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NOREF_generator_v4.py
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NOREF_generator_v4.py
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#noref pipline
#2013.01.06
#modified 2013.01.31
#modified 2013.5.24 by hanrui
#modified 2014.8.21 by yangying
#guoyang
import sys
import os
import os.path
import re
import argparse
root_dir=os.getcwd()
##################################################################################
#parse the arguments
parser = argparse.ArgumentParser(description="noref pipeline v1.5")
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=True)
parser.add_argument('--sample',help="sample names(sample1,sample2,...) warning: order sensitive!",required=True)
parser.add_argument('--seq',help="the original directory of the raw fastq reads for QC, [REQUIRED]",default=None)
parser.add_argument('--ad',help="the original directory of the adapter list for QC",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)",required=True)
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('--len',help="length of reads(n,n,...) for SNP, keep order in line with '--sample'",default=None)
parser.add_argument('--ex',help="the steps you do not wanna perform",default=None)
parser.add_argument('--group',help="sample classification, e.g. sample1:sample2,sample3 for differential expression analysis",default=None)
parser.add_argument('--groupname',help="group names, (default: group1,group2,... with 'sample repeat' or sample names directly without 'sample repeat'),for differential expression analysis",default=None)
parser.add_argument('--compare',help="group comparison strategy(1:2,1:3,...) warning: number only,for differential expression analysis",default=None)
parser.add_argument('--matrix',help="the score matrices for estscan program.",default='Hs')
parser.add_argument('--codon',help="the id indicates the genetic codon table.",default='1')
parser.add_argument('--ss',help='Probability of generating a read from the forward strand of a transcript.',choices=['0.0','0.5','1.0'],default='0.5')
parser.add_argument('--jc',help='(--jaccard_clip)set 1 if you have paired reads and you expect high gene density with UTR overlap (use FASTQ input file format for reads)(Default : 0)',choices=['0','1'],default='0')
parser.add_argument('--minkmercov',help='min count for K-mers to be assembled by Inchworm(Default : 2)',default='2')
parser.add_argument('--minglue',help='min number of reads needed to glue two inchworm contigs together(Default : 2)',default='2')
parser.add_argument('--db',help='Database (NR) used; choose "nr" for the whole database or "eu" for euKaryote only.',choices=['nr','eu'],default='eu')
parser.add_argument('--venn_cluster',help='compares groups for venn separately',default=None)
parser.add_argument('--generate_adapter',help='whether to generate the adpepter list y or 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 ,',default=None)
parser.add_argument('--ppi_number',help='the number of reference for PPI',default=None)
#extract, wash and check the parameter
argv=vars(parser.parse_args())
project=argv['project'].strip()
samples=[each.strip() for each in argv['sample'].strip().split(',') if each.strip() != '']
sample=','.join(samples)
assert not os.system('perl /PUBLIC/source/RNA/noRef/Pipeline_noRef/check.sample_name.pl -sample %s ' % (sample))
assert len(set(samples)) == len(samples)
generate_adapter=argv['generate_adapter']
assert argv['seq']!=None or argv['raw_dir'] != None
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['seq']!=None:
sequences=[]
seq=argv['seq'].strip()
for eachsample in samples:
sequences.append([seq+'/'+eachsample+'_1.fq.gz',seq+'/'+eachsample+'_2.fq.gz'])
if generate_adapter =='n':
adaptors=[]
for eachsample in samples:
adaptors.append([seq+'/'+eachsample+'_1.adapter.list.gz',seq+'/'+eachsample+'_2.adapter.list.gz'])
else:
assert not os.system('mkdir raw_data')
assert not os.system('perl /PUBLIC/source/RNA/noRef/QC/bin/ln_raw_data.pl %s %s pe raw_data' %(argv['mapfile'],argv['raw_dir']))
sequences=[]
for eachsample in samples:
sequences.append([root_dir+'/raw_data/'+eachsample+'_1.fq.gz',root_dir+'/raw_data/'+eachsample+'_2.fq.gz'])
if generate_adapter =='n':
adaptors=[]
for eachsample in samples:
adaptors.append([root_dir+'/raw_data/'+eachsample+'_1.adapter.list.gz',root_dir+'/raw_data/'+eachsample+'_2.adapter.list.gz'])
assert len(samples) == len(sequences)
for each1 in sequences:
for each2 in each1:
assert os.path.isfile(each2)
sequence=','.join([':'.join(each) for each in sequences])
if argv['ad'] != None :
ad=argv['ad'].strip()
adaptors=[]
