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DGE_generate_v3.py
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DGE_generate_v3.py
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import os
import sys
import os.path
import re
import argparse
import linecache
root_dir=os.getcwd()
##########################################################################
##########################################################################
#parse the arguments
parser = argparse.ArgumentParser(description="DGE pipline v3.0")
parser.add_argument('--project',help='project name, maybe same with the name of root dir, which will be displayed in the final report title, [REQUIRED]',required=True)
parser.add_argument('--sample',help="sample names(sample1,sample2,...) warning: order sensitive!",required=True)
parser.add_argument('--fq',help="the original directory of the raw fastq reads, [REQUIRED]",default=None)
parser.add_argument('--mapfile',help="mapfile files (mapfile1,mapfile2.The first column of mapfile is the NH number ,the second column of mapfile is the sample name)",default=None)
parser.add_argument('--raw_dir',help="the original directory of the raw fastq reads keep order in line with mapfile files (raw_dir1,raw_dir2)",default=None)
parser.add_argument('--ad',help="the original directory of the adapter list, ",default=None)
parser.add_argument('--generate_adapter',help='whether to generate the adpepter list y or n',choices=['y','n'],default='n')
parser.add_argument('--index',help='the index number of the fastq files,if you want to generate the adapter list,the parameter will be necessary,diffrent samples split by ,warning: order sensitive!',default=None)
parser.add_argument('--ss',help="strand specific, [REQUIRED]",choices=['no','yes','reverse'],default='no')
parser.add_argument('--number',help="chromosome number, [REQUIRED for density plot]",required=True)
parser.add_argument('--length',help="the length of sequenced reads",required=True)
parser.add_argument('--fa',help="the reference FASTA file, [REQUIRED for mapping]",required=True)
parser.add_argument('--gtf',help="the annotation GTF file, [REQUIRED for mapping]",required=True)
parser.add_argument('--group',help="sample classification, e.g. sample1:sample2,sample3, [REQUIRED]",default=None)
parser.add_argument('--groupname',help="group names, [group1,group2,... ]",default=None)
parser.add_argument('--compare',help="group comparison strategy 1:2,1:3,..., [REQUIRED]",default=None)
parser.add_argument('--venn',help="venn and cluster mode, defult is all groups, 1:2_1:3,1:3_2:3,... ",default=None)
parser.add_argument('--goann',help="gene to GO annotations file, [REQUIRED]",default=None)
parser.add_argument('--species',help="abbreviation for species, for kegg pathway. (note: all species: /PUBLIC/database/RNA/kobas2.0-data-20120208/seq_pepi_v2), [defalut=ko]",default='kaas')
parser.add_argument('--ppi_number',help="species code, (ref file: /PUBLIC/database/RNA/string_ppi/species.v9.0.txt)",default=None)
parser.add_argument('--ppi_blast',help="whether to run blast to get the protein-protein interactions",choices=['y','n'],default=None)
parser.add_argument('--genenamefile',help="genenamefile, 1st col is geneID, 2nd col is genename",default=None)
parser.add_argument('--ex',help="the steps you do not wanna perform",default=None)
def checkSample(sample):
PatChar = r'^(CON|PRN|AUX|CLOCK\$|NUL|COM[1-9]|LPT1|[\W]+)$'
PatNum = r'^\d+'
MAXLEN = 8
message = '''can only use word/digit/underscore in sample, start with word.
Max length is 8, no windows reserved words like CON PRN...'''
if re.search(PatChar,sample) or re.search(PatNum,sample) or len(sample) > MAXLEN:
print '%s<==invalid name' % s
print message
exit()
# extract, check and display the parameters
argv = vars(parser.parse_args())
project=argv['project'].strip()
display = open(root_dir + '/' + 'DGE_command.txt','w')
display.write('project: %s\n' % (project))
sample=argv['sample'].strip()
samples=sample.split(',')
samples_tmp=list(set(samples))
for s in samples:
checkSample(s)
assert len(samples)==len(samples_tmp)
display.write('sample: %s\n' % (sample))
mapfiles=[each.strip() for each in argv['mapfile'].strip().split(',') if each.strip() != '']
mapfile=' '.join(mapfiles)
assert not os.system('cat %s |sort -u |sed \'/^$/d\' >%s' % (mapfile,root_dir+'/libraryID'))
if argv['fq']:
fq = argv['fq'].strip()
fq = os.path.abspath(fq)
else:
assert not os.system('mkdir raw_data')
assert not os.system('perl /PUBLIC/source/RNA/RefRNA/ln_raw_data.pl %s %s se raw_data' %(argv['mapfile'],argv['raw_dir']))
fq = root_dir + '/raw_data'
for each in samples:
fq_tmp1=fq+'/'+each+'.fq.gz'
# fq_tmp2=fq+'/'+each+'_2.fq.gz'
assert os.path.isfile(fq_tmp1)
# assert os.path.isfile(fq_tmp2)
display.write('fq: %s\n' % (fq))
display.write('adapter: ')
if argv['ad']:
ad = argv['ad'].strip()
ad = os.path.abspath(ad)
for each in samples:
ad_tmp1=ad+'/'+each+'.adapter.list.gz'
# ad_tmp2=ad+'/'+each+'_2.adapter.list.gz'
assert os.path.isfile(ad_tmp1)
# assert os.path.isfile(ad_tmp2)
display.write('%s' % (ad))
display.write('\n')
if argv['generate_adapter']:
generate_adapter = argv['generate_adapter'].strip()
else:
generate_adapter = 'n'
display.write('generate_adapter: %s\n' % (generate_adapter))
display.write('index: \n')
if argv['index']:
index=argv['index'].strip()
indexes=index.split(',')
assert len(samples)==len(indexes)
for i,index_tmp in enumerate(samples):
display.write('%s:\t%s\n' % (index_tmp,indexes[i]))
display.write('\n')
if generate_adapter == 'y':
if argv['ad'] !=None:
print 'Error: the parameters --ad and --generate_adapter are not consensus!\n'
exit()
if argv['index'] == None:
print 'Error: the parameters --index and --generate_adapter are not consensus!\n'
exit()
else:
if argv['index'] != None:
print 'Error: the parameters --index and --generate_adapter are not consensus!\n'
exit()
#-----------------------------------------------------------------------
all_content=set([1,2,3,4,5,6])
if argv['ex'] != None:
excludes=argv['ex'].strip().strip(',').strip().split(',')
excludes=[int(each.strip()) for each in excludes]
for each1 in excludes:
assert each1 in all_content
