except:
print 'align failed'
Message('align failed',email)
raise
#======== (4) Convert sam to sorted bam ==================
try:
sort_bams = sam2bam_sort(map_sam,thread)
print 'sort bam files succeed'
print 'sort_bams is: ',sort_bams
except:
print 'sort bam files failed'
Message('sort bam files failed',email)
raise
#======== (5) Markduplicates using picard ================
try:
dedup_files = markduplicates(picard,sort_bams)
print 'mark duplicates succeed'
print 'dedup_files is: ',dedup_files
remove(sort_bams)
except:
print 'mark duplicates failed'
Message('mark duplicates failed',email)
raise
#======== 2. Indel realignment ====================================
#======== (1) Create a target list of intervals===========
try:
interval = RealignerTargetCreator(gatk,dedup_files,ref_fa,thread)
print 'RealignerTarget Creator succeed'
print 'interval is: ',interval
except:
print 'RealignerTarget Creator failed'
except:
print 'align failed'
Message('align failed', email)
raise
#======== (4) Convert sam to sorted bam ==================
try:
sort_bams = sam2bam_sort(map_sam, thread)
print 'sort bam files succeed'
print 'sort_bams is: ', sort_bams
except:
print 'sort bam files failed'
Message('sort bam files failed', email)
raise
#======== (5) Markduplicates using picard ================
try:
dedup_files = markduplicates(picard, sort_bams)
print 'mark duplicates succeed'
print 'dedup_files is: ', dedup_files
remove(sort_bams)
except:
print 'mark duplicates failed'
Message('mark duplicates failed', email)
raise
#======== 2. Indel realignment ====================================
#======== (1) Create a target list of intervals===========
try:
interval = RealignerTargetCreator(gatk, dedup_files, ref_fa, thread)
print 'RealignerTarget Creator succeed'
print 'interval is: ', interval
except:
print 'RealignerTarget Creator failed'
sys.stdout.write("sort bam failed\n")
Message("sort bam failed", email)
sys.exit(1)
try:
group_bams = addReadGroup(picard, sort_bams, read_group)
sys.stdout.write("add group succeed\n")
sys.stdout.write("group_bams is: {group}\n".format(group=group_bams))
except:
sys.stdout.write("add group failed\n")
Message("add group failed", email)
sys.exit(1)
# ======== (2) mark duplicates ============================
try:
dedup_bams = markduplicates(picard, group_bams)
sys.stdout.write("mark duplicate succeed\n")
sys.stdout.write("dedup_bams is: {dedup}\n".format(dedup=dedup_bams))
remove(group_bams)
except:
sys.stdout.write("mark duplicate failed\n")
Message("mark duplicate failed", email)
sys.exit(1)
# ======== 3. Split 'N' Trim and reassign mapping qualiteies
try:
split_bams = splitN(gatk, dedup_bams, ref_fa)
sys.stdout.write("split N succeed\n")
sys.stdout.write("split N is: {N}\n".format(N=split_bams))
remove(dedup_bams)
except:
sys.stdout.write("split N failed\n")
sys.stdout.write('sort bam failed\n')
Message('sort bam failed', email)
raise
try:
group_bams = addReadGroup(picard, sort_bams, read_group)
sys.stdout.write('add group succeed\n')
sys.stdout.write('group_bams is: {group}\n'.format(group=group_bams))
except:
sys.stdout.write('add group failed\n')
Message('add group failed', email)
raise
#======== (2) mark duplicates ============================
try:
dedup_bams = markduplicates(picard, group_bams)
sys.stdout.write('mark duplicate succeed\n')
sys.stdout.write('dedup_bams is: {dedup}\n'.format(dedup=dedup_bams))
remove(group_bams)
except:
sys.stdout.write('mark duplicate failed\n')
Message('mark duplicate failed', email)
raise
#======== 3. Split 'N' Trim and reassign mapping qualiteies
try:
split_bams = splitN(gatk, dedup_bams, ref_fa)
sys.stdout.write('split N succeed\n')
sys.stdout.write('split N is: {N}\n'.format(N=split_bams))
remove(dedup_bams)
except:
sys.stdout.write('split N failed\n')
