details: http://www.bx.psu.edu/hg/galaxy/rev/5469b917d3fb changeset: 3793:5469b917d3fb user: fubar: ross Lazarus at gmail period com date: Thu May 20 12:41:51 2010 -0400 description: Removed redundant code from rgEigPCA.py now that it takes a pre-converted ldindep dataset. diffstat: tools/rgenetics/rgEigPCA.py | 67 +-------------------------------------------- 1 files changed, 1 insertions(+), 66 deletions(-) diffs (84 lines): diff -r 2d49a94c8d28 -r 5469b917d3fb tools/rgenetics/rgEigPCA.py --- a/tools/rgenetics/rgEigPCA.py Thu May 20 12:38:35 2010 -0400 +++ b/tools/rgenetics/rgEigPCA.py Thu May 20 12:41:51 2010 -0400 @@ -195,71 +195,6 @@ print >> sys.stdout, rlog -def getInfiles(basename=None,infpath=None,outfpath=None,plinke='plink',forcerebuild=False): - """ - openOrMakeLDreduced(basename,newfpath,plinke='plink',forcerebuild=False) - ingeno = getLDreduced(infile,plinke) - gbase,gext = os.path.splitext(ingeno) - if gext == '.bed': - inmap = '%s.bim' % gbase - inped = '%s.fam' % gbase - elif gext == '.ped': - inmap = '%s.map' % gbase - inped = '%s.ped' % gbase - elif gext == '.tped': - inmap = '%s.tmap' % gbase - inped = '%s.tfam' % gbase - """ - base,kind = getLDreducedFname(basename,infpath=infpath,outfpath=outfpath,plinke=plinke,forcerebuild=forcerebuild) - assert kind in ['lped','pbed','tped'],'## kind=%s - not lped,pbed,tped' % str(kind) - if kind=='lped': - return '%s.ped' % base,'%s.map' % base,'%s.ped' % base - elif kind=='pbed': - return '%s.bed' % base,'%s.bim' % base,'%s.fam' % base - elif kind == 'tped': - return '%s.tped' % base,'%s.tmap' % base,'%s.tfam' % base - - -def getInfilesOld(infile=None): - """given a basename, find the best input files - """ - mapexts = ['.map','.bim','.pedsnp'] - mapexts += [x.upper() for x in mapexts] # ya never know - genoexts = ['.ped','.bed','.pedsnp'] - genoexts += [x.upper() for x in genoexts] - indexts = ['.ped','.fam','.pedind'] - indexts += [x.upper() for x in indexts] - flist = glob.glob('%s*' % infile) # this should list all available rgenetics data files - exts = set([os.path.splitext(x)[-1] for x in flist]) # expect ['.ped','.map'] etc - mapext = None - genoext = None - indext = None - for e in mapexts: - if e in exts: - mapext = e - inmap = '%s%s' % (infile,e) - break - for e in genoexts: - if e in exts: - genoext = e - ingeno = '%s%s' % (infile,e) - break - for e in indexts: - if e in exts: - indext = e - inped = '%s%s' % (infile,e) - break - if mapext == None: - print '### no map (%s) file found - cannot run eigensoft' % ','.join(mapexts) - sys.exit(1) - if indext == None: - print '### no ind (%s) file found - cannot run eigensoft' % ','.join(indexts) - sys.exit(1) - if genoext == None: - print '### no geno (%s) file found - cannot run eigensoft' % ','.join(genoexts) - sys.exit(1) - return ingeno,inmap,inped - def getfSize(fpath,outpath): """ format a nice file size string @@ -331,7 +266,7 @@ ofname = sys.argv[5] progname = os.path.basename(sys.argv[0]) infile = sys.argv[1] - infpath,base_name = os.path.split(infile) # can't leave anything here - readonly on PSU - so leave in outdir instead + infpath,base_name = os.path.split(infile) # now takes precomputed or autoconverted ldreduced dataset title = sys.argv[2].translate(trantab) # must replace all of these for urls containing title outfile1 = sys.argv[3] newfilepath = sys.argv[4]