def doManQQ(input_fname,
chrom_col,
offset_col,
pval_cols,
title,
grey,
ctitle,
outdir,
beTidy=False):
"""
we may have an interval file or a tabular file - if interval, will have chr1... so need to adjust
to chrom numbers
draw a qq for pvals and a manhattan plot if chrom/offset <> 0
contains some R scripts as text strings - we substitute defaults into the calls
to make them do our bidding - and save the resulting code for posterity
this can be called externally, I guess...for QC eg?
"""
if debug:
print 'doManQQ', input_fname, chrom_col, offset_col, pval_cols, title, grey, ctitle, outdir
rcmd = '%s%s' % (
rcode, rcode2 %
(input_fname, chrom_col, offset_col, pval_cols, title, grey))
if debug:
print 'running\n%s\n' % rcmd
rlog, flist = RRun(rcmd=rcmd, title=ctitle, outdir=outdir)
rlog.append('## R script=')
rlog.append(rcmd)
return rlog, flist
def doManQQ(input_fname,chrom_col,offset_col,pval_cols,title,grey,ctitle,outdir,beTidy=False):
"""
we may have an interval file or a tabular file - if interval, will have chr1... so need to adjust
to chrom numbers
draw a qq for pvals and a manhattan plot if chrom/offset <> 0
contains some R scripts as text strings - we substitute defaults into the calls
to make them do our bidding - and save the resulting code for posterity
this can be called externally, I guess...for QC eg?
"""
if debug:
print 'doManQQ',input_fname,chrom_col,offset_col,pval_cols,title,grey,ctitle,outdir
ffd,filtered_fname = tempfile.mkstemp(prefix='rgManQQtemp')
f = open(filtered_fname,'w')
inf = open(input_fname,'r')
ohead = inf.readline().strip().split('\t') # see if we have a header
inf.seek(0) # rewind
newhead = ['pval%d' % (x+1) for x in pval_cols]
newhead.insert(0,'Offset')
newhead.insert(0,'Chrom')
havehead = 0
wewant = [chrom_col,offset_col]
wewant += pval_cols
try:
allnums = ['%d' % x for x in ohead] # this should barf if non numerics == header row?
f.write('\t'.join(newhead)) # for R to read
f.write('\n')
except:
havehead = 1
newhead = [ohead[chrom_col],ohead[offset_col]]
newhead += [ohead[x] for x in pval_cols]
f.write('\t'.join(newhead)) # use the original head
f.write('\n')
for i,row in enumerate(inf):
if i == 0 and havehead:
continue # ignore header
sr = row.strip().split('\t')
if len(sr) > 1:
if sr[chrom_col].lower().find('chr') <> -1:
sr[chrom_col] = sr[chrom_col][3:]
newr = [sr[x] for x in wewant] # grab cols we need
s = '\t'.join(newr)
f.write(s)
f.write('\n')
f.close()
pvc = [x+3 for x in range(len(pval_cols))] # 2 for offset and chrom, 1 for r offset start
pvc = 'c(%s)' % (','.join(map(str,pvc)))
rcmd = '%s%s' % (rcode,rcode2 % (filtered_fname,'1','2',pvc,title,grey))
if debug:
print 'running\n%s\n' % rcmd
rlog,flist = RRun(rcmd=rcmd,title=ctitle,outdir=outdir)
rlog.append('## R script=')
rlog.append(rcmd)
if beTidy:
os.unlink(filtered_fname)
return rlog,flist
def doManQQ(input_fname,chrom_col,offset_col,pval_cols,title,grey,ctitle,outdir,beTidy=False):
"""
we may have an interval file or a tabular file - if interval, will have chr1... so need to adjust
to chrom numbers
draw a qq for pvals and a manhattan plot if chrom/offset <> 0
contains some R scripts as text strings - we substitute defaults into the calls
to make them do our bidding - and save the resulting code for posterity
this can be called externally, I guess...for QC eg?
"""
ffd,filtered_fname = tempfile.mkstemp(prefix='rgManQQtemp')
f = open(filtered_fname,'w')
inf = open(input_fname,'r')
ohead = inf.readline().strip().split('\t') # see if we have a header
inf.seek(0) # rewind
newhead = ['pval%d' % (x+1) for x in pval_cols]
newhead.insert(0,'Offset')
newhead.insert(0,'Chrom')
havehead = 0
wewant = [chrom_col,offset_col]
wewant += pval_cols
try:
allnums = ['%d' % x for x in ohead] # this should barf if non numerics == header row?
f.write('\t'.join(newhead)) # for R to read
f.write('\n')
except:
havehead = 1
newhead = [ohead[chrom_col],ohead[offset_col]]
newhead += [ohead[x] for x in pval_cols]
f.write('\t'.join(newhead)) # use the original head
f.write('\n')
for i,row in enumerate(inf):
if i == 0 and havehead:
continue # ignore header
sr = row.strip().split('\t')
if len(sr) > 1:
if sr[chrom_col].lower().find('chr') <> -1:
sr[chrom_col] = sr[chrom_col][3:]
newr = [sr[x] for x in wewant] # grab cols we need
s = '\t'.join(newr)
f.write(s)
f.write('\n')
f.close()
pvc = [x+3 for x in range(len(pval_cols))] # 2 for offset and chrom, 1 for r offset start
pvc = 'c(%s)' % (','.join(map(str,pvc)))
rcmd = '%s%s' % (rcode,rcode2 % (filtered_fname,'1','2',pvc,title,grey))
rlog,flist = RRun(rcmd=rcmd,title=ctitle,outdir=outdir)
rlog.append('## R script=')
rlog.append(rcmd)
if beTidy:
os.unlink(filtered_fname)
return rlog,flist
def doManQQ(input_fname,chrom_col,offset_col,pval_cols,title,grey,ctitle,outdir,beTidy=False):
"""
we may have an interval file or a tabular file - if interval, will have chr1... so need to adjust
to chrom numbers
draw a qq for pvals and a manhattan plot if chrom/offset <> 0
contains some R scripts as text strings - we substitute defaults into the calls
to make them do our bidding - and save the resulting code for posterity
this can be called externally, I guess...for QC eg?
"""
if debug:
print 'doManQQ',input_fname,chrom_col,offset_col,pval_cols,title,grey,ctitle,outdir
rcmd = '%s%s' % (rcode,rcode2 % (input_fname,chrom_col,offset_col,pval_cols,title,grey))
if debug:
print 'running\n%s\n' % rcmd
rlog,flist = RRun(rcmd=rcmd,title=ctitle,outdir=outdir)
rlog.append('## R script=')
rlog.append(rcmd)
return rlog,flist
