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')