mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-21 05:45:37 +08:00
Fixes to rgQC top table ordering and add offset so can use rgManQQ to make plots
Fixes to rgManQQ to handle unsorted data - now sorts before manhattan plot
This commit is contained in:
Ross Lazarus
@@ -178,7 +178,7 @@ def add_file( dataset, json_file, output_path ):
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# See if we have a gzipped file, which, if it passes our restrictions, we'll uncompress
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is_gzipped, is_valid = check_gzip( dataset.path )
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if is_gzipped and not is_valid:
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file_err( 'The uploaded file contains inappropriate content', dataset, json_file )
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file_err( 'The gzipped uploaded file contains inappropriate content', dataset, json_file )
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return
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elif is_gzipped and is_valid:
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# We need to uncompress the temp_name file, but BAM files must remain compressed in the BGZF format
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@@ -206,7 +206,7 @@ def add_file( dataset, json_file, output_path ):
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# See if we have a zip archive
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is_zipped, is_valid, test_ext = check_zip( dataset.path )
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if is_zipped and not is_valid:
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file_err( 'The uploaded file contains inappropriate content', dataset, json_file )
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file_err( 'The zipped uploaded file contains inappropriate content', dataset, json_file )
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return
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elif is_zipped and is_valid:
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# Currently, we force specific tools to handle this case. We also require the user
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@@ -231,7 +231,7 @@ def add_file( dataset, json_file, output_path ):
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if len( parts ) > 1:
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ext = parts[1].strip().lower()
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if ext not in unsniffable_binary_formats:
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file_err( 'The uploaded file contains inappropriate content', dataset, json_file )
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file_err( 'The uploaded binary file contains inappropriate content', dataset, json_file )
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return
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elif ext in unsniffable_binary_formats and dataset.file_type != ext:
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err_msg = "You must manually set the 'File Format' to '%s' when uploading %s files." % ( ext.capitalize(), ext )
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@@ -240,7 +240,7 @@ def add_file( dataset, json_file, output_path ):
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if not data_type:
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# We must have a text file
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if check_html( dataset.path ):
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file_err( 'The uploaded file contains inappropriate content', dataset, json_file )
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file_err( 'The uploaded file contains inappropriate HTML content', dataset, json_file )
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return
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if data_type != 'binary' and data_type != 'zip':
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# don't convert newlines on data we're only going to symlink
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@@ -124,7 +124,14 @@ qq = function(pvector, title=NULL, spartan=F) {
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rcode2 = """rgqqMan = function(infile="%s",chromcolumn=%d, offsetcolumn=%d, pvalscolumns=%s,
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title="%s",grey=%d) {
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d = read.table(infile,head=T,sep='\t')
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rawd = read.table(infile,head=T,sep='\t')
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dn = names(rawd)
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cc = dn[chromcolumn]
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oc = dn[offsetcolumn]
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nams = c(cc,oc)
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d = rawd[do.call(order,rawd[nams]),]
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# mmmf - suggested by http://onertipaday.blogspot.com/2007/08/sortingordering-dataframe-according.html
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# in case not yet ordered
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print(paste('###',length(d[,1]),'values read from',infile,'read - now running plots',sep=' '))
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for (pvalscolumn in pvalscolumns) {
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if (pvalscolumn > 0)
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+21
-39
@@ -994,7 +994,7 @@ def markerRep(froot='cleantest',outfname="mrep",newfpath='.',logf=None,maplist=N
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mapdict = {}
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if maplist <> None:
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rslist = [x[1] for x in maplist]
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offset = [x[3] for x in maplist]
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offset = [(x[0],x[3]) for x in maplist]
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mapdict = dict(zip(rslist,offset))
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hwefile = '%s.hwe' % froot
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lmissfile = '%s.lmiss' % froot
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@@ -1009,8 +1009,9 @@ def markerRep(froot='cleantest',outfname="mrep",newfpath='.',logf=None,maplist=N
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lmenddict = {}
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Tops = {}
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Tnames = ['Ranked Marker MAF', 'Ranked Marker Missing Genotype', 'Ranked Marker HWE', 'Ranked Marker Mendel']
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Tsorts = [2,5,9,10]
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Tsorts = [3,6,10,11]
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Treverse = [False,True,True,True] # so first values are worse(r)
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#res.append([rs,chrom,offset,maf,a1,a2,f_missing,hwe_all[0],hwe_all[1],hwe_unaff[0],hwe_unaff[1],nmend])
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#rhead = ['snp','chrom','maf','a1','a2','missfrac','p_hwe_all','logp_hwe_all','p_hwe_unaff','logp_hwe_unaff','N_Mendel']
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# -------------------hwe--------------------------
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# hwe has SNP TEST GENO O(HET) E(HET) P_HWD
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@@ -1057,12 +1058,13 @@ def markerRep(froot='cleantest',outfname="mrep",newfpath='.',logf=None,maplist=N
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hwedict[rs] = {}
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markerlist.append(rs)
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chromlist.append(chrom) # one place to find it?
