def _do_test_builder__pop_option(setter):
builder = AtomicCmdBuilder("find")
setter(builder, "-empty", fixed = False)
setter(builder, "-size", "1", fixed = False)
setter(builder, "-name", "*.txt", fixed = False)
builder.pop_option("-size")
assert_equal(builder.call, ["find", "-empty", "-name", "*.txt"])
def _get_common_parameters(version):
global _DEPRECATION_WARNING_PRINTED
if version == VERSION_14:
version_check = _VERSION_14_CHECK
elif version == VERSION_15:
version_check = _VERSION_15_CHECK
else:
raise CmdError("Unknown version: %s" % version)
cmd = AtomicCmdBuilder("AdapterRemoval",
CHECK_VERSION=version_check)
# Trim Ns at read ends
cmd.set_option("--trimns", fixed=False)
# Trim low quality scores
cmd.set_option("--trimqualities", fixed=False)
try:
if not _DEPRECATION_WARNING_PRINTED and version_check.version < (2, 0):
import pypeline.ui as ui
ui.print_warn("\nWARNING: AdapterRemoval v1.5.x is deprecated;")
ui.print_warn(" Upgrading to 2.1.x is strongly adviced!\n")
ui.print_warn(" Download the newest version of AdapterRemoval at ")
ui.print_warn(" https://github.com/MikkelSchubert/adapterremoval\n")
_DEPRECATION_WARNING_PRINTED = True
except versions.VersionRequirementError:
pass
return cmd
def _bowtie2_template(call, prefix, iotype = "IN", **kwargs):
params = AtomicCmdBuilder(call, **kwargs)
for postfix in ("1.bt2", "2.bt2", "3.bt2", "4.bt2", "rev.1.bt2", "rev.2.bt2"):
key = "%s_PREFIX_%s" % (iotype, postfix.upper())
params.set_kwargs(**{key : (prefix + "." + postfix)})
return params
def _do_test_builder__pop_option(setter):
builder = AtomicCmdBuilder("find")
setter(builder, "-empty", fixed=False)
setter(builder, "-size", "1", fixed=False)
setter(builder, "-name", "*.txt", fixed=False)
builder.pop_option("-size")
assert_equal(builder.call, ["find", "-empty", "-name", "*.txt"])
def test_builder__set_kwargs__after_finalize():
expected = {"IN_PATH" : "/a/b/"}
builder = AtomicCmdBuilder("echo")
builder.set_kwargs(IN_PATH = "/a/b/")
builder.finalize()
assert_raises(AtomicCmdBuilderError, builder.set_kwargs, OUT_PATH = "/dst/file")
assert_equal(builder.kwargs, expected)
def _bowtie2_template(call, prefix, iotype="IN", **kwargs):
params = AtomicCmdBuilder(call, **kwargs)
for postfix in ("1.bt2", "2.bt2", "3.bt2", "4.bt2", "rev.1.bt2",
"rev.2.bt2"):
key = "%s_PREFIX_%s" % (iotype, postfix.upper())
params.set_kwargs(**{key: (prefix + "." + postfix)})
return params
def test_builder__set__kwargs__overwriting():
expected = {"IN_PATH": "/a/b/"}
builder = AtomicCmdBuilder("echo")
builder.set_kwargs(IN_PATH="/a/b/")
assert_raises(AtomicCmdBuilderError,
builder.set_kwargs,
IN_PATH="/dst/file")
assert_equal(builder.kwargs, expected)
def customize(cls, infile, intervals, outfile, dependencies = ()):
params = AtomicCmdBuilder(["bam_sample_regions"],
IN_PILEUP = infile,
IN_INTERVALS = intervals,
OUT_STDOUT = outfile)
params.set_option("--genotype", "%(IN_PILEUP)s")
params.set_option("--intervals", "%(IN_INTERVALS)s")
return {"command" : params}
def test_builder__add_multiple_options_with_sep():
values = ("file_a", "file_b")
expected = {"IN_FILE_01": "file_a", "IN_FILE_02": "file_b"}
builder = AtomicCmdBuilder("ls")
kwargs = builder.add_multiple_options("-i", values, sep="=")
assert_equal(kwargs, expected)
assert_equal(builder.kwargs, expected)
assert_equal(builder.call, ["ls", "-i=%(IN_FILE_01)s", "-i=%(IN_FILE_02)s"])
def test_builder__add_multiple_values_with_template():
values = ("file_a", "file_b")
expected = {"OUT_BAM_1": "file_a", "OUT_BAM_2": "file_b"}
builder = AtomicCmdBuilder("ls")
kwargs = builder.add_multiple_values(values, template="OUT_BAM_%i")
assert_equal(kwargs, expected)
assert_equal(builder.kwargs, expected)
assert_equal(builder.call, ["ls", "%(OUT_BAM_1)s", "%(OUT_BAM_2)s"])
def test_builder__add_multiple_values():