for eachsample in samples:
adaptors.append([ad+'/'+eachsample+'_1.adapter.list.gz',ad+'/'+eachsample+'_2.adapter.list.gz'])
assert len(samples) == len(adaptors)
for each1 in adaptors:
assert len(each1) == 2
if (each1[0].strip() != '') or (each1[1].strip() != ''):
for each2 in each1:
assert os.path.isfile(each2)
adaptor=','.join([':'.join(each) for each in adaptors])
else:
if argv['raw_dir'] !=None:
if generate_adapter =='n':
assert len(samples) == len(adaptors)
for each1 in adaptors:
assert len(each1) == 2
if (each1[0].strip() != '') or (each1[1].strip() != ''):
for each2 in each1:
assert os.path.isfile(each2)
adaptor=','.join([':'.join(each) for each in adaptors])
else:
assert argv['index']
indexs=[each.strip() for each in argv['index'].strip().split(',')]
assert len(samples) == len(indexs)
for each1 in indexs:
index=','.join(indexs)
adaptor=','.join([':' for i in range(len(samples))])
else:
if generate_adapter !='n':
assert argv['index']
indexs=[each.strip() for each in argv['index'].strip().split(',')]
assert len(samples) == len(indexs)
for each1 in indexs:
index=','.join(indexs)
adaptor=','.join([':' for i in range(len(samples))])
if argv['seq']!=None:
if generate_adapter =='n':
if argv['ad'] == None:
print 'Error: the parameters --ad and --generate_adapter are not consensus!\n'
exit()
################################
all_content=set([1,2,3,4,5,6,7,8,9,10])
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
################################
if set([1]).issubset(includes):
ss=argv['ss'].strip()
jc=argv['jc'].strip()
minkmercov=argv['minkmercov'].strip()
minglue=argv['minglue'].strip()
################################
'''
if set([1,3]).issubset(includes):
assert argv['len']
lengths=argv['len'].strip().strip(',').strip().split(',')
lengths=[each.strip() for each in lengths]
if len(lengths) == 1:
lengths=lengths*len(samples)
for each1 in lengths:
assert each1.isdigit()
length=','.join(lengths)
assert len(lengths) == len(samples)
'''
################################
if set([1,5,6]).issubset(includes):
if argv['group'] == None:
groups=samples
groups_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 len(groups_iter) == len(set(groups_iter))
assert set(groups_iter).issubset(samples)
group_iter=','.join(groups_iter)
if argv['groupname'] == None:
if flag_repeat == False:
groupnames=groups
else:
groupnames=['group'+str(k+1) for k in range(len(groups))]
else:
groupnames=[each.strip() for each in argv['groupname'].split(',') if each.strip() != '']
assert len(groupnames) == len(groups)
groupname=','.join(groupnames)
#############################
assert argv['compare']
compares=[each.strip().split(':') for each in argv['compare'].strip().split(',') if each.strip() != '']
M=[]
for each1 in compares:
assert len(each1) == 2
for each2 in each1:
assert each2.isdigit()
M.append(int(each2))
assert max(M) <= len(groupnames)
assert min(M) > 0
compare=','.join([':'.join(each) for each in compares])
temp2=[]
for each1 in compares:
temp1=[]
for each2 in each1:
temp1.append(groupnames[int(each2)-1])
temp2.append(':'.join(temp1))
compare_name=','.join(temp2)
#############################################
if argv['venn_cluster'] != None:
venn_cluster=argv['venn_cluster'].strip()
com_pairs=compare.split(',')
venn_clusters=[each.split('_') for each in venn_cluster.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(groupnames[int(temp3[0])-1]+':'+groupnames[int(temp3[1])-1])
temp1.append('_'.join(temp2))
venn_cluster_name=','.join(temp1)
else:
venn_cluster=compare.replace(',','_')
venn_cluster_name=compare_name.replace(',','_')
##########################################################################
if set([1,5,6,10]).issubset(includes):
assert argv['ppi_number'] !=None
ppi_number=argv['ppi_number']
########################################################################################
if set([1,2]).issubset(includes):
matrix=argv['matrix'].strip()
if (matrix not in ['At','Hs','Mm','Rn','Dm','Dr','Os','Zm']) and (not os.path.isfile(matrix)):
sys.exit('matrix fail...')
codon=argv['codon'].strip()
if codon not in ['1','2','3','4','5','6','9','10','11','12','13','14','15','16','21','22','23']:
sys.exit('codon fail...')
db=argv['db']
###########################################################################
#parameters display
display=open('parameters_display.txt','w')
display.write('project: '+project+'\n')
for i,eachsample in enumerate(samples):
display.write('sample: '+eachsample+'\n')
display.write('\traw data1: '+sequences[i][0]+'\n')
display.write('\traw data2: '+sequences[i][1]+'\n')
if argv['ad'] != None:
display.write('\tadaptor list1: '+adaptors[i][0]+'\n')
