def colselect(infile, col, cut, rev, tag):
"""Select the columns from input file"""
pTsvColSelect1 = pTsvColSelect.copy(tag=tag)
if str(col).isdigit():
pTsvColSelect1.input = [infile]
pTsvColSelect1.args.cols = [0, int(col)]
start = end = pTsvColSelect1
else:
pTsvHeader1 = pTsvHeader.copy(tag=tag)
pTsvHeader1.input = [infile]
start = pTsvHeader1
pShell1 = pShell.copy(tag=tag)
pShell1.depends = pTsvHeader1
pShell1.args.cmd = """
head -1 {{i.infile | quote}} > {{o.outfile | quote}}
echo "%s" >> {{o.outfile | quote}}
""" % col
pTsvColSelect1.depends = pShell1
pTsvColSelect1.input = 'infile:file, colfile:file'
pTsvColSelect1.input = lambda ch: ch.insert(0, infile)
start = pTsvHeader1
end = pTsvColSelect1
if cut and cut < 1:
pTsv1 = pTsv.copy(tag=tag)
pTsv1.depends = pTsvColSelect1
pTsv1.args.row = 'lambda row: float(row[%r]) < %f' % (col, cut)
end = pTsv1
elif cut and cut > 1:
pSort1 = pSort.copy(tag=tag)
pSort1.depends = pTsvColSelect1
pSort1.args.inopts.skip = 1
pSort1.args.params.k = '2g%s' % ('' if rev else 'r')
pShell2 = pShell.copy(tag=tag)
pShell2.depends = pSort1
pShell2.args.cmd = "head -n %d {{i.infile | quote}} > {{o.outfile | quote}}" % (
int(cut) + 1)
end = pShell2
if rev:
pTsv2 = pTsv.copy(tag=tag)
pTsv2.depends = end
pTsv2.args.row = 'lambda row: row.__setitem__({0!r}, "-" + row[{0!r}])'.format(
col)
end = pTsv2
return start, end
def colselect(infile, col, cut):
"""Select the columns from input file"""
tag = Path(infile).stem.split(".")[0]
pTsvColSelect1 = pTsvColSelect.copy(tag=tag)
if str(col).isdigit():
pTsvColSelect1.input = [infile]
pTsvColSelect1.args.cols = [0, int(col)]
start = pTsvColSelect1
else:
pTsvHeader1 = pTsvHeader.copy(tag=tag)
pTsvHeader1.input = [infile]
start = pTsvHeader1
pShell1 = pShell.copy(tag=tag)
pShell1.depends = pTsvHeader1
pShell1.args.cmd = """
head -1 {{i.infile | quote}} > {{o.outfile | quote}}
echo "%s" >> {{o.outfile | quote}}
""" % col
pTsvColSelect1.depends = pShell1
pTsvColSelect1.input = lambda ch: ch.insert(0, infile)
pTsv1 = pTsv.copy(tag=tag)
pTsv1.depends = pTsvColSelect1
pTsv1.args.row = "lambda row: float(row[1]) < %f" % cut
return [start], [pTsv1]
def ceQTL_filter_row(args, pCefile, hasAdjPval, starts):
if not args.row:
return pCefile
pFilterRow = pTsv.copy()
pFilterRow.depends = pCefile
pFilterRow.args.helper = args.helper
pFilterRow.args.row = args.row
if hasAdjPval:
pFilterRow.args.inopts.row = 'lambda r: setattr(r, "Pval", float(r.Pval)) or setattr(r, "AdjPval", float(r.AdjPval)) or r'
else:
pFilterRow.args.inopts.row = 'lambda r: setattr(r, "Pval", float(r.Pval)) or r'
return pFilterRow
def ceQTL_atsnp(args):
pGTMat2Bed.input = [args.cefile]
pGTMat2Bed.args.inopts.cnames = False
pGTMat2Bed.args.inopts.skip = 1
pGTMat2Bed.args.inopts.delimit = '.'
pGTMat2Bed.args.name = 'full'
pGTMat2Bed.args.ncol = 8
pSortSnp = pSort.copy()
pSortSnp.depends = pGTMat2Bed
pSortSnp.args.unique = True
pSortByTF.input = [args.cefile]
pFilterTFs = pTsvJoin.copy()
pFilterTFs.depends = pSortByTF
pFilterTFs.input = lambda ch: [ch.insert(0, args.tflist).flatten()]
pFilterTFs.args.inopts.cnames = False
pFilterTFs.args.inopts.skip = [0, 1]
pFilterTFs.args.inopts.delimit = ['\t', '.']
