diff rgGSEA/rgGSEA.py @ 2:71fa159646c9 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rgGSEA/rgGSEA.py	Sun Jun 09 02:01:13 2013 -0400
@@ -0,0 +1,495 @@
+"""
+April 2013
+eeesh GSEA does NOT respect the mode flag!
+
+Now realise that the creation of the input rank file for gsea needs to take the lowest p value for duplicate 
+feature names. To make Ish's life easier, remove duplicate gene ids from any gene set to stop GSEA from 
+barfing.
+
+October 14 2012
+Amazingly long time to figure out that GSEA fails with useless error message if any filename contains a dash "-"
+eesh.
+
+Added history .gmt source - requires passing a faked name to gsea 
+Wrapper for GSEA http://www.broadinstitute.org/gsea/index.jsp
+Started Feb 22 
+Copyright 2012 Ross Lazarus
+All rights reserved
+Licensed under the LGPL
+
+called eg as
+
+#!/bin/sh
+GALAXY_LIB="/data/extended/galaxy/lib"
+if [ "$GALAXY_LIB" != "None" ]; then
+    if [ -n "$PYTHONPATH" ]; then
+        PYTHONPATH="$GALAXY_LIB:$PYTHONPATH"
+    else
+        PYTHONPATH="$GALAXY_LIB"
+    fi
+    export PYTHONPATH
+fi
+
+cd /data/extended/galaxy/database/job_working_directory/027/27311
+python /data/extended/galaxy/tools/rgenetics/rgGSEA.py --input_tab "/data/extended/galaxy/database/files/033/dataset_33806.dat"  --adjpvalcol "5" --signcol "2"
+--idcol "1" --outhtml "/data/extended/galaxy/database/files/034/dataset_34455.dat" --input_name "actaearly-Controlearly-actalate-Controllate_topTable.xls"
+--setMax "500" --setMin "15" --nPerm "1000" --plotTop "20"
+--gsea_jar "/data/extended/galaxy/tool-data/shared/jars/gsea2-2.0.12.jar"
+--output_dir "/data/extended/galaxy/database/job_working_directory/027/27311/dataset_34455_files" --mode "Max_probe"
+ --title " actaearly-Controlearly-actalate-Controllate_interpro_GSEA" --builtin_gmt "/data/genomes/gsea/3.1/IPR_DOMAIN.gmt"
+
+
+"""
+import optparse
+import tempfile
+import os
+import sys
+import subprocess
+import time
+import shutil
+import glob
+import math
+import re
+
+KEEPSELECTION = False # detailed records for selection of multiple probes
+
+def timenow():
+    """return current time as a string
+    """
+    return time.strftime('%d/%m/%Y %H:%M:%S', time.localtime(time.time()))
+
+
+
+def fix_subdir(adir,destdir):
+    """ Galaxy wants everything in the same files_dir
+    if os.path.exists(adir):
+        for (d,dirs,files) in os.path.walk(adir):
+            for f in files:
+                sauce = os.path.join(d,f) 
+                shutil.copy(sauce,destdir)   
+    """
+
+    def fixAffycrap(apath=''):
+        """class='richTable'>RUNNING ES</th><th class='richTable'>CORE ENRICHMENT</th><tr><td class='lessen'>1</td>
+        <td><a href='https://www.affymetrix.com/LinkServlet?probeset=LBR'>LBR</a></td><td></td><td></td><td>1113</td>
+        <td>0.194</td><td>-0.1065</td><td>No</td></tr><tr><td class='lessen'>2</td><td>
+        <a href='https://www.affymetrix.com/LinkServlet?probeset=GGPS1'>GGPS1</a></td><td></td><td></td><td>4309</td><td>0.014</td><td>-0.4328</td>
+        <td>No</td></tr>
+        """
+        html = []
+        try:
+            html = open(apath,'r').readlines()       
+        except:
+             return html
+        for i,row in enumerate(html):
+            row = re.sub('https\:\/\/www.affymetrix.com\/LinkServlet\?probeset=',"http://www.genecards.org/index.php?path=/Search/keyword/",row)
+            html[i] = row
+        return html
+
+    cleanup = False
+    if os.path.exists(adir):
+        flist = os.listdir(adir) # get all files created
+        for f in flist:
