def trimmomatic_se(fastq1, crop_length, crop_length_tol, out_dir, nth=1, java_heap=None): prefix = os.path.join(out_dir, os.path.basename(strip_ext_fastq(fastq1))) crop_length_tol = abs(crop_length_tol) min_length = crop_length - crop_length_tol cropped = '{p}.crop_{cl}-{tol}bp.fastq.gz'.format(p=prefix, cl=crop_length, tol=crop_length_tol) if java_heap is None: java_heap_param = '-Xmx6G' else: java_heap_param = '-Xmx{}'.format(java_heap) cmd = 'java -XX:ParallelGCThreads=1 {param} -jar {jar} SE -threads {nth} ' cmd += '{fq1} {cropped} MINLEN:{ml} CROP:{cl}' cmd = cmd.format(param=java_heap_param, jar=locate_trimmomatic(), nth=nth, fq1=fastq1, cropped=cropped, ml=min_length, cl=crop_length) run_shell_cmd(cmd) return cropped
def trimmomatic_pe(fastq1, fastq2, crop_length, out_dir_R1, out_dir_R2, nth=1, java_heap=None): prefix_R1 = os.path.join(out_dir_R1, os.path.basename(strip_ext_fastq(fastq1))) prefix_R2 = os.path.join(out_dir_R2, os.path.basename(strip_ext_fastq(fastq2))) cropped_R1 = '{}.crop_{}bp.fastq.gz'.format(prefix_R1, crop_length) cropped_R2 = '{}.crop_{}bp.fastq.gz'.format(prefix_R2, crop_length) tmp_cropped_R1 = '{}.tmp'.format(cropped_R1) tmp_cropped_R2 = '{}.tmp'.format(cropped_R2) if java_heap is None: java_heap_param = '-Xmx6G' else: java_heap_param = '-Xmx{}'.format(java_heap) cmd = 'java -XX:ParallelGCThreads=1 {} -jar {} PE -threads {} ' cmd += '{} {} {} {} {} {} MINLEN:{} CROP:{}' cmd = cmd.format(java_heap_param, locate_trimmomatic(), nth, fastq1, fastq2, cropped_R1, tmp_cropped_R1, cropped_R2, tmp_cropped_R2, crop_length, crop_length) run_shell_cmd(cmd) rm_f([tmp_cropped_R1, tmp_cropped_R2]) return cropped_R1, cropped_R2
def trimmomatic_pe(fastq1, fastq2, crop_length, crop_length_tol, out_dir_R1, out_dir_R2, nth=1, java_heap=None): prefix_R1 = os.path.join(out_dir_R1, os.path.basename(strip_ext_fastq(fastq1))) prefix_R2 = os.path.join(out_dir_R2, os.path.basename(strip_ext_fastq(fastq2))) crop_length_tol = abs(crop_length_tol) min_length = crop_length - crop_length_tol cropped_R1 = '{p}.crop_{cl}-{tol}bp.fastq.gz'.format(p=prefix_R1, cl=crop_length, tol=crop_length_tol) cropped_R2 = '{p}.crop_{cl}-{tol}bp.fastq.gz'.format(p=prefix_R2, cl=crop_length, tol=crop_length_tol) tmp_cropped_R1 = '{}.tmp'.format(cropped_R1) tmp_cropped_R2 = '{}.tmp'.format(cropped_R2) if java_heap is None: java_heap_param = '-Xmx6G' else: java_heap_param = '-Xmx{}'.format(java_heap) cmd = 'java -XX:ParallelGCThreads=1 {param} -jar {jar} PE -threads {nth} ' cmd += '{fq1} {fq2} {cropped1} {tmp_cropped1} {cropped2} {tmp_cropped2} ' cmd += 'MINLEN:{ml} CROP:{cl}' cmd = cmd.format(param=java_heap_param, jar=locate_trimmomatic(), nth=nth, fq1=fastq1, fq2=fastq2, cropped1=cropped_R1, tmp_cropped1=tmp_cropped_R1, cropped2=cropped_R2, tmp_cropped2=tmp_cropped_R2, ml=min_length, cl=crop_length) run_shell_cmd(cmd) rm_f([tmp_cropped_R1, tmp_cropped_R2]) return cropped_R1, cropped_R2
def trimmomatic_se(fastq1, crop_length, out_dir, nth=1, java_heap=None): prefix = os.path.join(out_dir, os.path.basename(strip_ext_fastq(fastq1))) cropped = '{}.crop_{}bp.fastq.gz'.format(prefix, crop_length) if java_heap is None: java_heap_param = '-Xmx6G' else: java_heap_param = '-Xmx{}'.format(java_heap) cmd = 'java -XX:ParallelGCThreads=1 {} -jar {} SE -threads {} ' cmd += '{} {} MINLEN:{} CROP:{}' cmd = cmd.format(java_heap_param, locate_trimmomatic(), nth, fastq1, cropped, crop_length, crop_length) run_shell_cmd(cmd) return cropped
def trimmomatic_se(fastq1, crop_length, crop_length_tol, phred_score_format, out_dir, nth=1, java_heap=None): prefix = os.path.join(out_dir, os.path.basename(strip_ext_fastq(fastq1))) crop_length_tol = abs(crop_length_tol) min_length = crop_length - crop_length_tol cropped = '{p}.crop_{cl}-{tol}bp.fastq.gz'.format(p=prefix, cl=crop_length, tol=crop_length_tol) if java_heap is None: java_heap_param = '-Xmx6G' else: java_heap_param = '-Xmx{}'.format(java_heap) phred_score_format = phred_score_format.lower() if phred_score_format == 'auto': phred_score_param = '' elif phred_score_format == 'phred33': phred_score_param = '-phred33' elif phred_score_format == 'phred64': phred_score_param = '-phred64' else: raise ValueError('Wrong phred_score_format!') cmd = 'java -XX:ParallelGCThreads=1 {param} -jar {jar} SE -threads {nth} {phred_score_param} ' \ '{fq1} {cropped} MINLEN:{ml} CROP:{cl}'.format( param=java_heap_param, jar=locate_trimmomatic(), nth=nth, phred_score_param=phred_score_param, fq1=fastq1, cropped=cropped, ml=min_length, cl=crop_length, ) run_shell_cmd(cmd) return cropped