def execute(listoffiles,trimdir,interleavedir,diginormdir,assemblydir):
#files_dictionary=get_files(listoffiles,trimdir)
#print files_dictionary
#for sample in files_dictionary:
#fileslist=sorted(files_dictionary[sample])
#interleavefile=interleave_reads(trimdir,interleavedir,fileslist,sample)
interleave_files=os.listdir(interleavedir)
interleave_files_dictionary=get_files_population(interleave_files,interleavedir)
print interleave_files_dictionary
#diginorm_files=get_diginorm_files(diginormdir)
for population in interleave_files_dictionary.keys():
#fileslist=sorted(files_dictionary[population])
#get_orphans(fileslist,trimdir,sample)
#orphansfile=interleavedir+population+".trim.orphans.fq.gz"
#graph_count_filename=run_diginorm(diginormdir,orphansfile,interleavedir,population)
#diginorm_files=get_diginorm_files(diginormdir)
#for diginormfile in diginorm_files[sample]:
#run_filt_abund(diginormdir,graph_count_filename,population)
genus_species_dir=assemblydir+population+"/"
rename_command=get_rename(diginormdir,population)
process_name="split"
rename_command=[rename_command]
module_name_list=""
filename=population
#clusterfunc.sbatch_file(diginormdir,process_name,module_name_list,filename,rename_command)
split_command1=split_reads(diginormdir,population)
process_name="split"
module_name_list=""
split_command=[split_command1]
clusterfunc.sbatch_file(diginormdir,process_name,module_name_list,filename,split_command)
def combine_files(merge_dictionary, basedir, combine_dir):
for sample in merge_dictionary:
R1 = []
R2 = []
for i in merge_dictionary[sample]:
file_fields = i.split("/")
fields = file_fields[5].split("_")
if fields[3] == "R1":
R1.append(i)
elif fields[3] == "R2":
R2.append(i)
else:
print "Wrong field.", fields
print sample, "R1 files:", R1
print sample, "R2 files:", R2
fields_read = R1[0].split("/")[5].split("_")
sample = fields_read[0]
extension = fields_read[4][3:]
newfilename_R1 = combine_dir + sample + "_R1" + extension
newfilename_R2 = combine_dir + sample + "_R2" + extension
files_string_R1 = " ".join(R1)
files_string_R2 = " ".join(R2)
combine_string_R1 = "cat " + files_string_R1 + " > " + newfilename_R1
combine_string_R2 = "cat " + files_string_R2 + " > " + newfilename_R2
print combine_string_R1
print combine_string_R2
#s=subprocess.Popen(combine_string,shell=True)
#s.wait()
combine_command = [combine_string_R1, combine_string_R2]
module_load_list = [""]
process_name = "combine"
clusterfunc.sbatch_file(basedir, process_name, module_load_list,
sample, combine_command)
def run_filt_abund(sample_diginormdir,sample):
abund_filt=get_filter_abund(sample_diginormdir,sample)
abund_filt_command=[abund_filt]
process_name="abundfilt"
module_name_list=""
filename=sample
clusterfunc.sbatch_file(trimdir,process_name,module_name_list,filename,abund_filt_command)
def split_reads(assemblydir):
assemblydirs=os.listdir(assemblydir)
for genus_species in assemblydirs:
genus_species_dir=assemblydir+genus_species+"/"
listoffiles=os.listdir(genus_species_dir)
for filename in listoffiles:
if filename.endswith("pe.keep.abundfilt.fq"):
# next time you run this, specify output file,
# otherwise output will be put in sbatch_files directory
# moved manually 2/7/2016
split_command="""
split-paired-reads.py -1 {}{}.1 -2 {}{}.2 {}{}
""".format(genus_species_dir,filename,genus_species_dir,filename,genus_species_dir,filename)
process_name="split"
module_name_list=""
split_command=[split_command]
#clusterfunc.sbatch_file(genus_species_dir,process_name,module_name_list,filename,split_command)
#else:
# print "Not found:",filename
combine="""
cat {}*.1 > {}{}.left.fq
cat {}*.2 > {}{}.right.fq
gunzip -c {}*orphans.keep.abundfilt.fq.gz >> {}{}.left.fq
""".format(genus_species_dir,genus_species_dir,genus_species,genus_species_dir,genus_species_dir,genus_species,genus_species_dir,genus_species_dir,genus_species)
combine_command=[combine]
process_name="combine"
module_name_list=""
clusterfunc.sbatch_file(genus_species_dir,process_name,module_name_list,genus_species,combine_command)
def combine_orphans_after_diginorm(genus_species_diginormdir,sample): consolidate_command=consolidate(genus_species_diginormdir,sample) consolidate_command=[consolidate_command] process_name="gzip" module_name_list="" filename=sample clusterfunc.sbatch_file(genus_species_diginormdir,process_name,module_name_list,filename,consolidate_command)
def run_extract_paired(genus_species_dir,sample):
abund_filt_filename = genus_species_dir + sample + ".abundfilt"
extract_paired=get_extract_paired(genus_species_dir,sample,abund_filt_filename)
extract_command=[extract_paired]
process_name="extract"
module_name_list=""
filename=sample
clusterfunc.sbatch_file(genus_species_dir,process_name,module_name_list,filename,extract_command)
def interleave_reads(trimdir,interleavedir,files_list,sample): interleavefile=interleavedir+sample+".interleaved.fq.gz" paired_list=get_pairs(files_list,trimdir,sample) interleave_string=[get_interleave_string(paired_list,interleavefile)] process_name="interleave" module_name_list="" filename=sample clusterfunc.sbatch_file(interleavedir,process_name,module_name_list,filename,interleave_string) return interleavefile
