sys.stdout.write('list file succeed\n')
sys.stdout.write('fastqFiles is: {fq}\n'.format(fq=fastqFiles))
#======== (2) align using 2 pass STAR ====================
try:
map_sams= STAR2Pass(fastqFiles,starDb,ref_fa,thread)
sys.stdout.write('align succeed\n')
sys.stdout.write('map_sams is: {map}\n'.format(map=map_sams))
except:
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)
if aligner == 'gsnap':
map_files = gsnap(fastqFiles,db_path, db_name,gsnap_annotation,thread)
else:
if not os.path.exists(db_path): os.mkdir(db_path)
if os.listdir(db_path) == []:
STAR_Db(db_path,ref_fa,thread)
map_files = STAR(fastqFiles,db_path,thread,annotation,['--outSAMtype BAM SortedByCoordinate','--quantMode GeneCounts'])
print 'align succeed'
print 'map_files is: ',map_files
except:
print 'align failed'
Message('align failed',email)
raise
#=========== (3) samtools to sort the file ==========
try:
sorted_bams = sam2bam_sort(map_files,thread,'name')
print 'sorted succeed'
print 'sorted_bam is: ',sorted_bams
except:
print 'sorted failed'
Message('sorted failed',email)
raise
#=========== (4) get mapping stats ==================
try:
flagstat(sorted_bams)
print 'flagstat succeed'
except:
print 'flagstat failed'
Message('flagstat failed',email)
raise
#=========== (4) htseq_count ========================
else:
if not os.path.exists(db_path): os.mkdir(db_path)
if os.listdir(db_path) == []:
STAR_Db(db_path, ref_fa, thread)
map_files = STAR(
fastqFiles, db_path, thread, annotation,
['--outSAMtype BAM SortedByCoordinate', '--quantMode GeneCounts'])
print 'align succeed'
print 'map_files is: ', map_files
except:
print 'align failed'
Message('align failed', email)
raise
#=========== (3) samtools to sort the file ==========
try:
sorted_bams = sam2bam_sort(map_files, thread, 'name')
print 'sorted succeed'
print 'sorted_bam is: ', sorted_bams
except:
print 'sorted failed'
Message('sorted failed', email)
raise
#=========== (4) get mapping stats ==================
try:
flagstat(sorted_bams)
print 'flagstat succeed'
except:
print 'flagstat failed'
Message('flagstat failed', email)
raise
#=========== (4) htseq_count ========================