values = ("file_a", "file_b")
expected = {"IN_FILE_01": "file_a", "IN_FILE_02": "file_b"}
builder = AtomicCmdBuilder("ls")
kwargs = builder.add_multiple_values(values)
assert_equal(kwargs, expected)
assert_equal(builder.kwargs, expected)
assert_equal(builder.call, ["ls", "%(IN_FILE_01)s", "%(IN_FILE_02)s"])
def test_builder__add_multiple_values_with_template():
values = ("file_a", "file_b")
expected = {"OUT_BAM_1": "file_a", "OUT_BAM_2": "file_b"}
builder = AtomicCmdBuilder("ls")
kwargs = builder.add_multiple_values(values, template="OUT_BAM_%i")
assert_equal(kwargs, expected)
assert_equal(builder.kwargs, expected)
assert_equal(builder.call, ["ls", "%(OUT_BAM_1)s", "%(OUT_BAM_2)s"])
def test_builder__add_multiple_values():
values = ("file_a", "file_b")
expected = {"IN_FILE_01": "file_a", "IN_FILE_02": "file_b"}
builder = AtomicCmdBuilder("ls")
kwargs = builder.add_multiple_values(values)
assert_equal(kwargs, expected)
assert_equal(builder.kwargs, expected)
assert_equal(builder.call, ["ls", "%(IN_FILE_01)s", "%(IN_FILE_02)s"])
def test_builder__add_multiple_options_with_template_fixed():
values = ("file_a", "file_b")
expected = {"IN_FILE_01": "file_a", "IN_FILE_02": "file_b"}
builder = AtomicCmdBuilder("ls")
kwargs = builder.add_multiple_options("-i", values)
assert_equal(kwargs, expected)
assert_equal(builder.kwargs, expected)
assert_raises(AtomicCmdBuilderError, builder.add_multiple_options, "-i",
values)
def test_builder__add_multiple_options_with_sep():
values = ("file_a", "file_b")
expected = {"IN_FILE_01": "file_a", "IN_FILE_02": "file_b"}
builder = AtomicCmdBuilder("ls")
kwargs = builder.add_multiple_options("-i", values, sep="=")
assert_equal(kwargs, expected)
assert_equal(builder.kwargs, expected)
assert_equal(builder.call,
["ls", "-i=%(IN_FILE_01)s", "-i=%(IN_FILE_02)s"])
def test_builder__add_multiple_options_multiple_times():
expected = {"IN_FILE_01": "file_a", "IN_FILE_02": "file_b"}
builder = AtomicCmdBuilder("ls")
kwargs = builder.add_multiple_options("-i", ("file_a",))
assert_equal(kwargs, {"IN_FILE_01": "file_a"})
kwargs = builder.add_multiple_options("-i", ("file_b",))
assert_equal(kwargs, {"IN_FILE_02": "file_b"})
assert_equal(builder.kwargs, expected)
assert_equal(builder.call, ["ls", "-i", "%(IN_FILE_01)s", "-i", "%(IN_FILE_02)s"])
def test_builder__add_multiple_options_with_template_fixed():
values = ("file_a", "file_b")
expected = {"IN_FILE_01": "file_a", "IN_FILE_02": "file_b"}
builder = AtomicCmdBuilder("ls")
kwargs = builder.add_multiple_options("-i", values)
assert_equal(kwargs, expected)
assert_equal(builder.kwargs, expected)
assert_raises(AtomicCmdBuilderError,
builder.add_multiple_options, "-i", values)
def test_builder__add_option__overwrite():
builder = AtomicCmdBuilder("find")
builder.add_option("-name", "*.txt")
builder.add_option("-or")
builder.add_option("-name", "*.bat")
assert_equal(builder.call,
["find", "-name", "*.txt", "-or", "-name", "*.bat"])
def _get_bwa_template(call, prefix, iotype = "IN", **kwargs):
extensions = ["amb", "ann", "bwt", "pac", "sa"]
try:
if BWA_VERSION.version < (0, 6, 0):
extensions.extend(("rbwt", "rpac", "rsa"))
except versions.VersionRequirementError:
pass # Ignored here, handled elsewhere
params = AtomicCmdBuilder(call, **kwargs)
for postfix in extensions:
key = "%s_PREFIX_%s" % (iotype, postfix.upper())
params.set_kwargs(**{key : (prefix + "." + postfix)})
return params
def _get_bwa_template(call, prefix, iotype="IN", **kwargs):
extensions = ["amb", "ann", "bwt", "pac", "sa"]
try:
if BWA_VERSION.version < (0, 6, 0):
extensions.extend(("rbwt", "rpac", "rsa"))
except versions.VersionRequirementError:
pass # Ignored here, handled elsewhere
params = AtomicCmdBuilder(call, **kwargs)
for postfix in extensions:
key = "%s_PREFIX_%s" % (iotype, postfix.upper())