def execute(assemblydirs,assemblydir):
#files_dictionary=get_files(assemblydirs,assemblydir)
for genus_species in assemblydirs:
genus_species_dir=assemblydir+genus_species+"/"
cat_command=get_cat_command(genus_species_dir,genus_species)
command=[cat_command]
module_load_list=[""]
process_name="cat"
clusterfunc.sbatch_file(genus_species_dir,process_name,module_load_list,genus_species,command)
def combine_split():
combine="""
cat {}*.1 > {}{}.left.fq
cat {}*.2 > {}{}.right.fq
gunzip -c {}*orphans.keep.abundfilt.fq >> {}{}.left.fq
""".format(genus_species_dir,genus_species_dir,genus_species,genus_species_dir,genus_species_dir,genus_species,genus_species_dir,genus_species_dir,genus_species)
combine_command=[combine]
process_name="combine"
module_name_list=""
clusterfunc.sbatch_file(genus_species_dir,process_name,module_name_list,genus_species,combine_command)
def run_filt_abund(diginormdir,graph_count_filename,diginorm_sample):
# if diginormfile.endswith("orphans.fq.gz.keep"):
# abundfilt_filename=diginormdir+diginorm_sample+".orphans"
# else:
# abundfilt_filename=diginormdir+diginorm_sample
abund_filt=get_filter_abund(diginormdir,diginorm_sample)
abund_filt_command=[abund_filt]
process_name="abundfilt"
module_name_list=""
filename=diginorm_sample
clusterfunc.sbatch_file(diginormdir,process_name,module_name_list,filename,abund_filt_command)
def transrate(transratedir,transrate_out,trinity_fasta,sample,left,right):
transrate_command = """
transrate --assembly={} --threads=4 \
--left={} \
--right={} \
--output={}
""".format(trinity_fasta,left,right,transrate_out)
print transrate_command
commands = [transrate_command]
process_name = "transrate"
module_name_list = ""
filename = sample
clusterfunc.sbatch_file(transratedir, process_name,module_name_list, filename, commands)
def get_assemblies(assemblydir): #genus_species_dirs=os.listdir(assemblydir) genus_species_dirs=["F_heteroclitus.MDPP","F_heteroclitus.MDPL"] for genus_species in genus_species_dirs: print genus_species genus_species_dir=assemblydir+genus_species+"/" assemblyfile=genus_species_dir+"Trinity.fasta" bam_out=genus_species_dir+genus_species+".bam" flagstat_out=genus_species_dir+genus_species+".flagstat.txt" module_load_list=["bwa/0.7.9a","samtools/1.2"] bwa_command=[bwa_mem(assemblyfile,bam_out,flagstat_out)] process_name="bwa" clusterfunc.sbatch_file(genus_species_dir,process_name,module_load_list,genus_species,bwa_command)
def get_orphans(files_list,trimdir,sample):
orphans_list=[]
for filename in files_list:
#print filename
if filename.endswith("1U.fq"):
orphans_list.append(filename)
elif filename.endswith("2U.fq"):
orphans_list.append(filename)
orphans_string=[make_orphans(trimdir,orphans_list,sample)]
process_name="orphans"
module_name_list=""
filename=sample
clusterfunc.sbatch_file(trimdir,process_name,module_name_list,filename,orphans_string)
def quant_salmon(newdir,dirname,genus_species,trinity_fasta,species):
salmon_index_string,index=salmon_index(newdir,genus_species,trinity_fasta)
print salmon_index_string
salmon_string="""
for i in {}{}*.trim_1P.fq
do
BASE=$(basename $i .trim_1P.fq)
salmon quant -i {}{} --libType IU -1 {}$BASE.trim_1P.fq -2 {}$BASE.trim_2P.fq -o {}$BASE.quant;
done
""".format(dirname,species,newdir,index,dirname,dirname,newdir)
print salmon_string
salmonstring=[salmon_index_string,salmon_string]
process_name="salmon"
module_name_list=""
clusterfunc.sbatch_file(newdir,process_name,module_name_list,genus_species,salmonstring)
def run_trinity(assemblydir):
assemblydirs=os.listdir(assemblydir)
for genus_species in assemblydirs:
genus_species_dir=assemblydir+genus_species+"/"
listoffiles=os.listdir(genus_species_dir)
trinity_command="""
set -x
# stops execution if there is an error
set -e
if [ -f {}trinity_out/Trinity.fasta ]; then exit 0 ; fi
if [ -d {}trinity_out ]; then mv {}trinity_out_dir {}trinity_out_dir0 || true ; fi
Trinity --left {}{}.left.fq \\
--right {}{}.right.fq \\
--output {}trinity_out --seqType fq --max_memory 14G \\
--CPU ${{THREADS:-2}}
""".format(genus_species_dir,genus_species_dir,genus_species_dir,genus_species_dir,genus_species_dir,genus_species,genus_species_dir,genus_species,genus_species_dir)
print trinity_command
trinity_command=[trinity_command]
module_load_list=["rsem/1.2.23","trinity/2.0.5"]
process_name="trinity"
clusterfunc.sbatch_file(genus_species_dir,process_name,module_load_list,genus_species,trinity_command)
def fastqc_report(fastqcdir, fastq_file, sample_name):
fastqc_string = "fastqc -o " + fastqcdir + " " + fastq_file
process_string = [fastqc_string]
process_name = "fastqc"
module_load_list = ["fastqc/0.10.1"]
clusterfunc.sbatch_file(basedir, process_name, module_load_list, sample_name, process_string)
def run_trimmomatic(trimdir,file1,file2,sample): trimmomatic_string=get_trimmomatic(trimdir,file1,file2,sample) process_string=[trimmomatic_string] module_load_list="" process_name="trim" clusterfunc.sbatch_file(trimdir,process_name,module_load_list,sample,process_string)
