command='%s sampe %s %s %s %s %s %s | %s view -bS - > %s'%(BWA_bin, read_group_command, genome_file, sai_file1, sai_file2, fastq_file1,
fastq_file2, samtools_bin, bam_file)
else:
command='%s samse %s %s %s %s | %s view -bS - > %s'%(BWA_bin, read_group_command, genome_file, sai_file1, fastq_file1, samtools_bin,
bam_file)
return_code = command_runner.run_command( command)
if return_code is not 0:
run_fine = False
if sort:
files_and_dir.append(bam_file)
if picard_dir:
sorted_bam_file=os.path.join(output_dir,sample_name+'_sorted.bam')
return_code = utils.sort_bam_file_per_coordinate(picard_dir, bam_file, sorted_bam_file, overwrite=True)
else:
sorted_bam_file=os.path.join(output_dir,sample_name+'_sorted')
command='%s sort %s %s'%(samtools_bin, bam_file, sorted_bam_file)
return_code = command_runner.run_command( command)
if return_code is not 0:
run_fine = False
if run_fine and clean_up:
return_code = remove_file(files_and_dir)
if return_code is not 0:
run_fine = False
return run_fine
nb_fragment += len(second_reads)
output_reads(output_stream, first_reads, second_reads)
library_size = estimate_library_size(nb_fragment, total_nb_uniqs)
print "%s fragments" % (nb_fragment)
print "%s (%.2f%%) duplicates" % (total_nb_dups,
float(total_nb_dups) / nb_fragment * 100)
print "nb unique=%d" % (total_nb_uniqs)
print "library size=%d" % round(library_size, 0)
print "Sort the new bam file"
output_stream.flush()
output_stream.close()
if picard_dir:
output_bam_file = tmp + '_mrk_dup.bam'
return_code = utils.sort_bam_file_per_coordinate(
picard_dir,
tmp_bam_file,
output_bam_file,
overwrite=True,
validation_stringency="SILENT")
else:
output_bam_file = tmp + '_mrk_dup'
command = '%s sort %s %s' % (samtools_bin, tmp_bam_file,
output_bam_file)
return_code = command_runner.run_command(command)
if return_code == 0:
command_runner.run_command('rm -f %s' % (tmp_bam_file))
def find_duplicates(first_reads, second_reads, distance_threshold):
uniq_second_sequences = {}
all_second_reads = second_reads.values()
nb_duplicate = 0
if current_reference!='*':
nb_dups = find_duplicates(first_reads,second_reads, distance_threshold)
total_nb_dups+=nb_dups
nb_fragment+=len(second_reads)
output_reads(output_stream, first_reads, second_reads)
library_size = estimate_library_size(nb_fragment, total_nb_uniqs)
print "%s fragments"%(nb_fragment)
print "%s (%.2f%%) duplicates"%(total_nb_dups,float(total_nb_dups)/nb_fragment*100)
print "nb unique=%d"%(total_nb_uniqs)
print "library size=%d"%round(library_size,0)
print "Sort the new bam file"
output_stream.flush()
output_stream.close()
if picard_dir:
output_bam_file = tmp + '_mrk_dup.bam'
return_code = utils.sort_bam_file_per_coordinate(picard_dir, tmp_bam_file, output_bam_file, overwrite=True, validation_stringency="SILENT")
else:
output_bam_file = tmp + '_mrk_dup'
command='%s sort %s %s'%(samtools_bin, tmp_bam_file, output_bam_file)
return_code = command_runner.run_command( command)
if return_code==0:
command_runner.run_command( 'rm -f %s'%(tmp_bam_file))
def find_duplicates(first_reads,second_reads, distance_threshold):
uniq_second_sequences={}
all_second_reads=second_reads.values()
nb_duplicate=0
if len(all_second_reads)>0:
uniq_second_sequences[all_second_reads[0].get_query_sequence()]=[all_second_reads[0]]
for sam_record in all_second_reads[1:]:
else:
command = '%s samse %s %s %s %s | %s view -bS - > %s' % (
BWA_bin, read_group_command, genome_file, sai_file1, fastq_file1,
samtools_bin, bam_file)
return_code = command_runner.run_command(command)