display.write('\tadaptor list2: '+adaptors[i][1]+'\n')
if argv['generate_adapter'] !='n':
display.write('\tindex list: '+indexs[i]+'\n')
#if set([1,3]).issubset(includes):
#display.write('\tlength: '+lengths[i]+'\n')
display.write('\n\n')
if set([1]).issubset(includes):
display.write('trinity parameters:\n')
display.write('\tStrand-specific RNA-Seq read orientation: %s\n' % ss)
display.write('\tjaccard_clip: %s\n' % jc)
display.write('\tmin count for K-mers to be assembled by Inchworm: %s\n' % minkmercov)
display.write('\tmin number of reads needed to glue two inchworm contigs together: %s\n\n\n' % minglue)
if set([1,5,6]).issubset(includes):
display.write('group:samples\n')
for i,eachgroup in enumerate(groupnames):
display.write(eachgroup+': '+str(groups[i])+'\n')
display.write('\n')
display.write('group comparison strategy:\n')
display.write(compare+'\n')
display.write(compare_name+'\n')
display.write('\n\n')
display.write('venn cluster:\n')
display.write(venn_cluster.replace('_',' ').replace(',','\n'))
display.write('venn cluster name:\n')
display.write(venn_cluster_name.replace('_',' ').replace(',','\n'))
display.write('\n\n\n')
if set([1,2]).issubset(includes):
display.write('matrix: '+matrix+'\n')
display.write('codon: '+codon+'\n')
db_detail={'nr':'for the whole database','eu':'for eukaryote only'}
display.write('database: '+db+' ('+db_detail[db]+')\n')
display.write('E-value: 1e-5\n\n\n')
contents_detail={0:'QC (default)',1:'trinity assembly',2:'function annotation & CDS prediction',3:'SNP',4:'SSR',5:'RSEM',6:'DIFF_EXP',7:'RNAseq QC',8:'KEGG enrichment',9:'GO enrichment',10:'PPI'}
display.write('content(s) included:\n')
display.write('\tcontent0: QC (default)\n')
for eachone in includes:
display.write('\tcontent%s: %s\n' % (eachone,contents_detail[eachone]))
display.write('\n\n\n\n\n\n\n\n##########################################\n')
display.write(sample+'\n')
display.write(str(samples)+'\n')
display.write(sequence+'\n')
display.write(str(sequences)+'\n')
if argv['ad'] != None:
display.write(str(adaptors)+'\n')
display.write(adaptor+'\n')
if set([1]).issubset(includes):
display.write(ss+'\n')
display.write(jc+'\n')
display.write(minkmercov+'\n')
display.write(minglue+'\n')
'''
if set([1,3]).issubset(includes):
display.write(length+'\n')
display.write(str(lengths)+'\n')
'''
if set([1,5,6]).issubset(includes):
display.write(group+'\n')
display.write(str(groups)+'\n')
display.write(groupname+'\n')
display.write(str(groupnames)+'\n')
display.write(compare+'\n')
display.write(str(compares)+'\n')
display.write(compare_name+'\n')
display.write(venn_cluster+'\n')
display.write(venn_cluster_name+'\n')
if argv['ppi_number'] != None:
display.write('ppi_number: %s\n\n' % (ppi_number))
if set([1,2]).issubset(includes):
display.write(matrix+'\n')
display.write(codon+'\n')
display.write(db+'\n')
display.write(str(excludes)+'\n')
display.write(str(includes)+'\n')
display.close()
###########################################################################
#for QC (run)
code='''
import os
sample='%s'
samples=sample.split(',')
sequence='%s'
sequences=[each.split(':') for each in sequence.split(',')]
adaptor='%s'
adaptors=[each.split(':') for each in adaptor.split(',')]
root_dir='%s'
generate_adapter='%s'
''' % (sample,sequence,adaptor,root_dir,generate_adapter)
if generate_adapter != 'n':
code+='''
index='%s'
indexs=index.split(',')
''' % (index)
code+='''
assert not os.system('mkdir QC')
os.chdir('QC')
for i,eachsample in enumerate(samples):
assert not os.system('mkdir '+eachsample)
os.chdir(eachsample)
assert not os.system('ln -s %s %s' % (sequences[i][0],eachsample+'_1.fq.gz'))
assert not os.system('ln -s %s %s' % (sequences[i][1],eachsample+'_2.fq.gz'))
par_map=root_dir+'/libraryID'
par_a=eachsample+'_1.fq.gz'
par_b=eachsample+'_2.fq.gz'
par_n=samples[i]
if (adaptors[i][0].strip() != '') and (adaptors[i][1].strip() != ''):
par_ad1=adaptors[i][0]
par_ad2=adaptors[i][1]
f=open('qc_'+eachsample+'.sh','w')
f.write('perl /PUBLIC/source/RNA/noRef/QC/runQC_noref_v2.2.pl -a %s -b %s -ad1 %s -ad2 %s -n %s -mapfile %s' % (par_a,par_b,par_ad1,par_ad2,par_n,par_map))
f.close()
assert not os.system('sh qc_%s.sh' % (eachsample))
else:
f=open('qc_'+eachsample+'.sh','w')
f.write('perl /PUBLIC/source/RNA/noRef/QC/runQC_noref_v2.2.pl -a %s -b %s -n %s -mapfile %s' % (par_a,par_b,par_n,par_map))
if generate_adapter !='n':
par_index=indexs[i]
f.write(' -m_ad %s -index %s' % (generate_adapter,par_index))
f.close()
assert not os.system('sh qc_%s.sh' % (eachsample))
assert not os.system('qsub -V -cwd -l vf=2G -l p=3 runQC_noref.sh')
os.chdir('..')