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lpvals = 0
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if ps.upper() <> 'NA' and ps.upper() <> 'NAN': # worth keeping
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lpvals = '0'
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if ps <> '1':
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try:
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pval = float(ps)
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lpvals = '%f6' % -math.log10(pval)
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lpvals = '%f' % -math.log10(pval)
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except:
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pass
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hwedict[rs][test] = (ps,lpvals)
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@@ -1147,49 +1149,33 @@ def markerRep(froot='cleantest',outfname="mrep",newfpath='.',logf=None,maplist=N
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rhead = ['snp','chromosome','offset','maf','a1','a2','missfrac','p_hwe_all','logp_hwe_all','p_hwe_unaff','logp_hwe_unaff','N_Mendel']
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res = []
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fres = []
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for i in xrange(len(markerlist)): # for each snp in found order
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chrom = chromlist[i]
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rs = markerlist[i]
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for rs in markerlist: # for each snp in found order
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f_missing = lmissdict.get(rs,'NA')
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maf,a1,a2 = freqdict.get(rs,('NA','NA','NA'))
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hwe_all = hwedict[rs].get('ALL',('NA','NA')) # hope this doesn't change...
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hwe_unaff = hwedict[rs].get('UNAFF',('NA','NA'))
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nmend = lmenddict.get(rs,'NA')
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offset=mapdict.get(rs,'0')
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(chrom,offset)=mapdict.get(rs,('?','0'))
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res.append([rs,chrom,offset,maf,a1,a2,f_missing,hwe_all[0],hwe_all[1],hwe_unaff[0],hwe_unaff[1],nmend])
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try:
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fmaf = '%f' % float(maf)
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except:
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fmaf = 'NA'
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try:
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inmend = '%d' % int(nmend)
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except:
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inmend = 'NA'
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try:
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fhweall = '%f' % float(hwe_all[1]) # the log value
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except:
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fhweall = 'NA'
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try:
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fhweunaff = '%f' % float(hwe_unaff[1]) # the log value
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except:
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fhweunaff = 'NA'
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try:
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ff_missing = '%f' % float(f_missing) # the log value
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except:
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ff_missing = 'NA'
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#fres.append([rs,chrom,fmaf,a1,a2,ff_missing,hwe_all[0],hwe_all[1],hwe_unaff[0],fhwe,inmend])
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arow = [rs,chrom,offset,fmaf,a1,a2,ff_missing,hwe_all[0],fhweall,hwe_unaff[0],fhweunaff,inmend]
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fres.append(arow)
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ntokeep = max(10,len(res)/keepfrac)
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def msortk(item=None):
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"""
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deal with non numeric sorting
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"""
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try:
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return float(item)
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except:
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return item
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for i,col in enumerate(Tsorts):
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fres.sort(key=operator.itemgetter(col))
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res.sort(key=msortk(lambda x:x[col]))
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if Treverse[i]:
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fres.reverse()
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res.reverse()
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repname = Tnames[i]
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Tops[repname] = fres[0:ntokeep]
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#Tops[repname] = [map(str,x) for x in Tops[repname]]
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Tops[repname] = res[0:ntokeep]
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Tops[repname].insert(0,rhead)
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res.sort()
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res.sort(key=lambda x: '%s_%10d' % (x[1].ljust(4,'0'),int(x[2]))) # in chrom offset order
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res.insert(0,rhead)
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f = open(outfile,'w')
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f.write('\n'.join(['\t'.join(x) for x in res]))
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@@ -1315,10 +1301,6 @@ if __name__ == "__main__":
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dat = subjectTops.get(ttitle,None)
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if not dat:
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dat = markerTops.get(ttitle,None)
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if not dat:
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print '## iterating plotpage - cannot find title=%s/ttitle=%s' % (title,ttitle)
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else:
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print '## iterating plotpage - found title=%s/ttitle=%s' % (title,ttitle)
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imghref = '%s.jpg' % os.path.splitext(url)[0] # removes .pdf
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thumbnail = os.path.join(newfpath,imghref)
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if not os.path.exists(thumbnail): # for multipage pdfs, mogrify makes multiple jpgs - fugly hack
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@@ -0,0 +1,218 @@
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#!/bin/sh
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# script to generate all functional test outputs for each rgenetics tool
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# could be run at installation to ensure all dependencies are in place?