params.set_kwargs(**{key: (prefix + "." + postfix)})
return params
def customize(cls, reference, in_bam, in_vcf, outfile, dependencies = ()):
unicat = AtomicCmdBuilder(["unicat", "%(IN_VCF)s"],
IN_VCF = in_vcf,
OUT_STDOUT = AtomicCmd.PIPE)
vcfpileup = AtomicCmdBuilder(["vcf_create_pileup", "%(OUT_PILEUP)s"],
IN_REF = reference,
IN_BAM = in_bam,
IN_STDIN = unicat,
OUT_PILEUP = outfile,
OUT_TBI = outfile + ".tbi")
vcfpileup.add_value("%(IN_BAM)s")
vcfpileup.set_option("-f", "%(IN_REF)s")
return {"commands" : {"unicat" : unicat,
"pileup" : vcfpileup}}
def customize(self,
config,
reference,
input_files,
output_file,
directory,
dependencies=()):
stats_out_fname = "Stats_out_MCMC_correct_prob.csv"
command = AtomicCmdBuilder([
"mapDamage", "--rescale-only", "-i", "%(TEMP_IN_BAM)s", "-d",
"%(TEMP_DIR)s", "-r", "%(IN_REFERENCE)s", "--rescale-out",
"%(OUT_BAM)s"
],
IN_REFERENCE=reference,
TEMP_OUT_LOG="Runtime_log.txt",
TEMP_OUT_CSV=stats_out_fname,
OUT_BAM=output_file,
CHECK_VERSION=MAPDAMAGE_VERSION)
return {
"command": command,
"config": config,
"input_files": input_files,
"directory": directory,
"dependencies": dependencies
}
def customize(self, reference, directory, dependencies=()):
command = AtomicCmdBuilder(
[
"mapDamage", "--stats-only", "-r", "%(IN_REFERENCE)s", "-d",
"%(TEMP_DIR)s"
],
IN_REFERENCE=reference,
TEMP_OUT_FREQ_3p="3pGtoA_freq.txt",
TEMP_OUT_FREQ_5p="5pCtoT_freq.txt",
TEMP_OUT_COMP_USER="******",
TEMP_OUT_MISINCORP="misincorporation.txt",
TEMP_OUT_LOG="Runtime_log.txt",
TEMP_OUT_STDOUT="pipe_mapDamage.stdout",
TEMP_OUT_STDERR="pipe_mapDamage.stderr",
OUT_COMP_GENOME=os.path.join(directory, "dnacomp_genome.csv"),
OUT_MCMC_PROBS=os.path.join(directory,
"Stats_out_MCMC_correct_prob.csv"),
OUT_MCMC_HIST=os.path.join(directory, "Stats_out_MCMC_hist.pdf"),
OUT_MCMC_ITER=os.path.join(directory, "Stats_out_MCMC_iter.csv"),
OUT_MCMC_ITERSUM=os.path.join(directory,
"Stats_out_MCMC_iter_summ_stat.csv"),
OUT_MCMC_POSTPRED=os.path.join(directory,
"Stats_out_MCMC_post_pred.pdf"),
OUT_MCMC_TRACE=os.path.join(directory, "Stats_out_MCMC_trace.pdf"),
CHECK_RSCRIPT=RSCRIPT_VERSION,
CHECK_MAPDAMAGE=MAPDAMAGE_VERSION)
return {"command": command, "dependencies": dependencies}
def _build_cat_command():
"""Returns a AtomicCmdBuilder for the 'paleomix cat' command."""
return AtomicCmdBuilder([_PALEOMIX_PATH, "cat"],
EXEC_GZIP="gzip",
EXEC_BZIP="bzip2",
EXEC_CAT="cat",
CHECK_PALEOMIX=VERSION_PALEOMIX)
def _get_common_parameters(version):
if version == VERSION_14:
version_check = _VERSION_14_CHECK
elif version == VERSION_15:
version_check = _VERSION_15_CHECK
else:
raise CmdError("Unknown version: %s" % version)
cmd = AtomicCmdBuilder("AdapterRemoval",
CHECK_VERSION=version_check)
# Trim Ns at read ends
cmd.set_option("--trimns", fixed=False)
# Trim low quality scores
cmd.set_option("--trimqualities", fixed=False)
return cmd
def __init__(self,
config,
reference,
input_bam,
output_bam,
tags,
min_mapq=0,
filter_unmapped=False,
dependencies=()):
flt_params = AtomicCmdBuilder(("samtools", "view", "-bu"),
IN_BAM=input_bam,
OUT_STDOUT=AtomicCmd.PIPE)
if min_mapq:
flt_params.set_option("-q", min_mapq, sep="")
if filter_unmapped:
flt_params.set_option("-F", "0x4", sep="")
flt_params.add_value("%(IN_BAM)s")
jar_params = picard.picard_command(config, "AddOrReplaceReadGroups")
jar_params.set_option("INPUT", "/dev/stdin", sep="=")
# Output is written to a named pipe, since the JVM may, in some cases,
# emit warning messages to stdout, resulting in a malformed BAM.
jar_params.set_option("OUTPUT", "%(TEMP_OUT_BAM)s", sep="=")
jar_params.set_option("COMPRESSION_LEVEL", "0", sep="=")
# Ensure that the BAM is sorted; this is required by the pipeline, and
# needs to be done before calling calmd (avoiding pathologic runtimes).
jar_params.set_option("SORT_ORDER", "coordinate", sep="=")