os.chdir(root_dir)
'''
open('NOREF_step1.py','w').write(code)
##############################################################################
#for QC_report
code='''
import os
sample='%s'
project='%s'
os.chdir('QC')
f=open('QC_report.sh','w')
f.write('perl /PUBLIC/source/RNA/noRef/QC/noRef_QC_report_library.pl -n %%s -p %%s -dir .\\n' %% (sample, project))
f.write('perl /PUBLIC/source/RNA/noRef/QC/bin/clean_data_sum.pl -n %%s\\n' %% (sample))
f.close()
assert not os.system('sh QC_report.sh')
''' % (sample, project)
open('NOREF_step1_QCreport.py','w').write(code)
####################################################################
#for trinity (sh->py noly, not run) root_dir
code=''
if set([1]).issubset(includes):
code+='''
import os
import os.path
import sys
import argparse
import re
parser = argparse.ArgumentParser(description='run trinity and resource list required')
parser.add_argument('--vf',required=True,help='momery required for qsub')
parser.add_argument('--h',required=True,help="the fat node for qsub")
argv=vars(parser.parse_args())
vf=argv['vf']
h=argv['h']
root_dir='%s'
sample='%s'
samples=sample.split(',')
ss='%s'
jc='%s'
minkmercov='%s'
minglue='%s'
project='%s'
clean_left=[]
clean_right=[]
for eachsample in samples:
each_clean_left=root_dir+'/QC/'+eachsample+'/clean_data/'+eachsample+'_1.clean.fq'
assert os.path.isfile(each_clean_left)
clean_left.append(each_clean_left)
each_clean_right=root_dir+'/QC/'+eachsample+'/clean_data/'+eachsample+'_2.clean.fq'
assert os.path.isfile(each_clean_right)
clean_right.append(each_clean_right)
clean_left=','.join(clean_left)
clean_right=','.join(clean_right)
rRNA=root_dir+'/QC/'+project+'.QC_results/results/1dataTable/dataTable'
assert os.path.isfile(rRNA)
cluster_num=re.search(r'([1-9])',h).group(1)
P_mem='mem'+str(cluster_num)
q_mem=P_mem+'.q'
if cluster_num==str(3) or cluster_num==str(4):
P_mem='mem3'
q_mem='mem3.q'
assert not os.system('mkdir TRINITY')
os.chdir('TRINITY')
f=open('trinity.sh','w')
f.write('perl /PUBLIC/source/RNA/noRef/Trinity_CDS/runTrinity_cds_v2.pl -left %%s -right %%s -ss %%s -jc %%s -minkmercov %%s -minglue %%s -JM %%s -rRNA %%s' %% (clean_left,clean_right,ss,jc,minkmercov,minglue,vf,rRNA))
f.close()
assert not os.system('sh trinity.sh')
assert not os.system('/opt/gridengine/bin/lx26-amd64/qsub -cwd -l vf=%%s -l p=10 -P %%s -q %%s -V run_Trinity_cds.sh' %% (vf,P_mem,q_mem))
''' % (root_dir,sample,ss,jc,minkmercov,minglue,project)
open('NOREF_step2.py','w').write(code)
##########################################################################
#for RSEM and SSR and the first step of SNP and ANNOTATION(sh->py only, not run) root_dir
code='''
import os
import os.path
import sys
'''
if set([1,2]).issubset(includes):
code+='''
import argparse
parser = argparse.ArgumentParser(description='some in-time parameters for annotation')
parser.add_argument('--new',help='where to qsub the annotation script,(1 on the New cluster,0 on the old DELL )',choices=['0','1'],default='1')
parser.add_argument('--n',help="split sequence file into given number, only for blast NR",default='0')
argv=vars(parser.parse_args())
ibm=argv['new']
n=argv['n'].strip()
assert n.isdigit()
'''
code+='''
sample='%s'
samples=sample.split(',')
root_dir='%s'
project='%s'
''' % (sample,root_dir,project)
if set([1,2]).issubset(includes):
code+='''
##ANNOTATION
matrix='%s'
codon='%s'
db='%s'
assert not os.system('mkdir ANNOTATION_ALL')
os.chdir('ANNOTATION_ALL')
assert os.path.isfile(root_dir+'/TRINITY/assembly_INFO/unigene.fasta')
par_seq=root_dir+'/TRINITY/assembly_INFO/unigene.fasta'
num = n if int(n) else int(round(int(os.popen('grep -c \\">\\" '+par_seq).read().rstrip())/20000.0))
par_out=root_dir+'/ANNOTATION_ALL'
f=open('annot.sh','w')
f.write('perl /PUBLIC/source/RNA/noRef/ANNOTATION/annotation_v4.pl -seq %%s -out %%s -p %%s -matrix %%s -codon %%s -n %%s -db %%s -new %%s' %% (par_seq,par_out,project,matrix,codon,num,db,ibm))
f.close()
assert not os.system('sh annot.sh')
os.chdir(root_dir)
''' % (matrix,codon,db)
if set([1,5]).issubset(includes):
code+='''
##RSEM
ss='%s'
assert not os.system('mkdir RSEM')
os.chdir('RSEM')
assert os.path.isfile(root_dir+'/TRINITY/trinity.out/Trinity.fasta')
for eachsample in samples:
assert not os.system('mkdir %%s' %% eachsample)
os.chdir(eachsample)
assert os.path.isfile(root_dir+'/QC/'+eachsample+'/clean_data/'+eachsample+'_1.clean.fq')
assert os.path.isfile(root_dir+'/QC/'+eachsample+'/clean_data/'+eachsample+'_2.clean.fq')
par_a=root_dir+'/TRINITY/trinity.out/Trinity.fasta'
par_r=root_dir+'/QC/'+eachsample+'/clean_data/'+eachsample+'_1.clean.fq'+','+root_dir+'/QC/'+eachsample+'/clean_data/'+eachsample+'_2.clean.fq'
runRSEM=open('RSEM_'+eachsample+'.sh','w')
runRSEM.write('perl /PUBLIC/source/RNA/noRef/RSEM/runRSEM_v1.5.pl -a %%s -r %%s -n %%s -s %%s -ss %%s' %% (par_a,par_r,project,eachsample,ss))
runRSEM.close()
assert not os.system('qsub -V -cwd -l vf=4G -l p=2 RSEM_%%s.sh' %% eachsample)
os.chdir('..')
