def pair(args):
''' pairs two same files '''
# validate parameters.
assert os.path.isdir(args.base_dir), 'base_dir'
assert os.path.isfile(args.tmp1_sam), 'tmp1_sam'
assert os.path.isfile(args.tmp2_sam), 'tmp2_sam'
# relavent files.
base_dir = os.path.abspath(args.base_dir)
tmp1_sam = os.path.abspath(args.tmp1_sam)
tmp2_sam = os.path.abspath(args.tmp2_sam)
read1_sam = os.path.abspath('%s/read1.sam' % base_dir)
read2_sam = os.path.abspath('%s/read2.sam' % base_dir)
# pair the alignment.
pair_sam2(tmp1_sam, tmp2_sam, read1_sam, read2_sam, args.key_size)
def align(args):
''' aligns reads against reference '''
# validate parameters.
assert os.path.isdir(args.base_dir), 'base_dir'
assert os.path.isfile(args.ctg_fasta), 'ctg_fasta'
assert os.path.isfile(args.read1_fastq), 'read1_fastq'
assert os.path.isfile(args.read2_fastq), 'read2_fastq'
assert os.path.isfile(args.size_file), 'size_file'
# relavent files.
base_dir = os.path.abspath(args.base_dir)
size_file = os.path.abspath(args.size_file)
ctg_fasta = os.path.abspath(args.ctg_fasta)
read1_fastq = os.path.abspath(args.read1_fastq)
read2_fastq = os.path.abspath(args.read2_fastq)
tmp1_sam = os.path.abspath('%s/tmp1.sam' % base_dir)
tmp2_sam = os.path.abspath('%s/tmp2.sam' % base_dir)
read1_sam = os.path.abspath('%s/read1.sam' % base_dir)
read2_sam = os.path.abspath('%s/read2.sam' % base_dir)
ant_dir = '%s/ant' % base_dir
idx_dir = '%s/index' % base_dir
idx_file = '%s/index' % idx_dir
# build index if not present.
if os.path.isdir(idx_dir) == False:
subprocess.call(["mkdir", "-p", idx_dir])
create_idx(ctg_fasta, idx_file)
# remove annotation dir if present.
if os.path.isdir(ant_dir) == True:
subprocess.call(["rm", "-rf", ant_dir])
subprocess.call(["mkdir", "-p", ant_dir])
# perform alignment.
create_aln(size_file, idx_file, read1_fastq, tmp1_sam, ant_dir, args.num_cpu)
create_aln(size_file, idx_file, read2_fastq, tmp2_sam, ant_dir, args.num_cpu)
# pair the alignment.
pair_sam2(tmp1_sam, tmp2_sam, read1_sam, read2_sam, args.key_size)