# All tags are overwritten; ID is set since the default (e.g. '1')
# causes problems with pysam due to type inference (is read as a length
# 1 string, but written as a character).
for tag in ("ID", "SM", "LB", "PU", "PL"):
jar_params.set_option(tag, tags[tag], sep="=")
jar_params.set_kwargs(IN_STDIN=flt_params, TEMP_OUT_BAM="bam.pipe")
calmd = AtomicCmdBuilder(
["samtools", "calmd", "-b", "%(TEMP_IN_BAM)s", "%(IN_REF)s"],
IN_REF=reference,
TEMP_IN_BAM="bam.pipe",
OUT_STDOUT=output_bam)
commands = [cmd.finalize() for cmd in (flt_params, jar_params, calmd)]
description = "<Cleanup BAM: %s -> '%s'>" \
% (input_bam, output_bam)
PicardNode.__init__(self,
command=ParallelCmds(commands),
description=description,
dependencies=dependencies)
def customize(cls, pileup, infile, outfile, interval, dependencies = ()):
unicat = AtomicCmdBuilder(["unicat", "%(IN_VCF)s"],
IN_VCF = infile,
OUT_STDOUT = AtomicCmd.PIPE)
vcffilter = AtomicCmdBuilder(["vcf_filter", "--pileup", "%(IN_PILEUP)s"],
IN_PILEUP = pileup,
IN_STDIN = unicat,
OUT_STDOUT = AtomicCmd.PIPE)
for contig in interval.get("Homozygous Contigs", ()):
vcffilter.set_option("--homozygous-chromosome", contig)
bgzip = AtomicCmdBuilder(["bgzip"],
IN_STDIN = vcffilter,
OUT_STDOUT = outfile)
return {"commands" : {"unicat" : unicat,
"filter" : vcffilter,
"bgzip" : bgzip}}
def customize(cls, options, infile, interval, outfile, padding, dependencies = ()):
prefix = "{Genome}.{Name}".format(**interval)
intervals = os.path.join(options.intervals_root, prefix + ".bed")
params = AtomicCmdBuilder(["bam_genotype_regions"],
IN_VCFFILE = infile,
IN_TABIX = infile + ".tbi",
IN_INTERVALS = intervals,
OUT_STDOUT = outfile)
params.set_option("--genotype", "%(IN_VCFFILE)s")
params.set_option("--intervals", "%(IN_INTERVALS)s")
if interval.get("Protein coding"):
params.set_option("--whole-codon-indels-only")
if not interval.get("Indels"):
params.set_option("--ignore-indels")
return {"command" : params}
def test_builder__finalize__calls_atomiccmd():
was_called = []
class _AtomicCmdMock:
def __init__(self, *args, **kwargs):
assert_equal(args, (["echo", "-out", "%(OUT_FILE)s", "%(IN_FILE)s"],))
assert_equal(kwargs, {"IN_FILE" : "/in/file", "OUT_FILE" : "/out/file", "set_cwd" : True})
was_called.append(True)
with Monkeypatch("pypeline.atomiccmd.builder.AtomicCmd", _AtomicCmdMock):
builder = AtomicCmdBuilder("echo", set_cwd = True)
builder.add_option("-out", "%(OUT_FILE)s")
builder.add_value("%(IN_FILE)s")
builder.set_kwargs(OUT_FILE = "/out/file",
IN_FILE = "/in/file")
builder.finalize()
assert was_called
def _get_common_parameters(version):
global _DEPRECATION_WARNING_PRINTED
if version == VERSION_14:
version_check = _VERSION_14_CHECK
elif version == VERSION_15:
version_check = _VERSION_15_CHECK
else:
raise CmdError("Unknown version: %s" % version)
cmd = AtomicCmdBuilder("AdapterRemoval", CHECK_VERSION=version_check)
# Trim Ns at read ends
cmd.set_option("--trimns", fixed=False)
# Trim low quality scores
cmd.set_option("--trimqualities", fixed=False)
try:
if not _DEPRECATION_WARNING_PRINTED and version_check.version < (2, 0):
import pypeline.ui as ui
ui.print_warn("\nWARNING: AdapterRemoval v1.5.x is deprecated;")
ui.print_warn(" Upgrading to 2.1.x is strongly adviced!\n")
ui.print_warn(
" Download the newest version of AdapterRemoval at ")
ui.print_warn(
" https://github.com/MikkelSchubert/adapterremoval\n")
_DEPRECATION_WARNING_PRINTED = True
except versions.VersionRequirementError:
pass
return cmd
def test_builder__finalize__calls_atomiccmd():
was_called = []
class _AtomicCmdMock:
def __init__(self, *args, **kwargs):
assert_equal(args,
(["echo", "-out", "%(OUT_FILE)s", "%(IN_FILE)s"], ))
assert_equal(kwargs, {
"IN_FILE": "/in/file",
"OUT_FILE": "/out/file",
"set_cwd": True
})
was_called.append(True)
with Monkeypatch("pypeline.atomiccmd.builder.AtomicCmd", _AtomicCmdMock):
builder = AtomicCmdBuilder("echo", set_cwd=True)
builder.add_option("-out", "%(OUT_FILE)s")
builder.add_value("%(IN_FILE)s")
builder.set_kwargs(OUT_FILE="/out/file", IN_FILE="/in/file")
builder.finalize()
assert was_called
def customize(cls,
options,
infile,
interval,
outfile,
padding,
dependencies=()):
prefix = "{Genome}.{Name}".format(**interval)
intervals = os.path.join(options.intervals_root, prefix + ".bed")
params = AtomicCmdBuilder(["bam_genotype_regions"],
IN_VCFFILE=infile,
IN_TABIX=infile + ".tbi",
IN_INTERVALS=intervals,
OUT_STDOUT=outfile)
params.set_option("--genotype", "%(IN_VCFFILE)s")
params.set_option("--intervals", "%(IN_INTERVALS)s")
if interval.get("Protein coding"):
params.set_option("--whole-codon-indels-only")
if not interval.get("Indels"):
params.set_option("--ignore-indels")
return {"command": params}
def customize(cls, reference, infile, outfile, filters, options, dependencies = ()):
# filter reads
percentile = str(options.makefile['vcf_percentile_threshold'])
flt = AtomicCmdBuilder(['vcf_qual_percentile'],
IN_VCF = infile,
OUT_VCF = outfile
)
for key,val in filters.items():
flt.add_option(key,val)
flt.set_option('--out','%(OUT_VCF)s')
flt.add_option(infile)
return {
'commands':{
'Filter': flt
}
}
def customize(cls, input_alignment, output_tree, dependencies=()):
"""
Arguments:
input_alignment -- An alignment file in a format readable by RAxML.