os.chdir(root_dir)
''' % (ss)
if set([1,3]).issubset(includes):
code+='''
##the first step of SNP
#length='%s'
#lengths=length.split(',')
assert not os.system('mkdir SNP')
os.chdir('SNP')
assert os.path.isfile(root_dir+'/TRINITY/assembly_INFO/unigene.fasta')
assert not os.system('mkdir bam')
par_bamdir=root_dir+'/SNP/bam'
par_D=root_dir+'/TRINITY/assembly_INFO/unigene.fasta'
par_dir=root_dir+'/SNP'
f=open('snp_step1.sh','w')
f.write('/PUBLIC/software/RNA/bowtie2-2.2.3/bowtie2-build %s %s\\n' % (par_D,par_D))
for i,eachsample in enumerate(samples):
#assert not os.system('mkdir %s' % eachsample)
#os.chdir(eachsample)
par_a=root_dir+'/QC/'+eachsample+'/clean_data/'+eachsample+'_1.clean.fq'
par_b=root_dir+'/QC/'+eachsample+'/clean_data/'+eachsample+'_2.clean.fq'
par_n=eachsample
#par_L=lengths[i]
par_sam=eachsample+'.sam'
par_bam='bam/'+eachsample+'.bam'
#par_i=root_dir+'/TRINITY/assembly_INFO/geneINFO'
#assert os.path.isfile(par_i)
f.write('/PUBLIC/software/RNA/bowtie2-2.2.3/bowtie2 -p 8 -x %s -1 %s -2 %s | samtools view -Sb - >%s\\n' % (par_D,par_a,par_b,par_bam))
#os.chdir('..')
f.write('perl /PUBLIC/source/RNA/noRef/GATKsnp/runGATK2_v1.pl -ref %s -t bam -i %s \\n' % (par_D,par_bamdir))
f.write('sh workflow.sh\\n')
f.close()
assert not os.system('qsub -V -cwd -l vf=12G -l p=8 snp_step1.sh')
os.chdir(root_dir)
'''
if set([1,4]).issubset(includes):
code+='''
##SSR
assert not os.system('mkdir SSR')
os.chdir('SSR')
assert os.path.isfile(root_dir+'/TRINITY/assembly_INFO/unigene.fasta')
f=open('ssr.sh','w')
f.write('perl /PUBLIC/source/RNA/noRef/SSR_Primer/runSSR_primer_v2.pl -a %s ' % (root_dir+'/TRINITY/assembly_INFO/unigene.fasta'))
f.close()
assert not os.system('sh ssr.sh')
assert not os.system('qsub -V -cwd -l vf=1G -l p=1 runSSR_primer.sh')
os.chdir(root_dir)
'''
open('NOREF_step3.py','w').write(code)
#########################################################
#for different expression (sh->py only, not run) root_dir
code=''
if set([1,5,6]).issubset(includes):
code+='''
import os
import os.path
import sys
assert not os.system('mkdir DIFF_EXP')
os.chdir('DIFF_EXP')
sample='%s'
samples=sample.split(',')
root_dir='%s'
group='%s'
groupname='%s'
compare='%s'
venn_cluster='%s'
readcount=[]
for eachsample in samples:
temp='%%s/RSEM/%%s/%%s.RSEM.out/%%s.Readcount_FPKM.xls' %% (root_dir,eachsample,eachsample,eachsample)
assert os.path.isfile(temp)
readcount.append(temp)
readcount=','.join(readcount)
geneinfo=root_dir+'/TRINITY/assembly_INFO/geneINFO'
assert os.path.isfile(geneinfo)
f=open('diff_exp.sh','w')
f.write('perl /PUBLIC/source/RNA/noRef/Diff_analysis/DE_analysis/runDE_analysis_v2.pl -i %%s -c %%s -group %%s -groupname %%s -g %%s -venn_cluster %%s' %% (readcount,geneinfo,group,groupname,compare,venn_cluster))
f.close()
assert not os.system('sh diff_exp.sh')
assert not os.system('qsub -V -cwd -l vf=2G -l p=2 Diff_Analysis.sh')
''' % (sample,root_dir,group,groupname,compare,venn_cluster)
open('NOREF_step4.py','w').write(code)
###########################################################
#for runAnnotationTable.sh,CDS prediction from ANNOTATION_ALL
code='''
import os
import os.path
sample='%s'
samples=sample.split(',')
root_dir='%s'
''' % (sample,root_dir)
if set([1,2]).issubset(includes):
code+='''
##runAnnotationTable.sh
os.chdir('ANNOTATION_ALL')
assert os.path.isfile('runAnnotationTable.sh')
assert not os.system('qsub -V -cwd -l vf=1G -l p=2 runAnnotationTable.sh')
'''
#if set([1,3]).issubset(includes):
#code+='''
#SNPanalysis_step2.sh
#os.chdir(root_dir)
#for eachsample in samples:
#os.chdir(root_dir+'/SNP/'+eachsample)
#assert not os.system('qsub -V -cwd -l vf=1G -l p=1 SNPanalysis_step2.sh')
#'''
open('NOREF_step5.py','w').write(code)
##########################################################
#for the second step of SNP, KEGG, GO and RNA-seqQC
code='''
import os
import os.path
root_dir='%s'
project='%s'
sample='%s'
samples=sample.split(',')
''' % (root_dir,project,sample)
if set([1,2,5,7]).issubset(includes):
code+='''
##RNA-seqQC
assert not os.system('mkdir RNA_SEQ_QC')
os.chdir('RNA_SEQ_QC')