+           apath = os.path.join(adir,f)
+           dest = os.path.join(destdir,f)
+           if not os.path.isdir(apath):
+               if os.path.splitext(f)[1].lower() == '.html':
+                   html = fixAffycrap(apath)
+                   fixed = open(apath,'w')
+                   fixed.write('\n'.join(html))
+                   fixed.write('\n')
+                   fixed.close()
+               if not os.path.isfile(dest):
+                   shutil.copy(apath,dest)
+           else:
+               fix_subdir(apath,destdir)
+        if cleanup:
+            try:
+                shutil.rmtree(path=adir,ignore_errors=True)
+            except:
+                pass
+
+
+
+def getFileString(fpath, outpath):
+    """
+    format a nice file size string
+    """
+    size = ''
+    fp = os.path.join(outpath, fpath)
+    s = fpath
+    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
+
+class gsea_wrapper:
+    """
+    GSEA java desktop client has a CL interface. CL can be gleaned by clicking the 'command line' button after setting up an analysis
+    We don't want gsea to do the analysis but it can read .rnk files containing rows of identifiers and an evidence weight such as the signed t statistic from limma for differential expression
+(vgalaxy)rlazarus@iaas1:~/public_html/idle_illumina_analysis$ cat gseaHumanREFSEQ.sh 
+#!/bin/bash
+for RNK in `ls *.rnk`
+do
+DIRNAME=${RNK%.*}
+echo $DIRNAME
+qsub -cwd -b y java -Xmx4096m -cp /data/app/bin/gsea2-2.07.jar xtools.gsea.GseaPreranked -gmx ../msigdb.v3.0.symbols.gmt -collapse true -mode Max_probe -norm meandiv 
+-nperm 1000 -rnk $RNK -scoring_scheme weighted -rpt_label $RNK -chip ../RefSeq_human.chip -include_only_symbols true -make_sets true -plot_top_x 20 -rnd_seed timestamp 
+-set_max 500 -set_min 15 -zip_report false -out gseaout/${DIRNAME} -gui false
+done
+    """
+    
+    def __init__(self,myName=None,opts=None):
+        """ setup cl for gsea
+        """
+        self.idcol = 0
+        self.signcol = 0
+        self.adjpvalcol = 0
+        self.progname=myName
+        self.opts = opts
+        remove_duplicates=True
+        if not os.path.isdir(opts.output_dir):
+            try:
+                os.makedirs(opts.output_dir)
+            except:
+                print >> sys.stderr,'##Error: GSEA wrapper unable to create or find output directory %s. Stopping' % (opts.output_dir)
+                sys.exit(1)
+        fakeGMT = re.sub('[^a-zA-Z0-9_]+', '', opts.input_name) # gives a more useful title for the GSEA report
+        fakeGMT = os.path.join(opts.output_dir,fakeGMT) 
+        fakeRanks = '%s.rnk' % fakeGMT
+        if not fakeGMT.endswith('.gmt'):
+            fakeGMT = '%s.gmt' % fakeGMT
+        if opts.builtin_gmt and opts.history_gmt:
+            newfile = open(fakeGMT,'w')
+            subprocess.call(['cat',opts.builtin_gmt,opts.history_gmt],stdout=newfile)
+            newfile.close()
+        elif opts.history_gmt:
+           subprocess.call(['cp',opts.history_gmt,fakeGMT])
+        else:       
+           subprocess.call(['cp',opts.builtin_gmt,fakeGMT])
+        # remove dupes from each gene set
+        gmt = open(fakeGMT,'r').readlines()
+        gmt = [x for x in gmt if len(x.split('\t')) > 3]
+        ugmt = []
+        for i,row in enumerate(gmt):
+            rows = row.rstrip().split('\t')
+            gmtname = rows[0]
+            gmtcomment = rows[1]
+            glist = list(set(rows[2:]))
+            newgmt = [gmtname,gmtcomment]
+            newgmt += glist
+            ugmt.append('\t'.join(newgmt))
+        gmt = open(fakeGMT,'w')