output_tree -- Filename for the output newick tree."""
command = AtomicCmdBuilder("parsimonator", set_cwd=True)
command.set_option("-s", "%(TEMP_OUT_ALN)s")
command.set_option("-n", "output")
# Random seed for the stepwise addition process
command.set_option("-p", int(random.random() * 2**31 - 1), fixed=False)
command.set_kwargs( # Auto-delete: Symlinks
TEMP_OUT_ALN=os.path.basename(input_alignment),
# Input files, are not used directly (see below)
IN_ALIGNMENT=input_alignment,
# Final output file, are not created directly
OUT_TREE=output_tree)
return {"command": command}
def customize(cls, infile, intervals, outfile, dependencies=()):
params = AtomicCmdBuilder(["bam_sample_regions"],
IN_PILEUP=infile,
IN_INTERVALS=intervals,
OUT_STDOUT=outfile)
params.set_option("--genotype", "%(IN_PILEUP)s")
params.set_option("--intervals", "%(IN_INTERVALS)s")
return {"command": params}
def test_builder__set_kwargs__after_finalize():
expected = {"IN_PATH": "/a/b/"}
builder = AtomicCmdBuilder("echo")
builder.set_kwargs(IN_PATH="/a/b/")
builder.finalize()
assert_raises(AtomicCmdBuilderError,
builder.set_kwargs,
OUT_PATH="/dst/file")
assert_equal(builder.kwargs, expected)
def customize(cls, input_file, output_file, algorithm = "auto", dependencies = ()):
command = AtomicCmdBuilder(_PRESETS[algorithm.lower()])
command.add_value("%(IN_FASTA)s")
command.set_kwargs(IN_FASTA = input_file,
OUT_STDOUT = output_file,
CHECK_VERSION = MAFFT_VERSION)
return {"command" : command,
"dependencies" : dependencies}
def customize(cls, reference, in_bam, in_vcf, outfile, dependencies=()):
unicat = AtomicCmdBuilder(["unicat", "%(IN_VCF)s"],
IN_VCF=in_vcf,
OUT_STDOUT=AtomicCmd.PIPE)
vcfpileup = AtomicCmdBuilder(["vcf_create_pileup", "%(OUT_PILEUP)s"],
IN_REF=reference,
IN_BAM=in_bam,
IN_STDIN=unicat,
OUT_PILEUP=outfile,
OUT_TBI=outfile + ".tbi")
vcfpileup.add_value("%(IN_BAM)s")
vcfpileup.set_option("-f", "%(IN_REF)s")
return {"commands": {"unicat": unicat, "pileup": vcfpileup}}
def customize(cls, input_alignment, output_tree, dependencies = ()):
"""
Arguments:
input_alignment -- An alignment file in a format readable by RAxML.
output_tree -- Filename for the output newick tree."""
command = AtomicCmdBuilder("parsimonator", set_cwd = True)
command.set_option("-s", "%(TEMP_OUT_ALN)s")
command.set_option("-n", "output")
# Random seed for the stepwise addition process
command.set_option("-p", int(random.random() * 2**31 - 1), fixed = False)
command.set_kwargs(# Auto-delete: Symlinks
TEMP_OUT_ALN = os.path.basename(input_alignment),
# Input files, are not used directly (see below)
IN_ALIGNMENT = input_alignment,
# Final output file, are not created directly
OUT_TREE = output_tree)
return {"command" : command}
def customize(self,
config,
reference,
input_files,
output_directory,
title="mapDamage",
dependencies=()):
command = AtomicCmdBuilder(
[
"mapDamage",
"--no-stats",
# Prevent references with many contigs from using excessive
# amounts of memory, at the cost of per-contig statistics:
"--merge-reference-sequences",
"-t",
title,
"-i",
"%(TEMP_IN_BAM)s",
"-d",
"%(TEMP_DIR)s",
"-r",
"%(IN_REFERENCE)s"
],
IN_REFERENCE=reference,
OUT_FREQ_3p=os.path.join(output_directory, "3pGtoA_freq.txt"),
OUT_FREQ_5p=os.path.join(output_directory, "5pCtoT_freq.txt"),
OUT_COMP_USER=os.path.join(output_directory, "dnacomp.txt"),
OUT_PLOT_FRAG=os.path.join(output_directory,
"Fragmisincorporation_plot.pdf"),
OUT_PLOT_LEN=os.path.join(output_directory, "Length_plot.pdf"),
OUT_LENGTH=os.path.join(output_directory, "lgdistribution.txt"),
OUT_MISINCORP=os.path.join(output_directory,
"misincorporation.txt"),
OUT_LOG=os.path.join(output_directory, "Runtime_log.txt"),
TEMP_OUT_STDOUT="pipe_mapDamage.stdout",
TEMP_OUT_STDERR="pipe_mapDamage.stderr",
CHECK_RSCRIPT=RSCRIPT_VERSION,
CHECK_MAPDAMAGE=MAPDAMAGE_VERSION)
return {
"command": command,
"config": config,
"input_files": input_files,
"dependencies": dependencies
}
def __init__(self, config, reference, input_bam, output_bam, tags,
min_mapq=0, filter_unmapped=False, dependencies=()):
flt_params = AtomicCmdBuilder(("samtools", "view", "-bu"),
IN_BAM=input_bam,
OUT_STDOUT=AtomicCmd.PIPE)
if min_mapq:
flt_params.set_option("-q", min_mapq, sep="")
if filter_unmapped:
flt_params.set_option("-F", "0x4", sep="")
flt_params.add_value("%(IN_BAM)s")
jar_params = picard.picard_command(config, "AddOrReplaceReadGroups")
jar_params.set_option("INPUT", "/dev/stdin", sep="=")
