def generate_trim_commands(forward_seqs, reverse_seqs, map_file,
out_dir, parameters):
"""Generates the QC_Trim commands
Parameters
----------
forward_seqs : list of str
The list of forward seqs filepaths
reverse_seqs : list of str
The list of reverse seqs filepaths
map_file : str
The path to the mapping file
out_dir : str
The job output directory
parameters : dict
The command's parameters, keyed by parameter name
Returns
-------
cmds: list of str
The QC_Trim commands
samples: list of tup
list of 4-tuples with run prefix, sample name, fwd read fp, rev read fp
Notes
-----
Currently this is requiring matched pairs in the make_read_pairs_per_sample
step but implicitly allowing empty reverse reads in the actual command
generation. This behavior may allow support of situations with empty
reverse reads in some samples, for example after trimming and QC.
"""
# we match filenames, samples, and run prefixes
samples = make_read_pairs_per_sample(forward_seqs, reverse_seqs, map_file)
cmds = []
param_string = _format_params(parameters, ATROPOS_PARAMS)
for run_prefix, sample, f_fp, r_fp in samples:
if r_fp is None:
cmds.append("atropos trim %s -o %s -se %s" % (
param_string, join(out_dir, '%s.R1.fastq.gz' % run_prefix),
f_fp))
else:
cmds.append('atropos trim %s -o %s -p %s -pe1 %s -pe2 %s'
% (param_string, join(out_dir, '%s.R1.fastq.gz' %
run_prefix), join(out_dir, '%s.R2.fastq.gz' %
run_prefix), f_fp, r_fp))
return cmds, samples
def test_format_filter_params(self):
db_path = os.environ["QC_FILTER_DB_DP"]
obs = _format_params(self.params, BOWTIE2_PARAMS)
exp = ('-p 1 -x %sphix/phix') % db_path
self.assertEqual(obs, exp)
def generate_filter_commands(forward_seqs, reverse_seqs, map_file, out_dir,
temp_dir, parameters):
"""Generates the QC_Filter commands
Parameters
----------
forward_seqs : list of str
The list of forward seqs filepaths
reverse_seqs : list of str
The list of reverse seqs filepaths
map_file : str
The path to the mapping file
out_dir : str
The job output directory
parameters : dict
The command's parameters, keyed by parameter name
Returns
-------
cmds: list of str
The QC_Filter commands
samples: list of tup
list of 4-tuples with run prefix, sample name, fwd read fp, rev read fp
Notes
-----
Currently this is requiring matched pairs in the make_read_pairs_per_sample
step but implicitly allowing empty reverse reads in the actual command
generation. This behavior may allow support of situations with empty
reverse reads in some samples, for example after trimming and QC.
"""
# we match filenames, samples, and run prefixes
samples = make_read_pairs_per_sample(forward_seqs, reverse_seqs, map_file)
cmds = []
param_string = _format_params(parameters, BOWTIE2_PARAMS)
threads = parameters['Number of threads']
for run_prefix, sample, f_fp, r_fp in samples:
cmds.append(
'bowtie2 {params} --very-sensitive -1 {fwd_ip} -2 {rev_ip}'
' | samtools view -f 12 -F 256 -b -o {bow_op}; '
'samtools sort -T {sample_path} -@ {thrds} -n -o {sam_op} '
'{sam_un_op}; '
'bedtools bamtofastq -i {sam_op} -fq {bedtools_op_one} '
'-fq2 {bedtools_op_two}; '
'pigz -p {thrds} -c {bedtools_op_one} > {gz_op_one}; '
'pigz -p {thrds} -c {bedtools_op_two} > {gz_op_two};'.format(
params=param_string,
thrds=threads,
fwd_ip=f_fp,
rev_ip=r_fp,
bow_op=join(temp_dir, '%s.unsorted.bam' % sample),
sample_path=join(temp_dir, '%s' % sample),
sam_op=join(temp_dir, '%s.bam' % sample),
sam_un_op=join(temp_dir, '%s.unsorted.bam' % sample),
bedtools_op_one=join(temp_dir,
'%s.R1.trimmed.filtered.fastq' % sample),
bedtools_op_two=join(temp_dir,
'%s.R2.trimmed.filtered.fastq' % sample),
gz_op_one=join(out_dir,
'%s.R1.trimmed.filtered.fastq.gz' % sample),
gz_op_two=join(out_dir,
'%s.R2.trimmed.filtered.fastq.gz' % sample)))
return cmds, samples
def test_format_trim_params(self):
obs = _format_params(self.params, ATROPOS_PARAMS)
exp = ('-A GATCGGAAGAGCGTCGTGTAGGGAAAGGAGTGT --adapter GATCGGAAGAGCACA'
'CGTCTGAACTCCAGTCAC --max-n 80 --minimum-length 80 '
'--pair-filter any --quality-cutoff 15 --threads 5 --trim-n')
self.assertEqual(obs, exp)