par_b=[]
for eachsample in samples:
assert os.path.isfile(root_dir+'/RSEM/'+eachsample+'/'+eachsample+'.RSEM.out/'+eachsample+'.transcript.bam')
par_b.append(root_dir+'/RSEM/'+eachsample+'/'+eachsample+'.RSEM.out/'+eachsample+'.transcript.bam')
par_b=','.join(par_b)
par_s=sample
par_a=root_dir+'/ANNOTATION_ALL/'+project+'.swissprot.xml'
assert os.path.isfile(par_a)
par_gi=root_dir+'/TRINITY/assembly_INFO/geneINFO'
assert os.path.isfile(par_gi)
par_ti=root_dir+'/TRINITY/assembly_INFO/isoformINFO'
assert os.path.isfile(par_ti)
f=open('rnaseq_qc.sh','w')
f.write('perl /PUBLIC/source/RNA/noRef/Uni_saturation/uni_saturation_v1.5.pl -b %s -s %s -a %s -gi %s -ti %s' % (par_b,par_s,par_a,par_gi,par_ti))
f.close()
assert not os.system('sh rnaseq_qc.sh')
assert not os.system('qsub -V -cwd -l vf=1G -l p=1 step5_Uni_saturation.sh')
os.chdir(root_dir)
'''
if set ([1,2,3]).issubset(includes):
code+='''
##SNP step2
os.chdir('SNP')
f=open('run.snp_step2.sh','w')
f.write('perl /PUBLIC/source/RNA/noRef/GATKsnp/get_gtf.pl '+root_dir+'/ANNOTATION_ALL/CDSprediction/'+project+'.blast.cds.fasta >'+root_dir+'/SNP/ResultsQ30/blast.cds.gtf\\n')
f.write('perl /PUBLIC/source/RNA/noRef/GATKsnp/annotationSNP.pl --outdir '+root_dir+'/SNP/ResultsQ30/ --name SNPs_annotation --gff '+root_dir+'/SNP/ResultsQ30/blast.cds.gtf --snp '+root_dir+'/SNP/ResultsQ30/SNPs.xls --fa '+root_dir+'/TRINITY/assembly_INFO/unigene.fasta\\n')
f.write('perl /PUBLIC/source/RNA/noRef/GATKsnp/snp_annot.pl '+root_dir+'/SNP/ResultsQ30/SNPs.xls '+root_dir+'/SNP/ResultsQ30/SNPs_annotation.info.txt '+root_dir+'/SNP/ResultsQ30/SNPs_non_synonymous.xls '+root_dir+'/SNP/ResultsQ30/SNPs_non_synonymous.stat.xls\\n')
f.write('rm -rf '+root_dir+'/SNP/dedup\\n')
f.close()
assert not os.system('qsub -V -cwd -l vf=0.5G run.snp_step2.sh')
os.chdir(root_dir)
'''
if set([1,2,4]).issubset(includes):
code+='''
##SSR step2
os.chdir(root_dir+'/SSR/')
assert not os.system('python /PUBLIC/source/RNA/noRef/SSR_Primer/bin/SSR_position.py --project %s --root_dir %s'%(project,root_dir))
assert not os.system('qsub -V -cwd -l vf=1G -l p=1 SSR_utr.sh')
os.chdir(root_dir)
'''
if set([1,2,6]).issubset(includes):
code+='''
###check DIFFgene number
assert not os.system('perl /PUBLIC/source/RNA/noRef/Diff_analysis/DE_analysis/diffreport.pl -diffdir %s ' % (root_dir+'/DIFF_EXP/'))
'''
if set([1,2,5,6,9]).issubset(includes):
code+='''
##GO
compare_name='%s'
compare_names=[each.split(':') for each in compare_name.split(',')]
assert not os.system('mkdir GO_ENRICHMENT')
os.chdir('GO_ENRICHMENT')
assert not os.system('mkdir ALL')
os.chdir('ALL')
for each in compare_names:
temp='vs'.join(each)
par_i=root_dir+'/DIFF_EXP/Diff_analysis.out/'+temp+'/'+temp+'.DEGlist.txt'
assert os.path.isfile(par_i)
par_goann=root_dir+'/ANNOTATION_ALL/'+project+'.go.txt'
assert os.path.isfile(par_goann)
par_length=root_dir+'/TRINITY/assembly_INFO/geneINFO'
assert os.path.isfile(par_length)
assert not os.system('mkdir %%s' %% temp)
os.chdir(temp)
par_o=os.getcwd()
py=open('run_goseq_'+temp+'.sh','w')
py.write('perl /PUBLIC/software/RNA/GOseq/goseq_graph_v3.pl -i %%s -goann %%s -o %%s -length %%s -p %%s' %% (par_i,par_goann,par_o,par_length,temp))
py.close()
assert not os.system('qsub -V -cwd -l vf=2G -l p=1 run_goseq_%%s.sh' %% temp)
os.chdir('..')
os.chdir('..')
assert not os.system('mkdir UP')
os.chdir('UP')
for each in compare_names:
temp='vs'.join(each)
par_i=root_dir+'/DIFF_EXP/Diff_analysis.out/'+temp+'/'+temp+'.DEGlist_up.txt'
assert os.path.isfile(par_i)
par_goann=root_dir+'/ANNOTATION_ALL/'+project+'.go.txt'
assert os.path.isfile(par_goann)
par_length=root_dir+'/TRINITY/assembly_INFO/geneINFO'
assert os.path.isfile(par_length)
assert not os.system('mkdir %%s' %% temp)
os.chdir(temp)
par_o=os.getcwd()
py=open('run_goseq_up_'+temp+'.sh','w')
py.write('perl /PUBLIC/software/RNA/GOseq/goseq_graph_v3.pl -i %%s -goann %%s -o %%s -length %%s -p %%s' %% (par_i,par_goann,par_o,par_length,temp+'_up'))
py.close()
assert not os.system('qsub -V -cwd -l vf=2G -l p=1 run_goseq_up_%%s.sh' %% temp)
os.chdir('..')
os.chdir('..')