else:
excludes=[] #list
includes=all_content-set(excludes) #set
#-----------------------------------------------------------------------
ss = argv['ss'].strip()
display.write('ss: %s\n' % (ss))
number = argv['number'].strip()
display.write('chr number: %s\n' % (number))
if argv['length']:
length = argv['length'].strip()
else:
length = '100'
display.write('length: %s\n' % (length))
fa = argv['fa'].strip()
fa = os.path.abspath(fa)
suffix_fa=['.1.bt2','.2.bt2','.3.bt2','.4.bt2','.rev.1.bt2','.rev.2.bt2']
for each in suffix_fa:
fa_tmp=fa+each
assert os.path.isfile(fa_tmp)
display.write('fa: %s\n' % (fa))
gtf = argv['gtf'].strip()
gtf = os.path.abspath(gtf)
assert os.path.isfile(gtf)
display.write('gtf: %s\n' % (gtf))
#-----------------------------------------------------------------------
if set([2]).issubset(includes):
if argv['group'] == None:
group=samples
group_iter=samples
group=sample
flag_repeat=False
else:
groups_iter=[]
if ':' in argv['group'].strip(':'):
flag_repeat=True
groups=[each.strip().split(':') for each in argv['group'].strip().strip(':').split(',') if each.strip() != '']
for each in groups:
groups_iter+=each
group_iter_n=[]
for each in groups_iter:
if each not in group_iter_n:
group_iter_n.append(each)
groups_iter=group_iter_n
group=','.join([':'.join(each) for each in groups])
else:
flag_repeat=False
groups=[each.strip() for each in argv['group'].strip().split(',') if each.strip() != '']
for each in groups:
groups_iter.append(each)
group=','.join(groups)
assert set(groups_iter).issubset(samples)
group_iter=','.join(groups_iter)
if argv['groupname'] == None:
if flag_repeat == False:
groupname_tmp=groups
else:
groupname_tmp=['group'+str(k+1) for k in range(len(groups))]
else:
groupname_tmp=[each.strip() for each in argv['groupname'].split(',') if each.strip() != '']
assert len(groupname_tmp) == len(groups)
groupname=','.join(groupname_tmp)
compare = argv['compare'].strip()
compare_samples=[each.strip().split(':') for each in argv['compare'].strip().split(',') if each.strip() != '']
M=[]
for each1 in compare_samples:
temp1=[]
for each2 in each1:
assert each2.isdigit()
M.append(int(each2))
assert max(M) <= len(groupname_tmp)
assert min(M) > 0
compare_sample=','.join([','.join(each) for each in compare_samples])
temp2=[]
for each1 in compare_samples:
temp1=[]
for each2 in each1:
temp1.append(groupname_tmp[int(each2)-1])
temp2.append(':'.join(temp1))
compares_name=','.join(temp2)
if argv['venn']:
venn = argv['venn'].strip()
com_pairs=compare.split(',')
venn_clusters=[each.split('_') for each in venn.split(',')]
temp1=[]
for each1 in venn_clusters:
temp2=[]
for each2 in each1:
assert each2 in com_pairs
temp3=each2.split(':')
assert len(temp3) == 2
temp2.append(groupname_tmp[int(temp3[0])-1]+':'+groupname_tmp[int(temp3[1])-1])
temp1.append('_'.join(temp2))
venn_cluster_name=','.join(temp1)
else:
venn = compare.replace(',','_')
venn_cluster_name=compares_name.replace(',','_')
groups=group.split(',')
groupnames=groupname.split(',')
compares=compare.split(',')
venns=venn.split(',')
for each in groups:
temp=each.split(':')
assert len(temp)==len(list(set(temp)))
for each2 in temp:
assert each2 in samples
assert len(groups)==len(groupnames)
display.write('\ngroups:\n')
assert len(groupnames)==len(list(set(groupnames)))
for i,each in enumerate(groupnames):
group_tmp=groups[i]
group_tmp=group_tmp.replace(':',',')
display.write('%s: %s\n' % (each,group_tmp))
display.write('\ncompare:\n')
compare_name=[]
for i,each in enumerate(compares):
display.write('%s: \t' % (each))
compare_tmp=each
compare_tmp=compare_tmp.split(':')
assert len(compare_tmp)==2
compare_name=groupnames[int(compare_tmp[0])-1]+'vs'+groupnames[int(compare_tmp[1])-1]
display.write('%s\n' % (compare_name))
display.write('\nvenn:\n')
for i,each in enumerate(venns):
display.write('%s: \t' % (each))
venn_tmp=each
venn_tmp=venn_tmp.split('_')
for each2 in venn_tmp:
assert each2 in compares
venn_tmp2=each2.split(':')
venn_name=groupnames[int(venn_tmp2[0])-1]+'vs'+groupnames[int(venn_tmp2[1])-1]
display.write('%s,' % (venn_name))
display.write('\n')
display.write('\n')
#-----------------------------------------------------------------------
if set([1,2,4]).issubset(includes):
goann = argv['goann'].strip()
goann = os.path.abspath(goann)
assert os.path.isfile(goann)
display.write('goann: %s\n' % (goann))
if set([1,2,5]).issubset(includes):
if argv['species']:
species = argv['species'].strip()
else:
species = 'kaas'
display.write('KEGG species: %s\n' % (species))
if set([1,2,6]).issubset(includes):
display.write('PPI number: ')
if argv['ppi_number']:
ppi_number = argv['ppi_number'].strip()
display.write('%s' % (ppi_number))
display.write('\n')
display.write('PPI blast: ')
if argv['ppi_blast']:
ppi_blast = argv['ppi_blast'].strip()
display.write('%s' % (ppi_blast))
display.write('\n')
if argv['ppi_blast']:
if argv['ppi_number'] == None:
print 'Error: the parameters --ppi_blast and --ppi_number are not consensus!\n'
exit()
else:
if argv['ppi_number']:
print 'Error: the parameters --ppi_blast and --ppi_number are not consensus!\n'
exit()
display.write('genenamefile: ')
if argv['genenamefile']:
genenamefile = argv['genenamefile'].strip()
genenamefile = os.path.abspath(genenamefile)
assert os.path.isfile(genenamefile)
display.write('%s' % (genenamefile))
display.write('\n')
display.close()
#################################################################################################
#for QC
code='''
import os
fq='%s'
ss='%s'
fa='%s'
gtf='%s'
sample='%s'
root_dir='%s'
''' % (fq,ss,fa,gtf,sample,root_dir)
if argv['ad']:
code+='''
ad='%s'
''' % (ad)
if generate_adapter != 'n':
code+='''
index='%s'
''' % (index)
if argv['mapfile']:
code+='''
mapfile='%s'
''' % (root_dir+'/libraryID')
code+='''
assert not os.system('mkdir QC_DGE')
os.chdir('QC_DGE')
f=open(root_dir+'/QC_DGE/generate_QC.sh','w')
f.write('perl /PUBLIC/source/RNA/QC/QC_v2/allrunQC_v2.1.pl -fq %s -se-pe se -n %s -o %s -spe %s -R %s -G %s -bed %s ' %(fq,sample,root_dir+'/QC_DGE',ss,fa,gtf,root_dir+'/QC_DGE/sorted.bed'))
'''
if argv['mapfile']:
code+='''
f.write('-mapfile %s ' % (mapfile))
'''
if argv['ad']:
code+='''