+        gmt.write('\n'.join(ugmt))
+        gmt.write('\n')
+        gmt.close()
+        if opts.input_ranks:
+            infname = opts.input_ranks
+            rdat = open(opts.input_ranks,'r').readlines() # suck in and remove blank ids that cause gsea to barf rml april 10 2012
+            rdat = [x.rstrip().split('\t') for x in rdat[1:]] # ignore head
+            dat = [[x[0],x[1],x[1]] for x in rdat] 
+            # fake same structure as input tabular file
+            try:
+                pvals = [float(x[1]) for x in dat]
+                signs = [float(x[1]) for x in dat]
+            except:
+                print >> sys.stderr, '## error converting floating point - cannot process this input'
+                sys.exit(99)
+        else: # read tabular
+            self.idcol = int(opts.idcol) - 1
+            self.signcol = int(opts.signcol) - 1
+            self.adjpvalcol = int(opts.adjpvalcol) - 1
+            maxcol = max(self.idcol,self.signcol,self.adjpvalcol)
+            infname = opts.input_tab
+            indat = open(opts.input_tab,'r').readlines()
+            dat = [x.rstrip().split('\t') for x in indat[1:]]
+            dat = [x for x in dat if len(x) > maxcol]
+            dat = [[x[self.idcol],x[self.adjpvalcol],x[self.signcol]] for x in dat] # reduce to rank form 
+            pvals = [float(x[1]) for x in dat]
+            outofrange = [x for x in pvals if ((x < 0.0) or (x > 1.0))]
+            assert len(outofrange) == 0, '## p values outside 0-1 encountered - was that the right column for adjusted p value?'
+            signs = [float(x[2]) for x in dat]
+            outofrange = [i for i,x in enumerate(signs) if (not x) and (dat[i][self.signcol] <> '0')]
+            bad = [dat[x][2] for x in outofrange] 
+            assert len(outofrange) == 0, '## null numeric values encountered for sign - was that the right column? %s' % bad 
+        ids = [x[0] for x in dat]
+        res = []
+        self.comments = []
+        useme = []
+        for i,row in enumerate(dat):
+            if row[1].upper() != 'NA' and row[2].upper() != 'NA' and row[0] != '' :
+                useme.append(i)
+        lost = len(dat) - len(useme)
+        if lost <> 0:
+            newdat = [dat[x] for x in useme]
+            del dat
+            dat = newdat  
+            print >> sys.stdout, '## %d lost - NA values or null id' % lost
+        if remove_duplicates:
+            uids = list(set(ids)) # complex procedure to get min pval for each unique id
+            if len(uids) <> len(ids): # dupes - deal with mode
+                print >> sys.stdout,'## Dealing with %d uids in %d ids' % (len(uids),len(ids))
+                ures = {}
+                for i,id in enumerate(ids):
+                    p = pvals[i]
+                    ures.setdefault(id,[])
+                    ures[id].append((p,signs[i]))
+                for id in uids:
+                    tlist = ures[id]
+                    tp = [x[0] for x in tlist]
+                    ts = [x[1] for x in tlist]
+                    if len(tp) == 1:
+                        p = tp[0]
+                        sign = ts[0]
+                    else:
+                        if  opts.mode == "Max_probe":
+                            p = min(tp)
+                            sign = ts[tp.index(p)]
+                        else: # guess median - too bad if even count
+                            tp.sort()
+                            ltp = len(tp)
+                            ind = ltp/2 # yes, this is wrong for evens but what if sign wobbles?