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case $# in 0) echo "USAGE: ${0##*/} TooltoTest"; exit 1;;
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[2-10]*) echo "Too many arguments - name of tool only"; exit 2;;
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*)
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esac
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GALAXYROOT=`pwd`
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echo "using $GALAXYROOT"
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# change this as needed for your local install
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INPATH="${GALAXYROOT}/test-data"
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BINPATH="${GALAXYROOT}/tool-data/rg/bin"
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TOOLPATH="${GALAXYROOT}/tools/rgenetics"
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OROOT="${GALAXYROOT}/test-data/rgtestouts"
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NORMALOROOT="${GALAXYROOT}/test-data"
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case "$1" in
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'rgManQQ')
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TOOL="rgManQQ"
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NPRE=${TOOL}test1
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OUTPATH="$OROOT/$TOOL"
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rm -rf $OUTPATH/*
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CL="python $TOOLPATH/$TOOL.py "$INPATH/smallwgaP.xls" $NPRE ${OUTPATH}/${NPRE}.html $OUTPATH 1 2 5,7 0"
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# rgManQQ.py '$input_file' "$name" '$out_html' '$out_html.files_path' '$chrom_col' '$offset_col'
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# '$pval_col'
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#python /opt/galaxy/tools/rgenetics/rgManQQ.py /opt/galaxy/test-data/smallwgaP.xls rgManQQtest1
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#/opt/galaxy/test-data/rgtestouts/rgManQQ/rgManQQtest1.html /opt/galaxy/test-data/rgtestouts/rgManQQ 1 2 5,7
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echo "Testing $TOOL using $CL"
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python $TOOLPATH/$TOOL.py "$INPATH/smallwgaP.xls" $NPRE ${OUTPATH}/${NPRE}.html $OUTPATH 1 2 5,7 0
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;;
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'rgfakePhe')
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TOOL="rgfakePhe"
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NPRE=${TOOL}test1
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OUTPATH="$OROOT/$TOOL"
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rm -rf $OUTPATH/*
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PSSCRIPT="$OUTPATH/script_file"
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echo "{'pN':'normtest','pT':'rnorm','pP':\"{'Mean':'100', 'SD':'10'}\"}" > $PSSCRIPT
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echo "{'pN':'cattest','pT':'cat','pP':\"{'values':'red,green,blue'}\"}" >> $PSSCRIPT
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echo "{'pN':'uniftest','pT':'$f.series.phetype','pP':\"{'low':'1','hi':'100'}\"}" >> $PSSCRIPT
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echo "{'pN':'gammatest','pT':'rgamma','pP':\"{'Alpha':'1', 'Beta':'0.1'}\"}" >> $PSSCRIPT
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echo "{'pN':'poissontest','pT':'poisson','pP':\"{'lamb':'1.0',}\"}" >> $PSSCRIPT
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echo "{'pN':'exptest','pT':'exponential','pP':\"{'Mean':'100.0',}\"}" >> $PSSCRIPT
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echo "{'pN':'weibtest','pT':'weibull','pP':\"{'Alpha':'1.0', 'Beta':'0.1'}\"}" >> $PSSCRIPT
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echo "now doing $TOOL"
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python $TOOLPATH/$TOOL.py ${INPATH}/tinywga $NPRE $NPRE.pphe $OUTPATH $PSSCRIPT
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# <command interpreter="python">rgfakePhe.py '$infile1.extra_files_path/$infile1.metadata.base_name'