f.write('-ad %s\\n' % (ad))
'''
if argv['index']:
code+='''
f.write('-m_ad y -index %s\\n' % (index))
'''
code+='''
f.write('\\n')
f.close()
assert not os.system('sh %s/generate_QC.sh' %(root_dir+'/QC_DGE'))
samples=sample.split(',')
for eachsample in samples:
os.chdir(root_dir+'/QC_DGE/'+eachsample)
assert not os.system('qsub -V -l vf=5g,p=8 -cwd %s' % (eachsample+'_QC_se.sh'))
os.chdir(root_dir)
'''
open('DGE_step1_QC.py','w').write(code)
#################################################################################################
#for QCreport
code='''
import os
sample='%s'
project='%s'
root_dir='%s'
''' % (sample,project,root_dir)
code+='''
assert not os.system('mkdir QC_DGE/QCreport')
os.system('sh /PUBLIC/source/RNA/QC/QC_v2/QCreport/DGE_QCreport.sh -dir %s -sample %s -title %s -results %s' %(root_dir+'/QC_DGE',sample,project,root_dir+'/QC_DGE/QCreport'))
'''
open('DGE_step1_QCreport.py','w').write(code)
#################################################################################################
#for Diff analysis and Curves
code=''
code='''
import re
import os
sample='%s'
ss='%s'
gtf='%s'
group='%s'
groupname='%s'
compare='%s'
venn='%s'
fa='%s'
n='%s'
length='%s'
root_dir='%s'
''' % (sample,ss,gtf,group,groupname,compare,venn,fa,number,length,root_dir)
if argv['genenamefile']:
code+='''
genenamefile='%s'
''' % (genenamefile)
if set([1,2]).issubset(includes):
code+='''
##Diff
sam=root_dir+'/QC_DGE/sam'
samples = sample.split(',')
readcount=[]
for eachsample in samples:
temp='%s/Diff_DGE/readcount/%s.readcount' % (root_dir,eachsample)
readcount.append(temp)
readcount=','.join(readcount)
assert not os.system('mkdir Diff_DGE')
os.chdir('Diff_DGE')
f=open(root_dir+'/Diff_DGE/generate_Diff.sh','w')
f.write('perl /PUBLIC/source/RNA/RefRNA/DGE/DiffExpression/runDiff_analysis_v2.2.pl -fa %s -sam %s -g %s -o %s -group %s -groupname %s -compare %s -venn %s -spe %s -i %s ' % (fa,sam,gtf,root_dir+'/Diff_DGE',group,groupname,compare,venn,ss,readcount))
'''
if argv['genenamefile']:
code+='''
f.write(' -genenamefile %s ' % (genenamefile))
'''
code+='''
f.write('\\n')
f.close()
assert not os.system('sh generate_Diff.sh')
assert not os.system('qsub -V -cwd -l vf=5G -l p=1 runDiff_analysis.sh')
os.chdir(root_dir)
'''
if set([1,2,3]).issubset(includes):
code+='''
##Curve
bam=root_dir+'/QC_DGE/bam'
assert not os.system('mkdir Curve_DGE')
os.chdir('Curve_DGE')
f=open(root_dir+'/Curve_DGE/generate_Curve.sh','w')
f.write('perl /PUBLIC/source/RNA/RefRNA/DGE/Curve/runCurve_v2.pl -bam %s -sample %s -n %s -r %s -fa %s -gtf %s -o %s\\n' % (bam,sample,n,length,fa,gtf,root_dir+'/Curve_DGE'))
f.close()
assert not os.system('sh generate_Curve.sh')
assert not os.system('qsub -V -cwd -l vf=10G -l p=1 runSaturation.sh')
assert not os.system('qsub -V -cwd -l vf=5G -l p=1 rundensity.sh')
os.chdir(root_dir)
'''
open('DGE_step2_Diff_Curves.py','w').write(code)
#################################################################################################
#for Enrichment and PPI
code='''
import os
fa='%s'
goann='%s'
groupname='%s'
compare='%s'
root_dir='%s'
''' % (fa,goann,groupname,compare,root_dir)
code+='''
groupnames=groupname.split(',')
compares=compare.split(',')
'''
if set([1,2,4]).issubset(includes):
code+='''
##GOSeq
assert not os.system('mkdir GOSeq_DGE')
os.chdir('GOSeq_DGE')
go=open(root_dir+'/GOSeq_DGE/runGOSeq.sh','w')
for each in compares:
temp=each.split(':')
dir=groupnames[int(temp[0])-1]+'vs'+groupnames[int(temp[1])-1]
id=root_dir+'/Diff_DGE/Diff/'+dir+'/'+dir+'.diffgeneID'
out=root_dir+'/GOSeq_DGE/'+dir
length=root_dir+'/Diff_DGE/Diff/genelength'
result=root_dir+'/GOSeq_DGE/'+dir+'/'+dir+'.GO_enrichment_result.xls'
diff=root_dir+'/Diff_DGE/Diff/'+dir+'/'+dir+'.diffgene.xls'
go.write('###############%s#####################\\n' % (dir))
go.write('mkdir %s\\n' % (root_dir+'/GOSeq_DGE/'+dir))
go.write('perl /PUBLIC/source/RNA/RefRNA/DGE/Enrichment/goseq_graph_v3.pl -i %s -goann %s -n %s -o %s -length %s\\n' % (id,goann,dir,out,length))
go.write('perl /PUBLIC/source/RNA/RefRNA/DGE/Enrichment/changeGO_up_down.pl %s %s %s\\n' % (result,diff,root_dir+'/GOSeq_DGE/'+dir+'/'+dir+'.GO_enrichment_result_up_down.xls'))
go.write('/PUBLIC/software/public/System/R-2.15.3/bin/Rscript /PUBLIC/source/RNA/RefRNA/DGE/Enrichment/goBar.R %s %s %s\\n' % (result,out,dir))
go.write('/PUBLIC/software/public/System/R-2.15.3/bin/Rscript /PUBLIC/source/RNA/RefRNA/DGE/Enrichment/goBar2.R %s %s %s\\n' % (root_dir+'/GOSeq_DGE/'+dir+'/'+dir+'.GO_enrichment_result_up_down.xls',out,dir))
go.close()
assert not os.system('qsub -V -cwd -l vf=5G -l p=1 runGOSeq.sh')
os.chdir(root_dir)
'''
if argv['genenamefile'] == None:
code+='''
assert not os.system('mkdir Blast_DGE')
os.chdir('Blast_DGE')
f=open(root_dir+'/Blast_DGE/runBlast_swissprot.sh','w')
query=root_dir+'/Diff_DGE/Diff/diffgene_union.seq'
outdir1=root_dir+'/Blast_DGE/Blast_Swissprot/'
out=root_dir+'/Blast_DGE/Blast_Swissprot/diffgene_union.seq.blastout'
f.write('echo start blastx\\ndate\\n')
f.write('mkdir %s\\n' % (outdir1))
f.write('/PUBLIC/software/public/Alignment/ncbi-blast-2.2.28+/bin/blastx -query %s -db /PUBLIC/database/Common/SwissProt/uniprot_sprot.fasta -evalue 1e-5 -outfmt 5 -max_target_seqs 1 -num_threads 10 -out %s\\n' % (query,out))
f.write('echo blastx end\\ndate\\n')
f.write('perl /PUBLIC/source/RNA/RefRNA/DGE/scriptdir/extractIDsEVxml.pl %s %s\\n' % (out,outdir1+'/diffgene_union.genenames'))
compare=root_dir+'/Diff_DGE/Diff/compare.txt'
indir=root_dir+'/Diff_DGE/Diff/'
outdir2=root_dir+'/Diff_DGE/Diff/DiffGeneList'
f.write('mkdir %s\\n' % (outdir2))
f.write('perl /PUBLIC/source/RNA/RefRNA/DGE/scriptdir/getdiffGN.up_down_v2.pl %s %s %s %s\\n' % (indir,compare,outdir1+'/diffgene_union.genenames',outdir2))
f.close()
assert not os.system('qsub -V -cwd -l vf=5G -l p=10 runBlast_swissprot.sh')
os.chdir(root_dir)
'''
if set([1,2,5]).issubset(includes):
code+='''
species='%s'
''' % (species)
if argv['species'] == 'kaas':
code+='''
##KOBAS
assert not os.system('mkdir KOBAS_DGE')
os.chdir('KOBAS_DGE')
ko=open(root_dir+'/KOBAS_DGE/runKOBAS.sh','w')
path=open(root_dir+'/KOBAS_DGE/runpathway.sh','w')