# Output is written to a named pipe, since the JVM may, in some cases,
# emit warning messages to stdout, resulting in a malformed BAM.
jar_params.set_option("OUTPUT", "%(TEMP_OUT_BAM)s", sep="=")
jar_params.set_option("COMPRESSION_LEVEL", "0", sep="=")
# Ensure that the BAM is sorted; this is required by the pipeline, and
# needs to be done before calling calmd (avoiding pathologic runtimes).
jar_params.set_option("SORT_ORDER", "coordinate", sep="=")
# All tags are overwritten; ID is set since the default (e.g. '1')
# causes problems with pysam due to type inference (is read as a length
# 1 string, but written as a character).
for tag in ("ID", "SM", "LB", "PU", "PL"):
jar_params.set_option(tag, tags[tag], sep="=")
jar_params.set_kwargs(IN_STDIN=flt_params,
TEMP_OUT_BAM="bam.pipe")
calmd = AtomicCmdBuilder(["samtools", "calmd", "-b",
"%(TEMP_IN_BAM)s", "%(IN_REF)s"],
IN_REF=reference,
TEMP_IN_BAM="bam.pipe",
OUT_STDOUT=output_bam)
commands = [cmd.finalize() for cmd in (flt_params, jar_params, calmd)]
description = "<Cleanup BAM: %s -> '%s'>" \
% (input_bam, output_bam)
PicardNode.__init__(self,
command=ParallelCmds(commands),
description=description,
dependencies=dependencies)
def customize(cls, pileup, infile, outfile, regions, dependencies=()):
cat = factory.new("cat")
cat.add_value("%(IN_VCF)s")
cat.set_kwargs(IN_VCF=infile,
OUT_STDOUT=AtomicCmd.PIPE)
vcffilter = factory.new("vcf_filter")
vcffilter.add_option("--pileup", "%(IN_PILEUP)s")
for contig in regions["HomozygousContigs"]:
vcffilter.add_option("--homozygous-chromosome", contig)
vcffilter.set_kwargs(IN_PILEUP=pileup,
IN_STDIN=cat,
OUT_STDOUT=AtomicCmd.PIPE)
bgzip = AtomicCmdBuilder(["bgzip"],
IN_STDIN=vcffilter,
OUT_STDOUT=outfile)
return {"commands": {"cat": cat,
"filter": vcffilter,
"bgzip": bgzip}}
def _get_common_parameters(version):
if version == VERSION_14:
version_check = _VERSION_14_CHECK
elif version == VERSION_15:
version_check = _VERSION_15_CHECK
else:
raise CmdError("Unknown version: %s" % version)
cmd = AtomicCmdBuilder("AdapterRemoval", CHECK_VERSION=version_check)
# Trim Ns at read ends
cmd.set_option("--trimns", fixed=False)
# Trim low quality scores
cmd.set_option("--trimqualities", fixed=False)
return cmd
def customize(cls, pileup, infile, outfile, interval, dependencies=()):
unicat = AtomicCmdBuilder(["unicat", "%(IN_VCF)s"],
IN_VCF=infile,
OUT_STDOUT=AtomicCmd.PIPE)
vcffilter = AtomicCmdBuilder(
["vcf_filter", "--pileup", "%(IN_PILEUP)s"],
IN_PILEUP=pileup,
IN_STDIN=unicat,
OUT_STDOUT=AtomicCmd.PIPE)
for contig in interval.get("Homozygous Contigs", ()):
vcffilter.set_option("--homozygous-chromosome", contig)
bgzip = AtomicCmdBuilder(["bgzip"],
IN_STDIN=vcffilter,
OUT_STDOUT=outfile)
return {
"commands": {
"unicat": unicat,
"filter": vcffilter,
"bgzip": bgzip
}
}
def test_builder__set_option__overwrite():
builder = AtomicCmdBuilder("find")
builder.set_option("-name", "*.txt", fixed=False)
builder.set_option("-name", "*.bat")
assert_equal(builder.call, ["find", "-name", "*.bat"])
def test_builder__set_kwargs__called_twice():
expected = {"IN_PATH" : "/a/b/", "OUT_PATH" : "/dst/file"}
builder = AtomicCmdBuilder("echo")
builder.set_kwargs(OUT_PATH = "/dst/file")
builder.set_kwargs(IN_PATH = "/a/b/")
assert_equal(builder.kwargs, expected)
def test_builder__set_option():
builder = AtomicCmdBuilder("find")
builder.set_option("-name", "*.txt")
assert_equal(builder.call, ["find", "-name", "*.txt"])
def test_builder__set_option__overwrite():
builder = AtomicCmdBuilder("find")
builder.set_option("-name", "*.txt", fixed = False)
builder.set_option("-name", "*.bat")
assert_equal(builder.call, ["find", "-name", "*.bat"])
def test_builder__set_option__overwrite_fixed():
builder = AtomicCmdBuilder("find")