+                            if ltp % 2 == 1: # odd
+                                ind += 1 # take the median                            
+                            p = tp[ind]
+                            sign = ts[ind]
+                        if KEEPSELECTION:
+                              self.comments.append('## for id=%s, got tp=%s, ts=%s, chose p=%f, sign =%f'\
+                                   % (id,str(tp),str(ts),p,sign))
+                    if opts.input_ranks: # must be a rank file
+                        res.append((id,'%f' % p))
+                    else:
+                        if p == 0.0:
+                            p = 1e-99
+                        try:
+                            lp = -math.log10(p) # large positive if low p value
+                        except ValueError:
+                            lp = 0.0
+                        if sign < 0:
+                            lp = -lp # if negative, swap p to negative
+                        res.append((id,'%f' % lp))
+            else: # no duplicates
+                for i,row in enumerate(dat):
+                    (id,p,sign) = (row[0],float(row[1]),float(row[2]))
+                    if opts.input_ranks: # must be a rank file
+                        res.append((id,'%f' % p))
+                    else:
+                        if p == 0.0:
+                            p = 1e-99
+                        try:
+                            lp = -math.log10(p) # large positive if low p value
+                        except ValueError:
+                            lp = 0.0
+                        if sign < 0:
+                            lp = -lp # if negative, swap p to negative
+                        res.append((id,'%f' % lp))
+        else:
+            for i,row in enumerate(dat):
+                (id,p,sign) = (row[0],float(row[1]),float(row[2]))
+                if opts.input_ranks: # must be a rank file
+                    res.append((id,'%f' % p))
+                else:
+                    if p == 0.0:
+                        p = 1e-99
+                    try:
+                        lp = -math.log10(p) # large positive if low p value
+                    except ValueError:
+                        lp = 0.0
+                    if sign < 0:
+                        lp = -lp # if negative, swap p to negative
+                    res.append((id,'%f' % lp))
+        len1 = len(ids)
+        ranks = res # [x for x in res if len(x[0]) > 0 and len(x[1].strip()) > 0 and x[0].upper() <> 'NA']
+        # rd = dict(zip([x[0] for x in res],res)) # this does something mysterious to dupes - probably keeps last one
+        # ranks = rd.values()
+        len2 = len(ranks)
+        delta = len1 - len2
+        if delta <> 0:
+            print >> sys.stdout,'NOTE: %d of %d rank input file %s rows deleted - dup, null or NA IDs, pvals or logFCs' % (delta,len1,infname)
+        ranks = [(float(x[1]),x) for x in ranks] # decorate
+        ranks.sort()
+        ranks.reverse()
+        ranks = [x[1] for x in ranks] # undecorate
+        if opts.chip == '': # if mouse - need HUGO
+             ranks = [[x[0].upper(),x[1]] for x in ranks]
+             print >> sys.stdout, '## Fixed any lower case - now have',','.join([x[0] for x in ranks[:5]])
+        ranks = ['\t'.join(x) for x in ranks]
+        if len(ranks) < 2:
+             print >> sys.stderr,'Input %s has 1 or less rows with two tab delimited fields - please check the tool documentation' % infname
+             sys.exit(1)
+        rclean = open(fakeRanks,'w')
+        rclean.write('contig\tscore\n')
+        rclean.write('\n'.join(ranks)) 
+        rclean.write('\n')
+        rclean.close()
+        cl = []
+        a = cl.append  
+        a('java -Xmx6G -cp')
+        a(opts.gsea_jar)
+        a('xtools.gsea.GseaPreranked')
+        a('-gmx %s' % fakeGMT) # ensure .gmt extension as required by GSEA - gene sets to use
+        a('-gui false')    # use preranked file mode and no gui
+        a('-make_sets true -rnd_seed timestamp') # more things from the GUI command line display
+        a('-norm meandiv -zip_report false -scoring_scheme weighted')            # ? need to set these? 