query=root_dir+'/Diff_DGE/Diff/diffgene_union.seq'
blastout=root_dir+'/Blast_DGE/KOBAS_blast.xml'
ko.write('###############Run kaas#####################\\n')
ko.write('/PUBLIC/software/public/Annotation/kaas_sa2/bin/auto_annotate.pl -n -s %s\\n' % (query))
ko.write('python /PUBLIC/software/RNA/gene_annotation/scripts/convert2kobas_v1.py %s /PUBLIC/database/Common/KEGG/kos %s\\n' % (root_dir + '/Diff_DGE/Diff/diffgene_union.seq.ko',root_dir + '/KOBAS_DGE/koID.annotation'))
for each in compares:
temp=each.split(':')
dir=groupnames[int(temp[0])-1]+'vs'+groupnames[int(temp[1])-1]
id=root_dir+'/Diff_DGE/Diff/'+dir+'/'+dir+'.diffgeneID'
out=root_dir+'/KOBAS_DGE/'+dir
ko.write('###############%s#####################\\n' % (dir))
path.write('echo "###############%s#####################"\\n' % (dir))
path.write('cd %s\\n' % (out))
result=root_dir+'/KOBAS_DGE/'+dir+'/'+'add.'+dir+'.identify.xls'
diff=root_dir+'/Diff_DGE/Diff/'+dir+'/'+dir+'.diffgene.xls'
diffID=root_dir+'/Diff_DGE/Diff/'+dir+'/'+dir+'.diffgeneID'
path.write('python /PUBLIC/source/RNA/RefRNA/DGE/KEGG_Enrichment/bin/pathway_annotation_flow_parallel_annotationfault_tolerant3.pyc --table %s --diff %s\\n' % (result,diff))
path.write('mv %s %s\\n' % ('add.'+dir+'.identify.xls_rendered_html_detail.html',dir+'.html'))
ko.write('mkdir %s\\n' % (root_dir+'/KOBAS_DGE/'+dir))
ko.write('cd %s\\n' % (root_dir+'/KOBAS_DGE/'+dir))
ko.write('perl /PUBLIC/source/RNA/noRef/KEGG_enrichment/runKEGG_enrich.pl -diff %s -ko %s -g %s\\n' % (diffID,root_dir + '/KOBAS_DGE/koID.annotation',dir))
path.close()
ko.close()
assert not os.system('qsub -V -cwd -l vf=5G -l p=10 runKOBAS.sh')
os.chdir(root_dir)
'''
else:
code+='''
##KOBAS
assert not os.system('mkdir KOBAS_DGE')
os.chdir('KOBAS_DGE')
ko=open(root_dir+'/KOBAS_DGE/runKOBAS.sh','w')
path=open(root_dir+'/KOBAS_DGE/runpathway.sh','w')
query=root_dir+'/Diff_DGE/Diff/diffgene_union.seq'
blastout=root_dir+'/Blast_DGE/KOBAS_blast.xml'
ko.write('###############Run Blast#####################\\n')
ko.write('mkdir %s\\n' % (root_dir+'/Blast_DGE/'))
ko.write('perl /PUBLIC/source/RNA/RefRNA/DGE/KEGG_Enrichment/bin/KEGG_step1_blast.pl %s %s %s %s\\n' % (query,species,blastout,root_dir+'/Blast_DGE/KOBAS_blast.sh'))
ko.write('sh %s\\n' % (root_dir+'/Blast_DGE/KOBAS_blast.sh'))
for each in compares:
temp=each.split(':')
dir=groupnames[int(temp[0])-1]+'vs'+groupnames[int(temp[1])-1]
id=root_dir+'/Diff_DGE/Diff/'+dir+'/'+dir+'.diffgeneID'
out=root_dir+'/KOBAS_DGE/'+dir
ko.write('###############%s#####################\\n' % (dir))
path.write('echo "###############%s#####################"\\n' % (dir))
path.write('cd %s\\n' % (out))
result=root_dir+'/KOBAS_DGE/'+dir+'/'+'add.'+dir+'.identify.xls'
diff=root_dir+'/Diff_DGE/Diff/'+dir+'/'+dir+'.diffgene.xls'
path.write('python /PUBLIC/source/RNA/RefRNA/DGE/KEGG_Enrichment/bin/pathway_annotation_flow_parallel_annotationfault_tolerant3.pyc --table %s --diff %s\\n' % (result,diff))
path.write('mv %s %s\\n' % ('add.'+dir+'.identify.xls_rendered_html_detail.html',dir+'.html'))
ko.write('mkdir %s\\n' % (root_dir+'/KOBAS_DGE/'+dir))
script=root_dir+'/KOBAS_DGE/'+dir+'/run.sh'
ko.write('perl /PUBLIC/source/RNA/RefRNA/DGE/KEGG_Enrichment/bin/KEGG_step2_enrich.pl -id %s -out-dir %s -species %s -blast-result %s -sample-names %s>%s\\n' % (id,out,species,blastout,dir,script))
ko.write('sh %s\\n' % (script))
path.close()
ko.close()
assert not os.system('qsub -V -cwd -l vf=5G -l p=10 runKOBAS.sh')
os.chdir(root_dir)
'''
if set([1,2,6]).issubset(includes):
code+='''
ppi_number='%s'
ppi_blast='%s'
''' % (ppi_number,ppi_blast)
code+='''
##PPI
assert not os.system('mkdir PPI_DGE')
os.chdir('PPI_DGE')
ppi=open(root_dir+'/PPI_DGE/runPPI.sh','w')
for each in compares:
temp=each.split(':')
dir=groupnames[int(temp[0])-1]+'vs'+groupnames[int(temp[1])-1]
id=root_dir+'/Diff_DGE/Diff/'+dir+'/'+dir+'.diffgeneID'
seq=root_dir+'/Diff_DGE/Diff/Diff_Gene_Seq/'+dir+'.diffgene.seq'
out=root_dir+'/PPI_DGE/'+dir
ppi.write('mkdir %s\\n' % (out))
'''
if argv['ppi_blast'] == 'y':
code+='''
ppi.write('python /PUBLIC/source/RNA/RefRNA/DGE/Enrichment/BLASTX_TO_PPI_v4.py --species %s --fa %s --outdir %s --name %s\\n' % (ppi_number,seq,out,dir))
'''
else:
code+='''
ppi_dir='/PUBLIC/database/RNA/PPI_ref/PPI_99'
ppi.write('python /PUBLIC/source/RNA/RefRNA/DGE/Enrichment/get_my_PPI.py -p %s -g %s -o %s\\n' % (ppi_dir+'/PPI_'+ppi_number+'.txt',id,out+'/'+dir+'.ppi.txt'))
'''
code+='''
ppi.close()
assert not os.system('qsub -V -cwd -l vf=5G -l p=10 runPPI.sh')
os.chdir(root_dir)
'''
open('DGE_step3_Enrichment.py','w').write(code)
#################################################################################################
#for Report
code='''
import re
import os
import os.path
import glob
import sys
import gzip
import linecache
reload(sys)
sys.setdefaultencoding('utf-8')
from django.template import Template, Context, loader
from django.conf import settings
settings.configure(DEBUG=True, TEMPLATE_DEBUG=True,TEMPLATE_DIRS=('/PUBLIC/source/RNA/RefRNA/Report/template/DGE',))
fq='%s'
sample='%s'
groupname='%s'
compare='%s'
project='%s'
root_dir='%s'
ss='%s'
venn_cluster_name='%s'
flag_uniform=True
''' % (fq,sample,groupname,compare,project,root_dir,ss,venn_cluster_name)
code+='''
samples=sample.split(',')
##md5
dir=root_dir+'/QC_DGE'
cd_md5=open(root_dir+'/QC_DGE/cd_md5.sh','w')
rd_md5=open(root_dir+'/QC_DGE/rd_md5.sh','w')
os.chdir(dir)
cd_md5.write('cd %s/cleandata\\n' % (dir))
cd_md5.write('echo -e \"md5\\tfile\">cd_md5.txt\\n')
rd_md5.write('echo -e \"md5\\tfile\">rd_md5.txt\\n')
for each in samples:
cd_md5.write('md5sum %s.clean.fq>>cd_md5.txt\\n' % (each))
cd_md5.write('unlink %s.clean.fq\\n' %(each))
cd_temp=root_dir+'/QC_DGE/'+each+'/clean_data/'+each+'.clean.fq'
cd_md5.write('gzip %s\\n' % (cd_temp))
cd_md5.write('ln -s %s.gz %s\\n' % (cd_temp,dir+'/cleandata/'))
rd_md5.write('cd %s\\n' % (root_dir+'/QC_DGE/'+each))
rd_md5.write('md5sum %s>>%srd_md5.txt\\n' % (each+'.fq.gz',root_dir+'/QC_DGE/'))
cd_md5.close()
rd_md5.close()
#assert not os.system('qsub -V -l vf=3g,p=1 -cwd cd_md5.sh')
#assert not os.system('qsub -V -l vf=3g,p=1 -cwd rd_md5.sh')
os.chdir(root_dir)
os.chdir(root_dir+'/QC_DGE')