builder.set_option("-name", "*.txt")
assert_raises(AtomicCmdBuilderError, builder.set_option, "-name", "*.bat")
def customize(cls, input_alignment, input_partition, template, start = 0, bootstraps = 50, dependencies = ()):
command = AtomicCmdBuilder("raxmlHPC", set_cwd = True)
# Read and (in the case of empty columns) reduce input
command.set_option("-f", "j")
# Output files are saved with a .Pypeline postfix, and subsequently renamed
command.set_option("-n", "Pypeline")
# Model required, but not used
command.set_option("-m", "GTRGAMMA")
# Set random seed for bootstrap generation. May be set to a fixed value to allow replicability.
command.set_option("-b", int(random.random() * 2**31 - 1), fixed = False)
# Generate a single bootstrap alignment (makes growing the number of bootstraps easier).
command.set_option("-N", int(bootstraps), fixed = False)
# Symlink to sequence and partitions, to prevent the creation of *.reduced files outside temp folder
# In addition, it may be nessesary to remove the .reduced files if created
command.set_option("-s", "input.alignment")
command.set_option("-q", "input.partition")
bootstrap_files = {"IN_ALIGNMENT" : input_alignment,
"IN_PARTITION" : input_partition,
"TEMP_OUT_INF" : "RAxML_info.Pypeline",
"TEMP_OUT_ALN" : "input.alignment",
"TEMP_OUT_PAR" : "input.partition",
"CHECK_VERSION": RAXML_VERSION}
for (index, (_, filename)) in enumerate(cls._bootstraps(template, bootstraps, start)):
bootstrap_files["OUT_BS_%03i" % index] = filename
command.set_kwargs(**bootstrap_files)
return {"command" : command}
def customize(cls, input_alignment, input_partition, output_template, threads = 1, dependencies = ()):
"""
Arguments:
input_alignment -- An alignment file in a format readable by RAxML.
input_partition -- A set of partitions in a format readable by RAxML.
output_template -- A template string used to construct final filenames. Should consist
of a full path, including a single '%s', which is replaced with the
variable part of RAxML output files (e.g. 'info', 'bestTree', ...).
Example destination: '/disk/project/SN013420.RAxML.%s'
Example output: '/disk/project/SN013420.RAxML.bestTree'"""
if threads > 1:
command = AtomicCmdBuilder("raxmlHPC-PTHREADS")
command.set_option("-T", threads)
version = RAXML_PTHREADS_VERSION
else:
command = AtomicCmdBuilder("raxmlHPC")
version = RAXML_VERSION
# Perform rapid bootstrapping
command.set_option("-f", "a")
# Output files are saved with a .Pypeline postfix, and subsequently renamed
command.set_option("-n", "Pypeline")
# Ensures that output is saved to the temporary directory
command.set_option("-w", "%(TEMP_DIR)s")
# Symlink to sequence and partitions, to prevent the creation of *.reduced files outside temp folder
# In addition, it may be nessesary to remove the .reduced files if created
command.set_option("-s", "%(TEMP_OUT_ALN)s")
command.set_option("-q", "%(TEMP_OUT_PART)s")
command.set_kwargs(# Auto-delete: Symlinks and .reduced files that RAxML may generate
TEMP_OUT_PART = os.path.basename(input_partition),
TEMP_OUT_PART_R = os.path.basename(input_partition) + ".reduced",
TEMP_OUT_ALN = os.path.basename(input_alignment),
TEMP_OUT_ALN_R = os.path.basename(input_alignment) + ".reduced",
# Input files, are not used directly (see below)
IN_ALIGNMENT = input_alignment,
IN_PARTITION = input_partition,
# Final output files, are not created directly
OUT_INFO = output_template % "info",
OUT_BESTTREE = output_template % "bestTree",
OUT_BOOTSTRAP = output_template % "bootstrap",
OUT_BIPART = output_template % "bipartitions",
OUT_BIPARTLABEL = output_template % "bipartitionsBranchLabels",
CHECK_VERSION = version)
# Use the GTRGAMMAI model of NT substitution by default
command.set_option("-m", "GTRGAMMAI", fixed = False)
