def align_samples(self,
samples_dir,
output_dir,
genome_dir,
genome_fasta=None,
samples=None,
annotation_gtf=None,
sjdboverhang=None,
genomeSAindexNbases=None,
genomeChrBinNbits=None,
genome_size=None,
feature_from_gtf_to_use_as_exon=None,
exon_tag_to_use_as_transcript_id=None,
exon_tag_to_use_as_gene_id=None,
length_of_sequences_flanking_junction=None,
junction_tab_file_list=None,
three_prime_trim=None,
five_prime_trim=None,
adapter_seq_for_three_prime_clip=None,
max_mismatch_percent_for_adapter_trimming=None,
three_prime_trim_after_adapter_clip=None,
output_type="BAM",
sort_bam=True,
max_memory_for_bam_sorting=8000000000,
include_unmapped_reads_in_bam=True,
output_unmapped_reads=True,
two_pass_mode=True,
max_intron_length=None):
#STAR.threads = threads
#STAR.path = star_dir
if genome_fasta:
STAR.index(genome_dir,
genome_fasta,
annotation_gtf=annotation_gtf,
junction_tab_file=junction_tab_file_list,
sjdboverhang=sjdboverhang,
genomeSAindexNbases=genomeSAindexNbases,
genomeChrBinNbits=genomeChrBinNbits,
genome_size=genome_size)
sample_list = samples if samples else self.get_sample_list(samples_dir)
FileRoutines.safe_mkdir(output_dir)
for sample in sample_list:
print("Handling %s" % sample)
sample_dir = "%s/%s/" % (samples_dir, sample)
alignment_sample_dir = "%s/%s/" % (output_dir, sample)
FileRoutines.safe_mkdir(alignment_sample_dir)
filetypes, forward_files, reverse_files = FileRoutines.make_lists_forward_and_reverse_files(
sample_dir)
print "\tAligning reads..."
STAR.align(
genome_dir,
forward_files,
reverse_read_list=reverse_files,
annotation_gtf=annotation_gtf if not genome_fasta else None,
feature_from_gtf_to_use_as_exon=feature_from_gtf_to_use_as_exon,
exon_tag_to_use_as_transcript_id=
exon_tag_to_use_as_transcript_id,
exon_tag_to_use_as_gene_id=exon_tag_to_use_as_gene_id,
length_of_sequences_flanking_junction=
length_of_sequences_flanking_junction,
junction_tab_file_list=junction_tab_file_list,
three_prime_trim=three_prime_trim,
five_prime_trim=five_prime_trim,
adapter_seq_for_three_prime_clip=
adapter_seq_for_three_prime_clip,
max_mismatch_percent_for_adapter_trimming=
max_mismatch_percent_for_adapter_trimming,
three_prime_trim_after_adapter_clip=
three_prime_trim_after_adapter_clip,
output_type=output_type,
sort_bam=sort_bam,
max_memory_for_bam_sorting=max_memory_for_bam_sorting,
include_unmapped_reads_in_bam=include_unmapped_reads_in_bam,
output_unmapped_reads=output_unmapped_reads,
output_dir=alignment_sample_dir,
two_pass_mode=two_pass_mode,
max_intron_length=max_intron_length)
print "\tIndexing bam file..."
resulting_bam_file = "%s/Aligned.sortedByCoord.out.bam" % alignment_sample_dir
SamtoolsV1.index(resulting_bam_file)
sjdboverhang=None,
genomeSAindexNbases=None,
genomeChrBinNbits=None,
genome_size=args.genome_size)
sample_list = args.samples if args.samples else Pipeline.get_sample_list(
args.samples_dir)
FileRoutines.safe_mkdir(args.output_dir)
for sample in sample_list:
print("Handling %s" % sample)
sample_dir = "%s/%s/" % (args.samples_dir, sample)
alignment_sample_dir = "%s/%s/" % (args.output_dir, sample)
FileRoutines.safe_mkdir(alignment_sample_dir)
filetypes, forward_files, reverse_files = FileRoutines.make_lists_forward_and_reverse_files(
sample_dir)
print "\tAligning reads..."
STAR.align(
args.genome_dir,
forward_files,
reverse_read_list=reverse_files,
annotation_gtf=args.annotation_gtf if not args.genome_fasta else None,
feature_from_gtf_to_use_as_exon=None,
exon_tag_to_use_as_transcript_id=None,
exon_tag_to_use_as_gene_id=None,
length_of_sequences_flanking_junction=None,
junction_tab_file_list=args.junction_tab_file,
three_prime_trim=None,
five_prime_trim=None,