rdmd5=glob.glob('rd_md5.txt')
if not rdmd5:
assert not os.system('qsub -V -l vf=3g,p=1 -cwd rd_md5.sh')
os.chdir(root_dir+'/QC_DGE/cleandata')
cdmd5=glob.glob('cd_md5.txt')
if not cdmd5:
os.chdir(root_dir+'//QC_DGE')
assert not os.system('qsub -V -l vf=3g,p=1 -cwd cd_md5.sh')
os.chdir(root_dir)
'''
if set([1,2,5]).issubset(includes):
code+='''
##path
path=root_dir+'/KOBAS_DGE/runpathway.sh'
assert not os.system('sh %s' % (path))
'''
code+='''
#results
assert not os.system('mkdir '+project+'_DGE_result')
assert not os.system('mkdir '+project+'_DGE_result/'+project+'_results')
assert not os.system('mkdir '+project+'_DGE_result/'+project+'_report')
#assert not os.system('cp /PUBLIC/source/RNA/RefRNA/TransRef/Report/src %s' % (root_dir+'/'+project+'_DGE_result/'+project+'_report'))
os.chdir(project+'_DGE_result/'+project+'_results')
result_order=0
result_order+=1
assert not os.system('mkdir '+str(result_order)+'.OriginalData')
rd_order=str(result_order)
os.chdir(''+str(result_order)+'.OriginalData')
#assert not os.system('cp %s\\n' % (root_dir+'/QC_DGE/rd_md5.txt'))
for eachsample in samples:
f_in=gzip.open(root_dir+'/QC_DGE/'+eachsample+'/'+eachsample+'.fq.gz','rb')
f_out=[f_in.readline() for num in range(20)]
open(eachsample+'.example.fq.txt','w').writelines(f_out)
f_in.close()
assert not os.system('cp /PUBLIC/source/RNA/RefRNA/TransRef/README_v2/OriginalData.README.txt %s' % (root_dir+'/'+project+'_DGE_result/'+project+'_results/'+str(result_order)+'.OriginalData/'+str(result_order)+'.1OriginalData.README.txt'))
os.chdir(root_dir+'/'+project+'_DGE_result/'+project+'_results')
result_order+=1
assert not os.system('mkdir '+str(result_order)+'.QC')
qc_order=str(result_order)
os.chdir(''+str(result_order)+'.QC')
assert not os.system('mkdir '+str(result_order)+'.1.ErrorRate')
os.chdir(''+str(result_order)+'.1.ErrorRate')
for eachsample in samples:
assert not os.system('cp %s %s' % (root_dir+'/QC_DGE/'+eachsample+'/clean_data/'+eachsample+'.Error.png',eachsample+'.error_rate_distribution.png'))
assert not os.system('cp %s %s' % (root_dir+'/QC_DGE/'+eachsample+'/clean_data/'+eachsample+'.Error.pdf',eachsample+'.error_rate_distribution.pdf'))
assert not os.system('cp /PUBLIC/source/RNA/RefRNA/TransRef/README_v2/Error.README.txt %s' % (root_dir+'/'+project+'_DGE_result/'+project+'_results/'+str(result_order)+'.QC/'+str(result_order)+'.1.ErrorRate/'+str(result_order)+'.1ErrorRate.README.txt'))
os.chdir('..')
assert not os.system('mkdir '+str(result_order)+'.2.GC')
os.chdir(''+str(result_order)+'.2.GC')
for eachsample in samples:
assert not os.system('cp %s %s' % (root_dir+'/QC_DGE/'+eachsample+'/clean_data/'+eachsample+'.GC.png',eachsample+'.GC_content_distribution.png'))
assert not os.system('cp %s %s' % (root_dir+'/QC_DGE/'+eachsample+'/clean_data/'+eachsample+'.GC.pdf',eachsample+'.GC_content_distribution.pdf'))
assert not os.system('cp /PUBLIC/source/RNA/RefRNA/TransRef/README_v2/GC.README.txt %s' % (root_dir+'/'+project+'_DGE_result/'+project+'_results/'+str(result_order)+'.QC/'+str(result_order)+'.2.GC/'+str(result_order)+'.2GC.README.txt'))
os.chdir('..')
assert not os.system('mkdir '+str(result_order)+'.3.ReadsClassification')
os.chdir(''+str(result_order)+'.3.ReadsClassification')
for eachsample in samples:
assert not os.system('cp %s %s' % (root_dir+'/QC_DGE/'+eachsample+'/files/'+eachsample+'.pie3d.png',eachsample+'.raw_reads_classification.png'))
assert not os.system('cp %s %s' % (root_dir+'/QC_DGE/'+eachsample+'/files/'+eachsample+'.pie3d.pdf',eachsample+'.raw_reads_classification.pdf'))
assert not os.system('cp /PUBLIC/source/RNA/RefRNA/TransRef/README_v2/Filter.README.txt %s' % (root_dir+'/'+project+'_DGE_result/'+project+'_results/'+str(result_order)+'.QC/'+str(result_order)+'.3.ReadsClassification/'+str(result_order)+'.3ReadsClassification.README.txt'))
os.chdir('..')
assert not os.system('mkdir '+str(result_order)+'.4.DataTable')
os.chdir(''+str(result_order)+'.4.DataTable')
#for eachsample in samples:
# assert not os.system('cp %s %s' % (root_dir+'/QC_DGE/'+eachsample+'/files/dataTable',eachsample+'datatable.xls'))
alldataTable = [ root_dir + '/QC_DGE/' + sample + '/files/dataTable' for sample in samples]
alldataTable = ' '.join(alldataTable)
assert not os.system("cat %s|cut -f 1-8 > %s " % ( alldataTable,'datatable.xls.1'))
assert not os.system('cat %s %s > %s' % ('/PUBLIC/source/RNA/RefRNA/DGE/Report/datatable','datatable.xls.1','datatable.xls'))
assert not os.system('rm %s' % ('datatable.xls.1'))
assert not os.system('cp /PUBLIC/source/RNA/RefRNA/TransRef/README_v2/DataTable.README.txt %s' % (root_dir+'/'+project+'_DGE_result/'+project+'_results/'+str(result_order)+'.QC/'+str(result_order)+'.4.DataTable/'+str(result_order)+'.4DataTable.README.txt'))
os.chdir(root_dir+'/'+project+'_DGE_result/'+project+'_results')
result_order+=1
assert not os.system('mkdir '+str(result_order)+'.Mapping')
mp_order=str(result_order)
os.chdir(''+str(result_order)+'.Mapping')
assert not os.system('mkdir '+str(result_order)+'.1.MapStat')
os.chdir(''+str(result_order)+'.1.MapStat')
for eachsample in samples:
assert not os.system('cut -f 2 %s > %s' % (root_dir+'/QC_DGE/'+eachsample+'/files/'+eachsample+'.stat',eachsample+'.stat.2'))
assert not os.system('cut -f 1 %s > %s' % (root_dir+'/QC_DGE/'+samples[0]+'/files/'+samples[0]+'.stat','stat.1'))
allStat_2 = [ root_dir + '/' + project+'_DGE_result/'+project+'_results/'+str(result_order)+'.Mapping/'+str(result_order)+'.1.MapStat/'+sample+'.stat.2' for sample in samples ]
allStat_2 = ' '.join(allStat_2)
assert not os.system('paste %s %s > %s' % ('stat.1',allStat_2,'MapStat.xls'))
assert not os.system("sed -i -e '/^Reads mapped in proper pairs/d' %s" % ('MapStat.xls'))
assert not os.system("sed -i -e '/^Proper-paired reads map to different chrom/d' %s" % ('MapStat.xls'))
assert not os.system('rm stat.1')
assert not os.system('rm *.stat.2')
assert not os.system('cp /PUBLIC/source/RNA/RefRNA/TransRef/README_v2/MapStat.README.txt %s' % (root_dir+'/'+project+'_DGE_result/'+project+'_results/'+str(result_order)+'.Mapping/'+str(result_order)+'.1.MapStat/'+str(result_order)+'.1MapStat.README.txt'))
os.chdir('..')
