = snpIndex # so we know which col to find genos for this marker
snpIndex += 1
markers.sort()
rslist = [x[2] for x in markers] # drop decoration
rsdict = dict(zip(rslist,rslist))
mfile.close()
return markers,snpcols,rslist,rsdict