if return_code is not 0:
run_fine = False
if sort:
files_and_dir.append(bam_file)
if picard_dir:
sorted_bam_file = os.path.join(output_dir,
sample_name + '_sorted.bam')
return_code = utils.sort_bam_file_per_coordinate(picard_dir,
bam_file,
sorted_bam_file,
overwrite=True)
else:
sorted_bam_file = os.path.join(output_dir, sample_name + '_sorted')
command = '%s sort %s %s' % (samtools_bin, bam_file,
sorted_bam_file)
return_code = command_runner.run_command(command)
if return_code is not 0:
run_fine = False
if run_fine and clean_up:
return_code = remove_file(files_and_dir)
if return_code is not 0:
run_fine = False
return run_fine
file_to_remove = []
sam_file = run_smalt_paired(consensus_file, read1_fastq, read2_fastq)
file_to_remove.append(sam_file)
if os.path.exists(single_fastq):
sam_file_single = run_smalt_single(consensus_file, single_fastq)
file_to_remove.append(sam_file_single)
corrected_sam_file = correct_smalt_sam_file(sam_file, all_read_groups, sam_file_single)
else:
corrected_sam_file = correct_smalt_sam_file(sam_file, all_read_groups)
file_to_remove.append(corrected_sam_file)
name, ext = os.path.splitext(corrected_sam_file)
output_bam = os.path.join(name + "_sorted.bam")
sort_bam_file_per_coordinate(picard_dir, input_bam=corrected_sam_file, output_bam=output_bam, overwrite=True,
CREATE_INDEX="true")
file_to_remove.append(output_bam)
mark_dups_jar = os.path.join(picard_dir, 'MarkDuplicates.jar')
mark_dups_bam = os.path.join(name + '_sorted_mrk_dup.bam')
mark_dups_metric = os.path.join(name + '_sorted_mrk_dup.metric')
command = 'java -Xmx5G -jar %s I=%s O=%s METRICS_FILE=%s VALIDATION_STRINGENCY=LENIENT MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=100 CREATE_INDEX=true' % (
mark_dups_jar, output_bam,
mark_dups_bam, mark_dups_metric)
command_runner.run_command(command)
file_to_remove.append(mark_dups_bam)
fixed_bam = os.path.join(name + '_sorted_mrk_dup_fixed.bam')
#This command remove the duplicate flag when a read is mapped and its mate isn't
#It also remove the unmapped read from the bam file as this prevent the merging for some reason !!
command = """samtools view -h %s |
file_to_remove.append(sam_file)
if os.path.exists(single_fastq):
sam_file_single = run_smalt_single(consensus_file, single_fastq)
file_to_remove.append(sam_file_single)
corrected_sam_file = correct_smalt_sam_file(sam_file, all_read_groups,
sam_file_single)
else:
corrected_sam_file = correct_smalt_sam_file(sam_file, all_read_groups)
file_to_remove.append(corrected_sam_file)
name, ext = os.path.splitext(corrected_sam_file)
output_bam = os.path.join(name + "_sorted.bam")
sort_bam_file_per_coordinate(picard_dir,
input_bam=corrected_sam_file,
output_bam=output_bam,
overwrite=True,
CREATE_INDEX="true")
file_to_remove.append(output_bam)
mark_dups_jar = os.path.join(picard_dir, 'MarkDuplicates.jar')
mark_dups_bam = os.path.join(name + '_sorted_mrk_dup.bam')
mark_dups_metric = os.path.join(name + '_sorted_mrk_dup.metric')
command = 'java -Xmx5G -jar %s I=%s O=%s METRICS_FILE=%s VALIDATION_STRINGENCY=LENIENT MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=100 CREATE_INDEX=true' % (
mark_dups_jar, output_bam, mark_dups_bam, mark_dups_metric)
command_runner.run_command(command)
file_to_remove.append(mark_dups_bam)
fixed_bam = os.path.join(name + '_sorted_mrk_dup_fixed.bam')
#This command remove the duplicate flag when a read is mapped and its mate isn't
#It also remove the unmapped read from the bam file as this prevent the merging for some reason !!