assert not os.system('mkdir '+str(result_order)+'.2.MapReg')
mr_order=str(result_order)
os.chdir(''+str(result_order)+'.2.MapReg')
for eachsample in samples:
assert not os.system('cp %s %s' % (root_dir+'/QC_DGE/'+eachsample+'/files/'+eachsample+'.MR.png',eachsample+'.Mapped_Region.png'))
assert not os.system('cp %s %s' % (root_dir+'/QC_DGE/'+eachsample+'/files/'+eachsample+'.MR.pdf',eachsample+'.Mapped_Region.pdf'))
assert not os.system('cp /PUBLIC/source/RNA/RefRNA/TransRef/README_v2/MapReg.README.txt %s' % (root_dir+'/'+project+'_DGE_result/'+project+'_results/'+str(result_order)+'.Mapping/'+str(result_order)+'.2.MapReg/'+str(result_order)+'.2MappedRegion.README.txt'))
os.chdir('..')
assert not os.system('mkdir '+str(result_order)+'.3.ChrDen')
cd_order=str(result_order)
os.chdir(''+str(result_order)+'.3.ChrDen')
for eachsample in samples:
assert not os.system('cp %s .' % (root_dir+'/Curve_DGE/density/'+eachsample+'/'+eachsample+'.density.png'))
assert not os.system('cp %s .' % (root_dir+'/Curve_DGE/density/'+eachsample+'/'+eachsample+'.density.pdf'))
assert not os.system('cp %s .' % (root_dir+'/Curve_DGE/density/'+eachsample+'/'+eachsample+'.ReadsVSlength.png'))
assert not os.system('cp /PUBLIC/source/RNA/RefRNA/TransRef/README_v2/ChrDen.README.txt %s' % (root_dir+'/'+project+'_DGE_result/'+project+'_results/'+str(result_order)+'.Mapping/'+str(result_order)+'.3.ChrDen/'+str(result_order)+'.3ChrDen.README.txt'))
os.chdir('..')
assert not os.system('mkdir '+str(result_order)+'.4.IGV')
igv_order=str(result_order)
os.chdir(''+str(result_order)+'.4.IGV')
assert not os.system('cp /PUBLIC/source/RNA/RefRNA/TransRef/Report/IGVQuickStart.pdf %s' % (root_dir+'/'+project+'_DGE_result/'+project+'_results/'+str(result_order)+'.Mapping/'+str(result_order)+'.4.IGV'))
assert not os.system('cp /PUBLIC/source/RNA/RefRNA/TransRef/README_v2/IGV.README.txt %s' % (root_dir+'/'+project+'_DGE_result/'+project+'_results/'+str(result_order)+'.Mapping/'+str(result_order)+'.4.IGV/'+str(result_order)+'.4IGV.README.txt'))
os.chdir(root_dir+'/'+project+'_DGE_result/'+project+'_results')
'''
if set([1]).issubset(includes):
code+='''
result_order+=1
assert not os.system('mkdir '+str(result_order)+'.GeneExprQuatification')
HTSeq_order=str(result_order)
os.chdir(''+str(result_order)+'.GeneExprQuatification')
assert not os.system('cp %s .' % (root_dir+'/Diff_DGE/Diff/rpkm.xls'))
assert not os.system('cp %s .' % (root_dir+'/Diff_DGE/Diff/readcount.xls'))
assert not os.system('cp %s .' % (root_dir+'/Diff_DGE/Diff/rpkm.stat.xls'))
assert not os.system('cp /PUBLIC/source/RNA/RefRNA/TransRef/README_v2/Quatification.README.txt %s' % (root_dir+'/'+project+'_DGE_result/'+project+'_results/'+str(result_order)+'.GeneExprQuatification/'+str(result_order)+'.GeneExprQuatification.README.txt'))
os.chdir(root_dir+'/'+project+'_DGE_result/'+project+'_results')
'''
if set([1,3]).issubset(includes):
code+='''
result_order+=1
assert not os.system('mkdir '+str(result_order)+'.AdvancedQC')
os.chdir(''+str(result_order)+'.AdvancedQC')
assert not os.system('mkdir '+str(result_order)+'.1.SaturationCurve')
os.chdir(''+str(result_order)+'.1.SaturationCurve')
for eachsample in samples:
assert not os.system('cp %s %s' % (root_dir+'/Curve_DGE/SaturationCurve/'+eachsample+'/'+eachsample+'.saturation.png',eachsample+'.Saturation_curve.png'))
assert not os.system('cp %s %s' % (root_dir+'/Curve_DGE/SaturationCurve/'+eachsample+'/'+eachsample+'.saturation.pdf',eachsample+'.Saturation_curve.pdf'))
assert not os.system('cp /PUBLIC/source/RNA/RefRNA/TransRef/README_v2/SatCurve.README.txt %s' % (root_dir+'/'+project+'_DGE_result/'+project+'_results/'+str(result_order)+'.AdvancedQC/'+str(result_order)+'.1.SaturationCurve/'+str(result_order)+'.1SaturationCurve.README.txt'))
os.chdir('..')