+        a('-rnk %s' % fakeRanks) # input ranks file symbol (the chip file is the crosswalk for ids in first column)
+        a('-out %s' % opts.output_dir) 
+        a('-set_max %s' % opts.setMax)
+        a('-set_min %s' % opts.setMin)
+        a('-mode %s' % opts.mode)
+        if opts.chip > '':
+           #a('-chip %s -collapse true -include_only_symbols true' % opts.chip)   
+           a('-chip %s -collapse true' % opts.chip)   
+        else:
+           a("-collapse false") # needed if no chip 
+        a('-nperm %s' % opts.nPerm)
+        a('-rpt_label %s' % opts.title)
+        a('-plot_top_x %s' % opts.plotTop)
+        self.cl = cl
+        self.comments.append('## GSEA command line:')
+        self.comments.append(' '.join(self.cl))
+        self.fakeRanks = fakeRanks
+        self.fakeGMT = fakeGMT
+     
+    def grepIds(self):
+        """
+        """
+        found = []
+        allids = open(self.opts.input_ranks,'r').readlines()
+        allids = [x.strip().split() for x in allids]
+        allids = [x[0] for x in allids] # list of ids
+        gmtpath = os.path.split(self.opts.fakeGMT)[0] # get path to all chip
+
+    def run(self):
+        """
+        
+        """
+        tlog = os.path.join(self.opts.output_dir,"gsea_runner.log")
+        sto = open(tlog,'w')
+        x = subprocess.Popen(' '.join(self.cl),shell=True,stdout=sto,stderr=sto,cwd=self.opts.output_dir)
+        retval = x.wait()
+        sto.close()
+        d = glob.glob(os.path.join(self.opts.output_dir,'%s*' % self.opts.title))
+        if len(d) > 0:
+            fix_subdir(d[0],self.opts.output_dir)       
+        htmlfname = os.path.join(self.opts.output_dir,'index.html')     
+        try:
+            html = open(htmlfname,'r').readlines()
+            html = [x.strip() for x in html if len(x.strip()) > 0]
+            if len(self.comments) > 0:
+                s = ['<pre>']
+                s += self.comments
+                s.append('</pre>')
+                try:
+                    i = html.index('<div id="footer">')
+                except:
+                    i = len(html) - 7 # fudge
+                html = html[:i] + s + html[i:]
+        except:
+            html = []
+            htmlhead = '<html><head></head><body>'
+            html.append('## Galaxy GSEA wrapper failure')
+            html.append('## Unable to find index.html in %s - listdir=%s' % (d,' '.join(os.listdir(self.opts.output_dir))))
+            html.append('## Command line was %s' % (' '.join(self.cl)))
+            html.append('## commonly caused by mismatched ID/chip selection')
+            glog = open(os.path.join(self.opts.output_dir,'gsea_runner.log'),'r').readlines()
+            html.append('## gsea_runner.log=%s' % '\n'.join(glog))
+            #tryme = self.grepIds()
+            retval = 1
+            print >> sys.stderr,'\n'.join(html)
+            html = ['%s<br/>' % x for x in html]
+            html.insert(0,htmlhead)
+            html.append('</body></html>')
+        htmlf = file(self.opts.outhtml,'w')
+        htmlf.write('\n'.join(html))
+        htmlf.write('\n')
+        htmlf.close()
+        os.unlink(self.fakeRanks)
+        os.unlink(self.fakeGMT)
+        if opts.outtab_neg:
+            tabs = glob.glob(os.path.join(opts.output_dir,"gsea_report_for_*.xls"))
+            if len(tabs) > 0:
+                for tabi,t in enumerate(tabs):
+                    tkind = os.path.basename(t).split('_')[4].lower()
+                    if tkind == 'neg':