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# "$title1" '$ppheout' '$ppheout.files_path' '$script_file'
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#
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;;
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'rgQC')
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TOOL="rgQC"
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NPRE=${TOOL}test1
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echo "now doing $TOOL"
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OUTPATH="$OROOT/$TOOL"
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rm -rf $OUTPATH/*
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python $TOOLPATH/$TOOL.py -i "$INPATH/tinywga" -o $NPRE -s ${OUTPATH}/${NPRE}.html -p $OUTPATH
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# rgQC.py -i '$input_file.extra_files_path/$input_file.metadata.base_name' -o "$out_prefix"
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# -s '$html_file' -p '$html_file.files_path'
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#
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;;
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'rgGRR')
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TOOL="rgGRR"
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NPRE=${TOOL}test1
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echo "now doing $TOOL"
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OUTPATH="$OROOT/$TOOL"
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rm -rf $OUTPATH/*
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python $TOOLPATH/$TOOL.py "$INPATH/tinywga" "tinywga" $OUTPATH/${NPRE}.html $OUTPATH "$NPRE" '100' '6'
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# rgGRR.py $i.extra_files_path/$i.metadata.base_name "$i.metadata.base_name"
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#'$out_file1' '$out_file1.files_path' "$title" '$n' '$Z'
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;;
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'rgLDIndep')
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TOOL="rgLDIndep"
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NPRE=${TOOL}test1
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OUTPATH="$OROOT/$TOOL"
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rm -rf $OUTPATH/*
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python $TOOLPATH/$TOOL.py "$INPATH" "tinywga" "$NPRE" 1 1 0 0 1 1 $OUTPATH/${NPRE}.pbed $OUTPATH 10000 5000 0.1
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#rgLDIndep.py '$input_file.extra_files_path' '$input_file.metadata.base_name' '$title' '$mind'
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# '$geno' '$hwe' '$maf' '$mef' '$mei' '$out_file1'
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#'$out_file1.files_path' '$window' '$step' '$r2'
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;;
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'rgPedSub')
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TOOL="rgPedSub"
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NPRE=${TOOL}test1
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OUTPATH="$OROOT/$TOOL"
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rm -rf $OUTPATH/*
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PSSCRIPT="$OUTPATH/pedsub.script"
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echo "title~~~~$NPRE" > $PSSCRIPT
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echo "output1~~~~${OUTPATH}/${NPRE}.lped" >> $PSSCRIPT
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echo "outformat~~~~lped" >> $PSSCRIPT
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echo "basename~~~~tinywga" >> $PSSCRIPT
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echo "inped~~~~$INPATH/tinywga" >> $PSSCRIPT
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echo "outdir~~~~$OUTPATH" >> $PSSCRIPT
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echo "region~~~~" >> $PSSCRIPT
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echo "relfilter~~~~all" >> $PSSCRIPT
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echo "rslist~~~~rs2283802Xrs2267000Xrs16997606Xrs4820537Xrs3788347Xrs756632Xrs4820539Xrs2283804Xrs2267006Xrs4822363X" >> $PSSCRIPT