# Enable Rapid Boostrapping and set random seed. May be set to a fixed value to allow replicability.
command.set_option("-x", int(random.random() * 2**31 - 1), fixed = False)
# Set random seed for parsimony inference. May be set to a fixed value to allow replicability.
command.set_option("-p", int(random.random() * 2**31 - 1), fixed = False)
# Terminate bootstrapping upon convergence, rather than after a fixed number of repetitions
command.set_option("-N", "autoMRE", fixed = False)
return {"command" : command}
def customize(cls, input_alignment, input_partitions, output_tree, dependencies = ()):
command = AtomicCmdBuilder("raxmlHPC")
# Compute a randomized parsimony starting tree
command.set_option("-y")
# Output files are saved with a .Pypeline postfix, and subsequently renamed
command.set_option("-n", "Pypeline")
# Model required, but not used
command.set_option("-m", "GTRGAMMA")
# Ensures that output is saved to the temporary directory
command.set_option("-w", "%(TEMP_DIR)s")
# Set random seed for bootstrap generation. May be set to a fixed value to allow replicability.
command.set_option("-p", int(random.random() * 2**31 - 1), fixed = False)
# Symlink to sequence and partitions, to prevent the creation of *.reduced files outside temp folder
command.set_option("-s", "%(TEMP_OUT_ALIGNMENT)s")
command.set_option("-q", "%(TEMP_OUT_PARTITION)s")
command.set_kwargs(IN_ALIGNMENT = input_alignment,
IN_PARTITION = input_partitions,
# TEMP_OUT_ is used to automatically remove these files
TEMP_OUT_ALIGNMENT = "RAxML_alignment",
TEMP_OUT_PARTITION = "RAxML_partitions",
TEMP_OUT_INFO = "RAxML_info.Pypeline",
OUT_TREE = output_tree,
CHECK_VERSION = RAXML_VERSION)
return {"command" : command}
def customize(cls, input_alignment, input_partition, output_file, dependencies = ()):
"""
Arguments:
input_alignment -- An alignment file in a format readable by RAxML.
input_partition -- A set of partitions in a format readable by RAxML.
output_filename -- Filename for the output binary sequence."""
command = AtomicCmdBuilder("examlParser", set_cwd = True)
command.set_option("-s", "%(TEMP_OUT_ALN)s")
command.set_option("-q", "%(TEMP_OUT_PART)s")
# Output file will be named output.binary, and placed in the CWD
command.set_option("-n", "output")
# Substitution model
command.set_option("-m", "DNA", fixed = False)
command.set_kwargs(# Auto-delete: Symlinks
TEMP_OUT_PART = os.path.basename(input_partition),
TEMP_OUT_ALN = os.path.basename(input_alignment),
# Input files, are not used directly (see below)
IN_ALIGNMENT = input_alignment,
IN_PARTITION = input_partition,
# Final output file, are not created directly
OUT_BINARY = output_file,
CHECK_EXAML = PARSER_VERSION)
return {"command" : command}
def customize(cls, input_alignment, input_partition, output_alignment, output_partition, dependencies = ()):
command = AtomicCmdBuilder("raxmlHPC")
# Read and (in the case of empty columns) reduce input
command.set_option("-f", "c")
# Output files are saved with a .Pypeline postfix, and subsequently renamed
command.set_option("-n", "Pypeline")
# Model required, but not used
command.set_option("-m", "GTRGAMMA")
# Ensures that output is saved to the temporary directory
command.set_option("-w", "%(TEMP_DIR)s")
# Symlink to sequence and partitions, to prevent the creation of *.reduced files outside temp folder
# In addition, it may be nessesary to remove the .reduced files if created
command.set_option("-s", "%(TEMP_IN_ALIGNMENT)s")
command.set_option("-q", "%(TEMP_IN_PARTITION)s")
command.set_kwargs(IN_ALIGNMENT = input_alignment,
IN_PARTITION = input_partition,
TEMP_IN_ALIGNMENT = "RAxML_alignment",
TEMP_IN_PARTITION = "RAxML_partitions",
TEMP_OUT_INFO = "RAxML_info.Pypeline",
OUT_ALIGNMENT = output_alignment,
OUT_PARTITION = output_partition,
CHECK_VERSION = RAXML_VERSION)
return {"command" : command}
def test_builder__kwargs__set_cwd():
builder = AtomicCmdBuilder(["ls"], set_cwd=True)
assert_equal(builder.kwargs, {"set_cwd": True})
def test_builder__set_option():
builder = AtomicCmdBuilder("find")
builder.set_option("-name", "*.txt")
assert_equal(builder.call, ["find", "-name", "*.txt"])
def test_builder__set__kwargs__overwriting():
expected = {"IN_PATH" : "/a/b/"}
builder = AtomicCmdBuilder("echo")
builder.set_kwargs(IN_PATH = "/a/b/")
assert_raises(AtomicCmdBuilderError, builder.set_kwargs, IN_PATH = "/dst/file")
assert_equal(builder.kwargs, expected)
def test_builder__set_option__overwrite_fixed():
builder = AtomicCmdBuilder("find")
builder.set_option("-name", "*.txt")
assert_raises(AtomicCmdBuilderError, builder.set_option, "-name", "*.bat")
def test_builder__finalize__returns_singleton():
builder = AtomicCmdBuilder("echo")
assert builder.finalize() is builder.finalize()
