def post_aln_qc(args, bam_file, logger=None):
""" perform post alignment quality check """
post_aln_dir = os.path.join(args.workDir, 'post_alignment_qc')
if not os.path.isdir(post_aln_dir):
os.mkdir(post_aln_dir)
#Fix mate information for bam file
exit_code, fix_mate_out = post_alignment_qc.fix_mate_information(args.picard, bam_file,
args.id, args.workDir, logger)
if exit_code == 0:
os.remove(bam_file)
assert(not os.path.isfile(bam_file))
os.rename(fix_mate_out, bam_file)
assert(os.path.isfile(bam_file))
#validate the post-alignment BAM file
post_alignment_qc.validate_bam_file(args.picard, bam_file, args.id, post_aln_dir, logger)
#collect RNA-seq metrics
post_alignment_qc.collect_rna_seq_metrics(args.picard, bam_file, args.id,
post_aln_dir, args.ref_flat, logger)
#run rna_seq_qc from broad institute
post_alignment_qc.bam_index(bam_file, args.id, logger)
rna_seq_qc_dir = os.path.join(post_aln_dir, 'rna_seq_qc')
if not os.path.isdir(rna_seq_qc_dir):
os.mkdir(rna_seq_qc_dir)
exit_code = post_alignment_qc.rna_seq_qc(args.rna_seq_qc_path, bam_file, args.id, rna_seq_qc_dir,
args.ref_genome,args.rna_seq_qc_annotation, logger)
if not(exit_code == 0):
reordered_bam = post_alignment_qc.reorder_bam(args.picard, bam_file, args.id, args.workDir,
args.ref_genome, logger)
post_alignment_qc.bam_index(reordered_bam, args.id, logger)
post_alignment_qc.rna_seq_qc(args.rna_seq_qc_path, reordered_bam, args.id, rna_seq_qc_dir,
args.ref_genome,args.rna_seq_qc_annotation, logger)
if os.path.isfile(reordered_bam):
os.remove(reordered_bam)
if os.path.isfile('%s.bai' %reordered_bam):
os.remove('%s.bai' %reordered_bam)
def post_aln_qc(args, bam_file, logger=None):
""" perform post alignment quality check """
#validate the post-alignment BAM file
post_alignment_qc.validate_bam_file(args.picard, bam_file, args.id, args.workDir, logger)
#collect RNA-seq metrics
post_alignment_qc.collect_rna_seq_metrics(args.picard, bam_file, args.id,
args.workDir, args.ref_flat, logger)
#run rna_seq_qc from broad institute
post_alignment_qc.bam_index(bam_file, args.id, logger)
exit_code = post_alignment_qc.rna_seq_qc(args.rna_seq_qc_path, bam_file, args.id, args.workDir,
args.ref_genome,args.rna_seq_qc_annotation, logger)
if not(exit_code == 0):
reordered_bam = post_alignment_qc.reorder_bam(args.picard, bam_file, args.id, args.workDir,
args.ref_genome, logger)
post_alignment_qc.bam_index(reordered_bam, args.id, logger)
post_alignment_qc.rna_seq_qc(args.rna_seq_qc_path, reordered_bam, args.id, args.workDir,
args.ref_genome,args.rna_seq_qc_annotation, logger)