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)