if trim == 'True':
trim_fastqFiles = Trimmomatic(trimmomatic,
fastqFiles,
phred,
trimmoAdapter,
batch=6)
remove(fastqFiles)
else:
trim_fastqFiles = fastqFiles
print 'list file succeed'
print 'fastqFiles is: ', trim_fastqFiles
#======== (2) define group ===============================
#defined above
#======== (3) align using bwa ============================
try:
map_sam = bwa_vari(read_group, trim_fastqFiles, bwaIndex, thread)
print 'align succeed'
print 'map_sam is: ', map_sam
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
bwa_Db(bwa_path,ref_fa)
os.chdir(file_path)
#======== (1) read files ================================
fastqFiles = list_files(file_path)
if trim == 'True':
trim_fastqFiles = Trimmomatic(trimmomatic,fastqFiles,phred,trimmoAdapter,batch=6)
remove(fastqFiles)
else:
trim_fastqFiles = fastqFiles
print 'list file succeed'
print 'fastqFiles is: ',trim_fastqFiles
#======== (2) define group ===============================
#defined above
#======== (3) align using bwa ============================
try:
map_sam = bwa_vari(read_group,trim_fastqFiles,bwaIndex,thread)
print 'align succeed'
print 'map_sam is: ',map_sam
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
#======== 1. map and dedupping =====================================
#======== (0) enter the directory ========================
os.chdir(file_path)
Message(startMessage,email)
#======== (1) read files ================================
fastqFiles = list_files_human(file_path)
if trim == 'True':
fastqFiles = Trimmomatic(trimmomatic,fastqFiles,phred,trimmoAdapter)
print 'list file succeed'
print 'fastqFiles is: ',fastqFiles
#======== (2) define group ===============================
#defined above
#======== (3) align using bwa ============================
try:
map_sam = bwa_vari(read_group,fastqFiles,bwaDb,thread)
print 'align succeed'
print 'map_sam is: ',map_sam
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