if flag_uniform:
assert not os.system('mkdir '+str(result_order)+'.2.MeanCoverage')
os.chdir(''+str(result_order)+'.2.MeanCoverage')
for eachsample in samples:
assert not os.system('cp %s %s' % (root_dir+'/QC_DGE/'+eachsample+'/files/'+eachsample+'.MC.png',eachsample+'.Mean_coverage_distribution.png'))
assert not os.system('cp %s %s' % (root_dir+'/QC_DGE/'+eachsample+'/files/'+eachsample+'.MC.pdf',eachsample+'.Mean_coverage_distribution.pdf'))
assert not os.system('cp /PUBLIC/source/RNA/RefRNA/TransRef/README_v2/MeanCov.README.txt %s' % (root_dir+'/'+project+'_DGE_result/'+project+'_results/'+str(result_order)+'.AdvancedQC/'+str(result_order)+'.2.MeanCoverage/'+str(result_order)+'.2MeanCoverage.README.txt'))
os.chdir(root_dir+'/'+project+'_DGE_result/'+project+'_results')
if flag_uniform:
os.chdir(''+str(result_order)+'.AdvancedQC')
assert not os.system('mkdir '+str(result_order)+'.3.Correlation')
os.chdir(''+str(result_order)+'.3.Correlation')
for png in glob.iglob(root_dir+'/Diff_DGE/Diff/corr_plot/*.png'):
assert not os.system('cp %s .' % png)
for pdf in glob.iglob(root_dir+'/Diff_DGE/Diff/corr_plot/*.pdf'):
assert not os.system('cp %s .' % pdf)
assert not os.system( 'cp %s .' % (root_dir+ '/Diff_DGE/Diff/corr_plot/cor_pearson.xls' ) )
assert not os.system('cp /PUBLIC/source/RNA/RefRNA/TransRef/README_v2/DupCorr.README.txt %s' % (root_dir+'/'+project+'_DGE_result/'+project+'_results/'+str(result_order)+'.AdvancedQC/'+str(result_order)+'.3.Correlation/'+str(result_order)+'.3Correlation.README.txt'))
os.chdir(root_dir+'/'+project+'_DGE_result/'+project+'_results')
else:
os.chdir(''+str(result_order)+'.AdvancedQC')
assert not os.system('mkdir '+str(result_order)+'.2.Correlation')
os.chdir(''+str(result_order)+'.2.Correlation')
for png in glob.iglob(root_dir+'/Diff_DGE/Diff/corr_plot/*.png'):
assert not os.system('cp %s .' % png)
for pdf in glob.iglob(root_dir+'/Diff_DGE/Diff/corr_plot/*.pdf'):
assert not os.system('cp %s .' % pdf)
assert not os.system( 'cp %s .' % (root_dir+ '/Diff_DGE/Diff/corr_plot/cor_pearson.xls' ) )
assert not os.system('cp /PUBLIC/source/RNA/RefRNA/TransRef/README_v2/DupCorr.README.txt %s' % (root_dir+'/'+project+'_DGE_result/'+project+'_results/'+str(result_order)+'.AdvancedQC/'+str(result_order)+'.2.Correlation/'+str(result_order)+'.2Correlation.README.txt'))
os.chdir(root_dir+'/'+project+'_DGE_result/'+project+'_results')
'''
if set([1,2]).issubset(includes):
code+='''
groupnames=groupname.split(',')
compares=compare.split(',')
compare_names=[]
for each in compares:
temp=each.split(':')
compare_names.append(groupnames[int(temp[0])-1]+'vs'+groupnames[int(temp[1])-1])
#compare_names=','.join(compare_names)
venn_cluster_vs_names=[]
flag_venn=False
for each in venn_cluster_name.split(','):
if each.count(':') >= 2 and each.count(':') <= 5:
flag_venn=True
venn_cluster_vs_names.append(each.replace(':','vs'))
result_order+=1
assert not os.system('mkdir '+str(result_order)+'.DiffExprAnalysis')
os.chdir(''+str(result_order)+'.DiffExprAnalysis')
assert not os.system('mkdir '+str(result_order)+'.1.GeneExpContrast')
os.chdir(''+str(result_order)+'.1.GeneExpContrast')
assert not os.system('cp %s .' % (root_dir+'/Diff_DGE/Diff/boxplot.pdf'))
assert not os.system('cp %s .' % (root_dir+'/Diff_DGE/Diff/boxplot.png'))
assert not os.system('cp %s .' % (root_dir+'/Diff_DGE/Diff/density.pdf'))
assert not os.system('cp %s .' % (root_dir+'/Diff_DGE/Diff/density.png'))
assert not os.system('cp /PUBLIC/source/RNA/RefRNA/TransRef/README_v2/ExpLev.README.txt %s' % (root_dir+'/'+project+'_DGE_result/'+project+'_results/'+str(result_order)+'.DiffExprAnalysis/'+str(result_order)+'.1.GeneExpContrast/'+str(result_order)+'.1.GeneExpContrast.README.txt'))
os.chdir('..')
assert not os.system('mkdir '+str(result_order)+'.2.DEGsList')
os.chdir(''+str(result_order)+'.2.DEGsList')
for each in compare_names:
assert not os.system('cp %s %s' % (root_dir+'/Diff_DGE/Diff/DiffGeneList/'+each+'.diffgene.genename.xls',each+'.DEG.xls'))
assert not os.system('cp %s %s' % (root_dir+'/Diff_DGE/Diff/DiffGeneList/'+each+'.diffgene_up.genename.xls',each+'.DEG_up.xls'))
assert not os.system('cp %s %s' % (root_dir+'/Diff_DGE/Diff/DiffGeneList/'+each+'.diffgene_down.genename.xls',each+'.DEG_down.xls'))
assert not os.system('cp %s %s' % (root_dir+'/Diff_DGE/Diff/Diff_Gene_Seq/'+each+'.diffgene.seq',each+'.DEG.fasta'))
assert not os.system('cp %s . ' % (root_dir+'/Diff_DGE/Diff/'+each+'/'+each+'.Differential_analysis_results.xls'))
assert not os.system('cp /PUBLIC/source/RNA/RefRNA/TransRef/README_v2/DiffList.README.txt %s' % (root_dir+'/'+project+'_DGE_result/'+project+'_results/'+str(result_order)+'.DiffExprAnalysis/'+str(result_order)+'.2.DEGsList/'+str(result_order)+'.2DEGsList.README.txt'))
os.chdir('..')
assert not os.system('mkdir '+str(result_order)+'.3.DEGsFilter')
os.chdir(''+str(result_order)+'.3.DEGsFilter')
for each in compare_names:
assert not os.system('cp %s %s' % (root_dir+'/Diff_DGE/Diff/'+each+'/'+each+'.volcano.pdf',each+'.Volcanoplot.pdf'))
assert not os.system('cp %s %s' % (root_dir+'/Diff_DGE/Diff/'+each+'/'+each+'.volcano.png',each+'.Volcanoplot.png'))
assert not os.system('cp /PUBLIC/source/RNA/RefRNA/TransRef/README_v2/DiffFilt.README.txt %s' % (root_dir+'/'+project+'_DGE_result/'+project+'_results/'+str(result_order)+'.DiffExprAnalysis/'+str(result_order)+'.3.DEGsFilter/'+str(result_order)+'.3DEGsFilter.README.txt'))
os.chdir('..')
assert not os.system('mkdir '+str(result_order)+'.4.DEGcluster')
os.chdir(''+str(result_order)+'.4.DEGcluster')
assert not os.system('cp %s Union_for_cluster.xls' % ( root_dir+'/Diff_DGE/Diff/union_for_cluster' ))
assert not os.system('cp %s .' % (root_dir+'/Diff_DGE/Diff/heatCluster.pdf'))
assert not os.system('cp %s .' % (root_dir+'/Diff_DGE/Diff/heatCluster.png'))
os.system('cp %s .' % (root_dir+'/Diff_DGE/Diff/heatCluster.detail.pdf'))
assert not os.system('cp %s .' % (root_dir+'/Diff_DGE/Diff/union_for_cluster_hclust/h_show_plots.png'))
assert not os.system('cp %s .' % (root_dir+'/Diff_DGE/Diff/union_for_cluster_kmeans/kmeans_cluster_plots.pdf'))
assert not os.system('cp %s .' % (root_dir+'/Diff_DGE/Diff/union_for_cluster_som/som_cluster_plots.pdf'))
assert not os.system('cp %s %s' % (root_dir+'/Diff_DGE/Diff/union_for_cluster_hclust/h_subcluster_plots.pdf','h_cluster_plots.pdf'))
assert not os.system('cp /PUBLIC/source/RNA/RefRNA/TransRef/README_v2/Cluster.README.txt %s' % (root_dir+'/'+project+'_DGE_result/'+project+'_results/'+str(result_order)+'.DiffExprAnalysis/'+str(result_order)+'.4.DEGcluster/'+str(result_order)+'.4DEGcluster.README.txt'))
assert not os.system('mkdir '+'Subcluster')
assert not os.system('mkdir '+'Subcluster/kmeans')
assert not os.system('mkdir '+'Subcluster/hclust')
assert not os.system('mkdir '+'Subcluster/som')
assert not os.system('ls %s|while read a;do cut -f 1 $a>%s${a##*/}.xls;done' % (root_dir+'/Diff_DGE/Diff/union_for_cluster_kmeans/subcluster*','Subcluster/kmeans/'))
assert not os.system('ls %s|while read a;do cut -f 1 $a>%s${a##*/}.xls;done' % (root_dir+'/Diff_DGE/Diff/union_for_cluster_hclust/subcluster*','Subcluster/hclust/'))
assert not os.system('ls %s|while read a;do cut -f 1 $a>%s${a##*/}.xls;done' % (root_dir+'/Diff_DGE/Diff/union_for_cluster_som/subcluster*','Subcluster/som/'))
os.chdir('..')