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echo "now doing $TOOL"
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python $TOOLPATH/$TOOL.py $PSSCRIPT
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rm -rf $PSSCRIPT
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;;
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'rgfakePhe')
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TOOL="rgfakePhe"
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NPRE=${TOOL}test1
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OUTPATH="$OROOT/$TOOL"
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rm -rf $OUTPATH/*
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PSSCRIPT="$OUTPATH/script_file"
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echo "{'pN':'normtest','pT':'rnorm','pP':\"{'Mean':'100', 'SD':'10'}\"}" > $PSSCRIPT
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echo "{'pN':'cattest','pT':'cat','pP':\"{'values':'red,green,blue'}\"}" >> $PSSCRIPT
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echo "{'pN':'uniftest','pT':'$f.series.phetype','pP':\"{'low':'1','hi':'100'}\"}" >> $PSSCRIPT
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echo "{'pN':'gammatest','pT':'rgamma','pP':\"{'Alpha':'1', 'Beta':'0.1'}\"}" >> $PSSCRIPT
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echo "{'pN':'poissontest','pT':'poisson','pP':\"{'lamb':'1.0',}\"}" >> $PSSCRIPT
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echo "{'pN':'exptest','pT':'exponential','pP':\"{'Mean':'100.0',}\"}" >> $PSSCRIPT
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echo "{'pN':'weibtest','pT':'weibull','pP':\"{'Alpha':'1.0', 'Beta':'0.1'}\"}" >> $PSSCRIPT
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echo "now doing $TOOL"
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python $TOOLPATH/$TOOL.py $PSSCRIPT
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;;
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'rgClean')
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TOOL="rgClean"
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NPRE=${TOOL}test1
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OUTPATH="$OROOT/$TOOL"
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rm -rf $OUTPATH/*
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python $TOOLPATH/$TOOL.py $INPATH "tinywga" "$NPRE" 1 1 0 0 1 1 $OUTPATH/${NPRE}.pbed $OUTPATH 0 0 0 0
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# rgClean.py '$input_file.extra_files_path' '$input_file.metadata.base_name' '$title' '$mind'
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# '$geno' '$hwe' '$maf' '$mef' '$mei' '$out_file1' '$out_file1.files_path'
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# '${GALAXY_DATA_INDEX_DIR}/rg/bin/plink' '$relfilter' '$afffilter' '$sexfilter' '$fixaff'
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#
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;;
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'rgEigPCA')
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TOOL="rgEigPCA"
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NPRE=${TOOL}test1
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OUTPATH="$OROOT/$TOOL"
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rm -rf $OUTPATH/*
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python $TOOLPATH/$TOOL.py "$INPATH/tinywga" "$NPRE" ${OUTPATH}/${NPRE}.html $OUTPATH 4 2 2 2 $OUTPATH/rgEigPCAtest1.txt
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# rgEigPCA.py "$i.extra_files_path/$i.metadata.base_name" "$title" "$out_file1"
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# "$out_file1.files_path" "$k" "$m" "$t" "$s" "$pca"
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#
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;;
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'rgfakePed')
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TOOL="rgfakePed"
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NPRE=${TOOL}test1
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OUTPATH="$OROOT/$TOOL"