assert not os.system('mkdir DOWN')
os.chdir('DOWN')
for each in compare_names:
temp='vs'.join(each)
par_i=root_dir+'/DIFF_EXP/Diff_analysis.out/'+temp+'/'+temp+'.DEGlist_down.txt'
assert os.path.isfile(par_i)
par_goann=root_dir+'/ANNOTATION_ALL/'+project+'.go.txt'
assert os.path.isfile(par_goann)
par_length=root_dir+'/TRINITY/assembly_INFO/geneINFO'
assert os.path.isfile(par_length)
assert not os.system('mkdir %%s' %% temp)
os.chdir(temp)
par_o=os.getcwd()
py=open('run_goseq_down_'+temp+'.sh','w')
py.write('perl /PUBLIC/software/RNA/GOseq/goseq_graph_v3.pl -i %%s -goann %%s -o %%s -length %%s -p %%s' %% (par_i,par_goann,par_o,par_length,temp+'_down'))
py.close()
assert not os.system('qsub -V -cwd -l vf=2G -l p=1 run_goseq_down_%%s.sh' %% temp)
os.chdir('..')
os.chdir(root_dir)
''' % (compare_name)
if set([1,2,5,6,8]).issubset(includes):
code+='''
##KEGG
compare_name='%s'
compare_names=[each.split(':') for each in compare_name.split(',')]
assert not os.system('mkdir KEGG')
os.chdir('KEGG')
assert not os.system('mkdir ALL')
os.chdir('ALL')
for each in compare_names:
temp='vs'.join(each)
assert not os.system('mkdir %%s' %% temp)
os.chdir(temp)
par_diff=root_dir+'/DIFF_EXP/Diff_analysis.out/'+temp+'/'+temp+'.DEGlist.txt'
par_ko=root_dir+'/ANNOTATION_ALL/koID.annotation'
assert os.path.isfile(par_ko)
py=open('runKEGG_enrich_'+temp+'.sh','w')
py.write('perl /PUBLIC/source/RNA/noRef/KEGG_enrichment/runKEGG_enrich.pl -diff %%s -ko %%s -g %%s' %% (par_diff,par_ko,temp))
py.close()
assert not os.system('qsub -V -cwd -l vf=1G -l p=1 runKEGG_enrich_%%s.sh' %% temp)
os.chdir('..')
os.chdir('..')
assert not os.system('mkdir UP')
os.chdir('UP')
for each in compare_names:
temp='vs'.join(each)
assert not os.system('mkdir %%s' %% temp)
os.chdir(temp)
par_diff=root_dir+'/DIFF_EXP/Diff_analysis.out/'+temp+'/'+temp+'.DEGlist_up.txt'
par_ko=root_dir+'/ANNOTATION_ALL/koID.annotation'
assert os.path.isfile(par_ko)
py=open('runKEGG_enrich_up_'+temp+'.sh','w')
py.write('perl /PUBLIC/source/RNA/noRef/KEGG_enrichment/runKEGG_enrich.pl -diff %%s -ko %%s -g %%s' %% (par_diff,par_ko,temp+'_up'))
py.close()
assert not os.system('qsub -V -cwd -l vf=1G -l p=1 runKEGG_enrich_up_%%s.sh' %% temp)
os.chdir('..')
os.chdir('..')
assert not os.system('mkdir DOWN')
os.chdir('DOWN')
for each in compare_names:
temp='vs'.join(each)
assert not os.system('mkdir %%s' %% temp)
os.chdir(temp)
par_diff=root_dir+'/DIFF_EXP/Diff_analysis.out/'+temp+'/'+temp+'.DEGlist_down.txt'
par_ko=root_dir+'/ANNOTATION_ALL/koID.annotation'
assert os.path.isfile(par_ko)
py=open('runKEGG_enrich_down_'+temp+'.sh','w')
py.write('perl /PUBLIC/source/RNA/noRef/KEGG_enrichment/runKEGG_enrich.pl -diff %%s -ko %%s -g %%s' %% (par_diff,par_ko,temp+'_down'))
py.close()
assert not os.system('qsub -V -cwd -l vf=1G -l p=1 runKEGG_enrich_down_%%s.sh' %% temp)
os.chdir('..')
os.chdir(root_dir)
''' % (compare_name)
if set([1,2,5,6,10]).issubset(includes):
code+='''
##PPI
compare_name='%s'
compare_names=[each.split(':') for each in compare_name.split(',')]
ppi_number='%s'
assert not os.system('mkdir PPI')
os.chdir('PPI')
assert not os.system('mkdir ALL')
os.chdir('ALL')
for each in compare_names:
temp='vs'.join(each)
assert not os.system('mkdir %%s' %% temp)
os.chdir(temp)
par_diff=root_dir+'/DIFF_EXP/Diff_analysis.out/'+temp+'/'+temp+'.DEGlist.txt'
par_a=root_dir+'/TRINITY/assembly_INFO/unigene.fasta'
py=open('runPPI_'+temp+'.sh','w')
py.write('python /PUBLIC/source/RNA/guoyang_tools/BLASTX_TO_PPI_v4.py --entries %%s --species %%s --fa %%s --name %%s --output . \\n' %% (par_diff,ppi_number,par_a,temp))
py.write('cp %%s %%s' %% (root_dir+'/PPI/ALL/'+temp+'/'+temp+'.ppi.txt',root_dir+'/PPI/ALL/'+temp+'/'+temp+'.PPI.txt'))
py.close()
assert not os.system('qsub -V -cwd -l vf=1G -l p=4 runPPI_%%s.sh' %% temp)
os.chdir('..')
os.chdir('..')