+                       outtab = opts.outtab_neg
+                    elif tkind == 'pos':
+                       outtab = opts.outtab_pos
+                    else:
+                       print >> sys.stderr, '## tab file matched %s which is not "neg" or "pos" in 4th segment %s' % (t,tkind)
+                       sys.exit()
+                    content = open(t).readlines()
+                    tabf = open(outtab,'w')
+                    tabf.write(''.join(content))
+                    tabf.close()
+            else:
+                print >> sys.stdout, 'Odd, maketab = %s but no matches - tabs = %s' % (makeTab,tabs)
+        return retval
+        
+
+if __name__ == "__main__":
+    """ 
+    called as:
+   <command interpreter="python">rgGSEA.py --input_ranks "$input1"  --outhtml "$html_file"
+       --setMax "$setMax" --setMin "$setMin" --nPerm "$nPerm" --plotTop "$plotTop" --gsea_jar "$GALAXY_DATA_INDEX_DIR/shared/jars/gsea2-2.07.jar" 
+       --output_dir "$html_file.files_path" --use_gmt ""${use_gmt.fields.path}"" --chip "${use_chip.fields.path}"
+  </command>
+    """
+    op = optparse.OptionParser()
+    a = op.add_option
+    a('--input_ranks',default=None)
+    a('--input_tab',default=None)
+    a('--input_name',default=None)
+    a('--use_gmt',default=None)
+    a('--history_gmt',default=None)
+    a('--builtin_gmt',default=None)
+    a('--history_gmt_name',default=None)
+    a('--setMax',default="500")
+    a('--setMin',default="15")
+    a('--nPerm',default="1000") 
+    a('--title',default="GSEA report") 
+    a('--chip',default='')
+    a('--plotTop',default='20')
+    a('--outhtml',default=None)
+    a('--makeTab',default=None)
+    a('--output_dir',default=None)
+    a('--outtab_neg',default=None)
+    a('--outtab_pos',default=None)
+    a('--adjpvalcol',default=None)
+    a('--signcol',default=None)
+    a('--idcol',default=None)
+    a('--mode',default='Max_probe')
+    a('-j','--gsea_jar',default='/usr/local/bin/gsea2-2.07.jar')
+    opts, args = op.parse_args() 
+    assert os.path.isfile(opts.gsea_jar),'## GSEA runner unable to find supplied gsea java desktop executable file %s' % opts.gsea_jar
+    if opts.input_ranks:
+        inpf = opts.input_ranks
+    else:
+        inpf = opts.input_tab
+        assert opts.idcol <> None, '## GSEA runner needs an id column if a tabular file provided'
+        assert opts.signcol <> None, '## GSEA runner needs a sign column if a tabular file provided'
+        assert opts.adjpvalcol <> None, '## GSEA runner needs an adjusted p value column if a tabular file provided'
+    assert os.path.isfile(inpf),'## GSEA runner unable to open supplied input file %s' % inpf
+    if opts.chip > '':
+        assert os.path.isfile(opts.chip),'## GSEA runner unable to open supplied chip file %s' % opts.chip
+    some = None
+    if opts.history_gmt <> None:
+        some = 1
+        assert os.path.isfile(opts.history_gmt),'## GSEA runner unable to open supplied history gene set matrix (.gmt) file %s' % opts.history_gmt
+    if opts.builtin_gmt <> None:
+        some = 1
+        assert os.path.isfile(opts.builtin_gmt),'## GSEA runner unable to open supplied history gene set matrix (.gmt) file %s' % opts.builtin_gmt
+    assert some, '## GSEA runner needs a gene set matrix file - none chosen?'
+    opts.title = re.sub('[^a-zA-Z0-9_]+', '', opts.title)
+    myName=os.path.split(sys.argv[0])[-1]
+    gse = gsea_wrapper(myName, opts=opts)
+    retcode = gse.run()
+    if retcode <> 0:
+        sys.exit(retcode) # indicate failure to job runner
+    
+