pFilterTFs.args.outopts.cnames = False
pFilterTFs.args.match = 'lambda r1, r2: TsvJoin.compare(r1[1], r2[1])'
pFilterTFs.args.do = 'lambda out, r1, r2: out.write(r1)'
pAtSnp.depends = pFilterTFs, pSortSnp
pAtSnp.args.tfmotifs = args.motifdb
pAtSnp.args.fdr = False
pAtSnp.args.plot = False
pAtSnp.args.nthread = args.nthread
setOutfile(pAtSnp, args.outfile)
if args.man:
pToMan = pTsv.copy()
pToMan.depends = pAtSnp
pToMan.args.outopts.cnames = False
# [chr1, 12496021, rs6541023, 0.04]
pToMan.args.helper = 'snprec = lambda x: [x[0], int(x[1]) - 1, x[1], x[2], 0, "+"]'
pToMan.args.row = 'lambda r: snprec(r.Snp.split("_")[:3]) + [r.Pval_Diff]'
pBedSort.depends = pToMan
pBedSort.args.chrorder = params.chrorder.value
pManhattan.depends = pBedSort
if args.hifile:
pManhattan.input = lambda ch: ch.cbind(args.hifile)
pManhattan.args.gsize = params.gsize.value
setOutfile(pManhattan, args.man)
PyPPL().start(pGTMat2Bed, pSortByTF).run()
def pipeline(opts):
"""Construct the pipeline"""
start, end = colselect(opts.infile, opts.col, opts.cut)
# duplicate gold standard columns
pTsvGold = pTsv.copy()
pTsvGold.input = [opts.gold]
pTsvGold.args.inopts.cnames = False
pTsvGold.args.row = 'lambda row: [row[0], 1]'
start = [pTsvGold, start]
# add header
pTsvReplaceHeader.depends = pTsvGold
pTsvReplaceHeader.args.inopts.cnames = False
pTsvReplaceHeader.args.cnames = ['ROWNAME', 'GOLD']
pTsvCbind.depends = pTsvReplaceHeader, end
pTsvCbind.input = (lambda *chs: [[ch.get() for ch in chs]])
# prepare file for hypergeometric test
# replace NA with 0
# replace pvalues with 1 (presence)
pPrepHG = pTsv.copy()
pPrepHG.depends = pTsvCbind
pPrepHG.args.row = ('lambda row: row.__setitem__(1, int(row[1] == "1")) '
'or row.__setitem__(2, int(row[2] != "NA"))')
pHypergeom.depends = pPrepHG
pHypergeom.args.intype = 'raw'
if str(opts.bign).isdigit():
pHypergeom.args.N = int(opts.bign)
else:
bign = cmdy.wc(l = opts.bign).strip().split()[0]
pHypergeom.args.N = int(bign)
return start
def pipeline(opts):
"""Construct the pipeline"""
starts = []
ends = []
for i, infile in enumerate(opts.infiles):
start, end = colselect(infile, opts.cols[i],
opts.cuts[i] if opts.cuts else None, opts.rev,
"in%s" % (i + 1))
starts.append(start)
ends.append(end)
# duplicate gold standard columns
pTsvGold = pTsv.copy()
pTsvGold.input = [opts.gold]
pTsvGold.args.inopts.cnames = False
pTsvGold.args.row = 'lambda row: [row[0], 1]'
starts.append(pTsvGold)
pROC.args.params.bestCut = False
pROC.args.ggs.theme_bw = {}
pTsvCbind.args.inopts.dup = 'ignore'
if not opts.sep:
pSort.depends = ends
pSort.input = lambda *chs: [ch.get() for ch in chs]
pSort.args.inopts.skip = 1
pTsvJoin.depends = pSort
pTsvJoin.input = lambda ch: [ch.flatten()]
#pTsvJoin.args.outopts.cnames = ["ROWNAME"] + [Path(infile).stem for infile in opts.infiles]
pTsvJoin.args.inopts.cnames = True
pTsvJoin.args.do = "lambda writer, *rs: writer.write([rs[0][0]] + [r[1] for r in rs])"
pTsvCbind.depends = pTsvGold, pTsvJoin
pTsvCbind.input = lambda ch1, ch2: [ch1.cbind(ch2).flatten()]
pTsvCbind.args.inopts.cnames = False
pTsvCbind.args.inopts.rnames = True
pTsvCbind.args.fill = True
pTsvCbind.args.fn2cname = "NULL"
# set the non-hit record to 0
# and remove NAs from predictions
pTsvGoldFalse = pTsv.copy()
pTsvGoldFalse.depends = pTsvCbind
pTsvGoldFalse.args.row = ('lambda row: False '
'if any(r == "NA" for r in row[2:]) '
'else row.__setitem__(1, 0) '
'if row[1] == "NA" '
'else None')
pTsvReplaceHeader.depends = pTsvGoldFalse
pTsvReplaceHeader.args.cnames = ["ROWNAME", "GOLD"] + opts.names
pROC.depends = pTsvReplaceHeader
else:
# add header
pTsvReplaceHeader.depends = pTsvGold
pTsvReplaceHeader.args.inopts.cnames = False
pTsvReplaceHeader.args.cnames = ['ROWNAME', 'GOLD']
ends.insert(0, pTsvReplaceHeader)
pTsvCbind.depends = ends
pTsvCbind.output = 'outfile:file:{{i.infiles | [-1] | stem2 }}.cbound.txt'
pTsvCbind.input = (
lambda ch_gold, *chs: [ch_gold.cbind(ch).flatten() for ch in chs])
pTsvGoldFalse = pTsv.copy()
pTsvGoldFalse.depends = pTsvCbind
pTsvGoldFalse.config.export_dir = opts.outdir
pTsvGoldFalse.args.row = ('lambda row: False '
'if any(r == "NA" for r in row[2:]) '
'else row.__setitem__(1, 0) '
'if row[1] == "NA" '
'else None')
pROC.depends = pTsvGoldFalse
pROC.config.export_dir = opts.outdir
return starts