if flag_venn:
assert not os.system('mkdir '+str(result_order)+'.5.VennDiagram')
os.chdir(''+str(result_order)+'.5.VennDiagram')
for each in venn_cluster_vs_names:
assert not os.system('cp -r %s .' % (root_dir+'/Diff_DGE/Diff/Venn/'+each))
assert not os.system('cp /PUBLIC/source/RNA/RefRNA/TransRef/README_v2/Venn.README.txt %s' % (root_dir+'/'+project+'_DGE_result/'+project+'_results/'+str(result_order)+'.DiffExprAnalysis/'+str(result_order)+'.5.VennDiagram/'+str(result_order)+'.5VennDiagram.README.txt'))
os.chdir(root_dir+'/'+project+'_DGE_result/'+project+'_results')
'''
if set([1,2,4]).issubset(includes):
code+='''
result_order+=1
assert not os.system('mkdir '+str(result_order)+'.DEG_GOEnrichment')
os.chdir(''+str(result_order)+'.DEG_GOEnrichment')
assert not os.system('mkdir '+str(result_order)+'.1.DEG_GOList')
os.chdir(''+str(result_order)+'.1.DEG_GOList')
for each in compare_names:
assert not os.system('cp %s %s' % (root_dir+'/GOSeq_DGE/'+each+'/'+each+'.GO_enrichment_result_up_down.xls',each+'.DEG_GO_enrichment_result_up_down.xls'))
assert not os.system('cp /PUBLIC/source/RNA/RefRNA/TransRef/README_v2/GOList.README.txt %s' % (root_dir+'/'+project+'_DGE_result/'+project+'_results/'+str(result_order)+'.DEG_GOEnrichment/'+str(result_order)+'.1.DEG_GOList/'+str(result_order)+'.1DEG_GOList.README.txt'))
os.chdir('..')
assert not os.system('mkdir '+str(result_order)+'.2.DAG')
os.chdir(''+str(result_order)+'.2.DAG')
for each in compare_names:
os.system('cp %s .' % (root_dir+'/GOSeq_DGE/'+each+'/'+each+'.GObp_DAG.png'))
os.system('cp %s .' % (root_dir+'/GOSeq_DGE/'+each+'/'+each+'.GObp_DAG.pdf'))
os.system('cp %s .' % (root_dir+'/GOSeq_DGE/'+each+'/'+each+'.GOmf_DAG.png'))
os.system('cp %s .' % (root_dir+'/GOSeq_DGE/'+each+'/'+each+'.GOmf_DAG.pdf'))
os.system('cp %s .' % (root_dir+'/GOSeq_DGE/'+each+'/'+each+'.GOcc_DAG.png'))
os.system('cp %s .' % (root_dir+'/GOSeq_DGE/'+each+'/'+each+'.GOcc_DAG.pdf'))
assert not os.system('cp /PUBLIC/source/RNA/RefRNA/TransRef/README_v2/DAG.README.txt %s' % (root_dir+'/'+project+'_DGE_result/'+project+'_results/'+str(result_order)+'.DEG_GOEnrichment/'+str(result_order)+'.2.DAG/'+str(result_order)+'.2DAG.README.txt'))
os.chdir('..')
assert not os.system('mkdir '+str(result_order)+'.3.BAR')
os.chdir(''+str(result_order)+'.3.BAR')
for each in compare_names:
assert not os.system('cp %s .' % (root_dir+'/GOSeq_DGE/'+each+'/'+each+'.bar_graph.png'))
assert not os.system('cp %s .' % (root_dir+'/GOSeq_DGE/'+each+'/'+each+'.bar_graph.pdf'))
assert not os.system('cp %s .' % (root_dir+'/GOSeq_DGE/'+each+'/'+each+'.bar_graph_updown.png'))
assert not os.system('cp %s .' % (root_dir+'/GOSeq_DGE/'+each+'/'+each+'.bar_graph_updown.pdf'))
assert not os.system('cp /PUBLIC/source/RNA/RefRNA/TransRef/README_v2/BAR.README.txt %s' % (root_dir+'/'+project+'_DGE_result/'+project+'_results/'+str(result_order)+'.DEG_GOEnrichment/'+str(result_order)+'.3.BAR/'+str(result_order)+'.3BAR.README.txt'))
os.chdir(root_dir+'/'+project+'_DGE_result/'+project+'_results')
'''
if set([1,2,5]).issubset(includes):
code+='''
result_order+=1
assert not os.system('mkdir '+str(result_order)+'.DEG_KEGGEnrichment')
os.chdir(''+str(result_order)+'.DEG_KEGGEnrichment')
assert not os.system('mkdir '+str(result_order)+'.1.DEG_KEGGList')
os.chdir(''+str(result_order)+'.1.DEG_KEGGList')
for each in compare_names:
assert not os.system('cp %s %s' % (root_dir+'/KOBAS_DGE/'+each+'/add.'+each+'.identify.xls',each+'.DEG_KEGG_pathway_enrichment_result.xls'))
assert not os.system('cp /PUBLIC/source/RNA/RefRNA/TransRef/README_v2/KEGGList.README.txt %s' % (root_dir+'/'+project+'_DGE_result/'+project+'_results/'+str(result_order)+'.DEG_KEGGEnrichment/'+str(result_order)+'.1.DEG_KEGGList/'+str(result_order)+'.1DEG_KEGGList.README.txt'))
os.chdir('..')
assert not os.system('mkdir '+str(result_order)+'.2.DEG_KEGGScat')
os.chdir(''+str(result_order)+'.2.DEG_KEGGScat')
for each in compare_names:
os.system('cp %s .' % (root_dir+'/KOBAS_DGE/'+each+'/'+each+'.DEG_enriched_KEGG_pathway_scatterplot.png'))
os.system('cp %s .' % (root_dir+'/KOBAS_DGE/'+each+'/'+each+'.DEG_enriched_KEGG_pathway_scatterplot.pdf'))
assert not os.system('cp /PUBLIC/source/RNA/RefRNA/TransRef/README_v2/KEGGScat.README.txt %s' % (root_dir+'/'+project+'_DGE_result/'+project+'_results/'+str(result_order)+'.DEG_KEGGEnrichment/'+str(result_order)+'.2.DEG_KEGGScat/'+str(result_order)+'.2DEG_KEGGScat.README.txt'))
os.chdir('..')
assert not os.system('mkdir '+str(result_order)+'.3.DEG_KEGGPath')
os.chdir(''+str(result_order)+'.3.DEG_KEGGPath')
for each in compare_names:
assert not os.system('mkdir '+each)
assert not os.system('cp %s %s' % (root_dir+'/KOBAS_DGE/'+each+'/'+each+'.html',each))
assert not os.system('cp -r %s %s' % (root_dir+'/KOBAS_DGE/'+each+'/src',each))
assert not os.system('cp /PUBLIC/source/RNA/RefRNA/TransRef/README_v2/KEGGPath.README.txt %s' % (root_dir+'/'+project+'_DGE_result/'+project+'_results/'+str(result_order)+'.DEG_KEGGEnrichment/'+str(result_order)+'.3.DEG_KEGGPath/'+str(result_order)+'.3DEG_KEGGPath.README.txt'))
os.chdir(root_dir+'/'+project+'_DGE_result/'+project+'_results')
'''
if set([1,2,6]).issubset(includes):
code+='''
result_order+=1
assert not os.system('mkdir '+str(result_order)+'.DEG_PPI')
os.chdir(''+str(result_order)+'.DEG_PPI')
assert not os.system('cp /PUBLIC/source/RNA/RefRNA/TransRef/Report/CytoscapeQuickStart.pdf .')
for each in compare_names:
assert not os.system('cp %s .' % (root_dir+'/PPI_DGE/'+each+'/'+each+'.ppi.txt'))