assert not os.system('mkdir UP')
os.chdir('UP')
for each in compare_names:
temp='vs'.join(each)
assert not os.system('mkdir %%s' %% temp)
name=temp+'_up'
os.chdir(temp)
par_diff=root_dir+'/DIFF_EXP/Diff_analysis.out/'+temp+'/'+temp+'.DEGlist_up.txt'
par_a=root_dir+'/TRINITY/assembly_INFO/unigene.fasta'
py=open('runPPI_up_'+temp+'.sh','w')
py.write('python /PUBLIC/source/RNA/guoyang_tools/BLASTX_TO_PPI_v4.py --entries %%s --species %%s --fa %%s --name %%s --output . \\n' %% (par_diff,ppi_number,par_a,name))
py.write('cp %%s %%s' %% (root_dir+'/PPI/UP/'+temp+'/'+name+'.ppi.txt',root_dir+'/PPI/UP/'+temp+'/'+temp+'_up.PPI.txt'))
py.close()
assert not os.system('qsub -V -cwd -l vf=1G -l p=4 runPPI_up_%%s.sh' %% temp)
os.chdir('..')
os.chdir('..')
assert not os.system('mkdir DOWN')
os.chdir('DOWN')
for each in compare_names:
temp='vs'.join(each)
assert not os.system('mkdir %%s' %% temp)
name=temp+'_down'
os.chdir(temp)
par_diff=root_dir+'/DIFF_EXP/Diff_analysis.out/'+temp+'/'+temp+'.DEGlist_down.txt'
par_a=root_dir+'/TRINITY/assembly_INFO/unigene.fasta'
py=open('runPPI_down_'+temp+'.sh','w')
py.write('python /PUBLIC/source/RNA/guoyang_tools/BLASTX_TO_PPI_v4.py --entries %%s --species %%s --fa %%s --name %%s --output . \\n' %% (par_diff,ppi_number,par_a,name))
py.write('cp %%s %%s' %% (root_dir+'/PPI/DOWN/'+temp+'/'+name+'.ppi.txt',root_dir+'/PPI/DOWN/'+temp+'/'+temp+'_down.PPI.txt'))
py.close()
assert not os.system('qsub -V -cwd -l vf=1G -l p=4 runPPI_down_%%s.sh' %% temp)
os.chdir('..')
os.chdir(root_dir)
''' % (compare_name,ppi_number)
open('NOREF_step6.py','w').write(code)
####################################################
#for web Visualization for KEGG due to the network problem, can not qsub this step
code='''
import os
import os.path
root_dir='%s'
''' % (root_dir)
if set([1,2]).issubset(includes):
code+='''
os.chdir(root_dir+'/ANNOTATION_ALL')
par_ko=root_dir+'/ANNOTATION_ALL/Annotation_KO.xls'
assert os.path.isfile(par_ko)
assert not os.system('python /PUBLIC/source/RNA/guoyang_tools/pathway_ko_annotation_parallel_tolerant.pyc %s' % par_ko)
os.chdir(root_dir)
'''
if set([1,5,6,8]).issubset(includes):
code+='''
compare_name='%s'
compare_names=[each.split(':') for each in compare_name.split(',')]
for each in compare_names:
temp='vs'.join(each)
os.chdir(root_dir+'/KEGG/ALL/'+temp)
par_table=temp+'.DEG_KEGG_pathway_enrichment_add.xls'
par_diff=root_dir+'/DIFF_EXP/Diff_analysis.out/'+temp+'/'+temp+'.DEG.xls'
if os.path.isfile(par_table) and os.path.isfile(par_diff):
print '###'+temp+'###'
assert not os.system('python /PUBLIC/source/RNA/guoyang_tools/pathway_annotation_flow_parallel_annotationfault_tolerant.pyc --table %%s --diff %%s' %% (par_table,par_diff))
else:
print '!!!'+temp+'!!! file(s) unavailable...'
os.chdir(root_dir+'/KEGG/UP/'+temp)
par_table=temp+'_up.DEG_KEGG_pathway_enrichment_add.xls'
par_diff=root_dir+'/DIFF_EXP/Diff_analysis.out/'+temp+'/'+temp+'.DEG_up.xls'
if os.path.isfile(par_table) and os.path.isfile(par_diff):
print '###'+temp+' up###'
assert not os.system('python /PUBLIC/source/RNA/guoyang_tools/pathway_annotation_flow_parallel_annotationfault_tolerant.pyc --table %%s --diff %%s' %% (par_table,par_diff))
else:
print '!!!'+temp+' up!!! file(s) unavailable...'
os.chdir(root_dir+'/KEGG/DOWN/'+temp)
par_table=temp+'_down.DEG_KEGG_pathway_enrichment_add.xls'
par_diff=root_dir+'/DIFF_EXP/Diff_analysis.out/'+temp+'/'+temp+'.DEG_down.xls'
if os.path.isfile(par_table) and os.path.isfile(par_diff):
print '###'+temp+' down###'
assert not os.system('python /PUBLIC/source/RNA/guoyang_tools/pathway_annotation_flow_parallel_annotationfault_tolerant.pyc --table %%s --diff %%s' %% (par_table,par_diff))
else:
print '!!!'+temp+' down!!! file(s) unavailable...'
''' % (compare_name)
open('NOREF_step7.py','w').write(code)
####################################################
# for summary
code='''
import os
import os.path
import glob
import gzip
import sys
import re
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/noRef/Pipeline_noRef/report_v2',))
def fasta_trim(file,k,typ):
fa=[]
for eachLine in open(file):
if eachLine.startswith('>'):
k-=1
if k == 0:
break
if typ == 1:
fa.append(eachLine)
else:
fa.append(eachLine.strip()+'<br />')
return fa