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rm -rf $OUTPATH/*
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echo "now doing $TOOL"
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python $TOOLPATH/$TOOL.py --title "$NPRE" -o $OUTPATH/${NPRE}.lped -p $OUTPATH -c "20" -n "40" -s "10" -w "0" -v "0" -l "pbed" -d "T" -m "0" -M "0"
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#rgfakePed.py --title '$title1'
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# -o '$out_file1' -p '$out_file1.extra_files_path' -c '$ncases' -n '$ntotal'
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# -s '$nsnp' -w '$lowmaf' -v '$missingValue' -l '$outFormat'
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# -d '$mafdist' -m '$missingRate' -M '$mendelRate'
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;;
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'rgHaploView')
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TOOL="rgHaploView"
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NPRE=${TOOL}test1
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OUTPATH="$OROOT/$TOOL"
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rm -rf $OUTPATH/*
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python $TOOLPATH/$TOOL.py "" "rs2283802Xrs2267000Xrs16997606Xrs4820537Xrs3788347Xrs756632Xrs4820539Xrs2283804Xrs2267006Xrs4822363X" \
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"$NPRE" $OUTPATH/${NPRE}.html "$INPATH" "tinywga" 0.0 200000 "RSQ" "lo" "2048" "$OUTPATH" "noinfo" "0.8" \
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"YRI" $BINPATH/haploview.jar
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# rgHaploView.py "$ucsc_region" "$rslist" "$title" "$output1"
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# "$lhistIn.extra_files_path" "$lhistIn.metadata.base_name"
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# "$minmaf" "$maxdist" "$ldtype" "$hires" "$memsize" "$output1.files_path"
|
||||
# "$infoTrack" "$tagr2" "$hmpanel" ${GALAXY_DATA_INDEX_DIR}/rg/bin/haploview.jar
|
||||
# note these statistical tools do NOT generate composite outputs
|
||||
;;
|
||||
|
||||
'rgGLM')
|
||||
TOOL="rgGLM"
|
||||
NPRE=${TOOL}test1
|
||||
OUTPATH=$NORMALOROOT
|
||||
python $TOOLPATH/$TOOL.py "$INPATH/tinywga" $INPATH/tinywga "$NPRE" "c1" "" $OUTPATH/${NPRE}_GLM.xls \
|
||||
$OUTPATH/${NPRE}_GLM_log.txt "tinywga" "" "" "" 1 1 0 0 $OUTPATH/${NPRE}_GLM_topTable.gff
|
||||
## rgGLM.py '$i.extra_files_path/$i.metadata.base_name' '$phef.extra_files_path/$phef.metadata.base_name'
|
||||
## "$title1" '$predvar' '$covar' '$out_file1' '$logf' '$dbkey' '$i.metadata.base_name'
|
||||
## '$inter' '$cond' '$gender' '$mind' '$geno' '$maf' '$logistic' '$gffout'
|
||||
;;
|
||||
|
||||
'rgTDT')
|
||||
TOOL="rgTDT"
|
||||
NPRE=${TOOL}test1
|
||||
OUTPATH=$NORMALOROOT
|
||||
python $TOOLPATH/$TOOL.py -i "$INPATH/tinywga" -o "$NPRE" -r $OUTPATH/${NPRE}_TDT.xls \
|
||||
-l $OUTPATH/${NPRE}_TDT_log.txt -g $OUTPATH/${NPRE}_TDT_topTable.gff
|
||||
## rgTDT.py -i '$infile.extra_files_path/$infile.metadata.base_name' -o '$title'
|
||||
## -r '$out_file1' -l '$logf' -x '${GALAXY_DATA_INDEX_DIR}/rg/bin/plink'
|
||||
## -g '$gffout'
|
||||
;;
|
||||
|
||||
'rgCaCo')
|
||||
TOOL="rgCaCo"
|
||||
NPRE=${TOOL}test1
|
||||
OUTPATH=$NORMALOROOT
|
||||
echo "now doing $TOOL"
|
||||
python $TOOLPATH/rgCaCo.py $INPATH/tinywga "$NPRE" $OUTPATH/${NPRE}_CaCo.xls $OUTPATH/${NPRE}_CaCo_log.txt $OUTPATH $OUTPATH/${NPRE}_CaCo_topTable.gff
|
||||
# echo tp=$TOOLPATH t=$TOOL op=$OUTPATH b=$BINPATH
|
||||
# rgCaCo.py '$i.extra_files_path/$i.metadata.base_name' "$name" '$out_file1' '$logf' '$logf.files_path' '$gffout'
|
||||
;;
|
||||
|
||||
'rgQQ')
|
||||
TOOL="rgQQ"
|
||||
echo "now doing $TOOL"
|
||||
NPRE=${TOOL}test1
|
||||
OUTPATH=$NORMALOROOT
|
||||
CL="python $TOOLPATH/$TOOL.py "$INPATH/tinywga.pphe" "$NPRE" 1 3 $OUTPATH/$NPRE.pdf 8 10 "false" 1 $OUTPATH"
|
||||
echo "running $TOOL using $CL"
|
||||
python $TOOLPATH/$TOOL.py "$INPATH/tinywga.pphe" "$NPRE" 1 3 $OUTPATH/$NPRE.pdf 8 10 "false" 1 $OUTPATH
|
||||
# rgQQ.py "$input1" "$name" $sample "$cols" $allqq $height $width $log $allqq.id $__new_file_path__
|
||||
;;
|
||||
esac
|
||||
Reference in New Issue
Block a user