sys.stdout.write("align failed\n")
Message("align failed", email)
sys.exit(1)
# ======== 2. Add read groups, sort,mark duplicates, and create index
# ======== (1) sort and add group =========================
try:
sort_bams = sam2bam_sort(map_sams, thread)
sys.stdout.write("sort bam succeed\n")
sys.stdout.write("sort_bams is: {bam}\n".format(bam=sort_bams))
except:
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")
sys.stdout.write('align failed\n')
Message('align failed', email)
raise
#======== 2. Add read groups, sort,mark duplicates, and create index
#======== (1) sort and add group =========================
try:
sort_bams = sam2bam_sort(map_sams, thread)
sys.stdout.write('sort bam succeed\n')
sys.stdout.write('sort_bams is: {bam}\n'.format(bam=sort_bams))
except:
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')
sys.stdout.write('align failed\n')
Message('align failed',email)
raise
#======== 2. Add read groups, sort,mark duplicates, and create index
#======== (1) sort and add group =========================
# try:
# sort_bams = sam2bam_sort(map_sams,thread)
# sys.stdout.write('sort bam succeed\n')
# sys.stdout.write('sort_bams is: {bam}\n'.format(bam=sort_bams))
# remove(map_sams)
# except:
# sys.stdout.write('sort bam failed\n')
# Message('sort bam failed',email)
# raise
try:
group_bams = addReadGroup(picard,map_sams,read_group,batch=9)
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)
sys.stdout.write('align failed\n')
Message('align failed', email)
raise
#======== 2. Add read groups, sort,mark duplicates, and create index
#======== (1) sort and add group =========================
# try:
# sort_bams = sam2bam_sort(map_sams,thread)
# sys.stdout.write('sort bam succeed\n')
# sys.stdout.write('sort_bams is: {bam}\n'.format(bam=sort_bams))
# remove(map_sams)
# except:
# sys.stdout.write('sort bam failed\n')
# Message('sort bam failed',email)
# raise
try:
group_bams = addReadGroup(picard, map_sams, read_group, batch=9)
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)
