def __init__(self, config, reference, intervals, infiles, outfile,
dependencies=()):
self._basename = os.path.basename(outfile)
infiles = safe_coerce_to_tuple(infiles)
jar_file = os.path.join(config.jar_root, "GenomeAnalysisTK.jar")
command = AtomicJavaCmdBuilder(jar_file,
jre_options=config.jre_options)
command.set_option("-T", "IndelRealigner")
command.set_option("-R", "%(IN_REFERENCE)s")
command.set_option("-targetIntervals", "%(IN_INTERVALS)s")
command.set_option("-o", "%(OUT_BAMFILE)s")
command.set_option("--bam_compression", 0)
command.set_option("--disable_bam_indexing")
_set_input_files(command, infiles)
command.set_kwargs(IN_REFERENCE=reference,
IN_REF_DICT=fileutils.swap_ext(reference, ".dict"),
IN_INTERVALS=intervals,
OUT_BAMFILE=outfile,
CHECK_GATK=_get_gatk_version_check(config))
calmd = AtomicCmd(["samtools", "calmd", "-b",
"%(TEMP_IN_BAM)s", "%(IN_REF)s"],
TEMP_IN_BAM=self._basename,
IN_REF=reference,
TEMP_OUT_STDOUT=self._basename + ".calmd",
CHECK_VERSION=SAMTOOLS_VERSION)
description = "<Indel Realigner (aligning): %s -> %r>" \
% (describe_files(infiles), outfile)
CommandNode.__init__(self,
description=description,
command=ParallelCmds([command.finalize(), calmd]),
dependencies=dependencies)
def __init__(self, parameters):
commands = [parameters.commands['VariantRecal'].finalize()]
description = "<Variant Recalibrator: {}".format(os.path.basename(parameters.model_name))
CommandNode.__init__(self,
description = description,
command = ParallelCmds(commands),
dependencies = parameters.dependencies)
def __init__(self, parameters):
self._kwargs = parameters.command.paths
CommandNode.__init__(self,
command = parameters.command.finalize(),
description = "<RAxMLReduce: '%s' -> '%s'>" \
% (parameters.input_alignment, parameters.output_alignment),
dependencies = parameters.dependencies)
def __init__(self, parameters):
commands = [parameters.commands['Filter'].finalize()]
description = "<Variant Filter: {}".format(os.path.basename(parameters.outfile))
CommandNode.__init__(self,
description = description,
command = ParallelCmds(commands),
dependencies = parameters.dependencies)
def __init__(self, config, d_make, bedn, mappa, unique, dependencies=()):
inbedfile = d_make.bedfiles[bedn]
basename, extension = os.path.splitext(os.path.basename(inbedfile))
bname = "{}_MappaOnly{}".format(basename, extension)
dest = os.path.join(config.temp_local, bname)
d_make.bedfiles[bedn] = dest
call1 = [
"python",
os.path.join(PREFIX, "intersectmappabed.py"), "%(IN_BED)s",
"%(IN_MAPPA)s",
str(unique), "%(OUT_DEST)s"
]
cmd = AtomicCmd(call1,
IN_BED=inbedfile,
IN_MAPPA=mappa,
OUT_DEST=dest,
CHECK_VERSION=PYTHON_VERSION)
description = ("<CLEANBEDFILES: '%s' -> '%s', Uniqueness: '%s'>" %
(inbedfile, dest, unique))
CommandNode.__init__(self,
description=description,
command=cmd,
dependencies=dependencies)
def __init__(self,
infile,
outfile,
genome,
from_start=0,
from_end=0,
strand_relative=False,
dependencies=()):
if type(from_start) != type(from_end):
raise ValueError(
"'from_start' and 'from_end' should be of same type!")
call = [
"slopBed", "-i", "%(IN_FILE)s", "-g", "%(IN_GENOME)s", "-l",
str(from_start), "-r",
str(from_end)
]
if strand_relative:
call.append("-s")
if type(from_start) is float:
call.append("-pct")
command = AtomicCmd(call,
IN_FILE=infile,
IN_GENOME=genome,
OUT_STDOUT=outfile)
description = "<SlopBed: '%s' -> '%s'>" % (infile, outfile)
CommandNode.__init__(self,
description=description,
command=command,
dependencies=dependencies)
def __init__(self, parameters):
description = "<Merge BAMs: %i file(s) -> '%s'>" \
% (len(parameters.input_bams), parameters.output_bam)
CommandNode.__init__(self,
command=parameters.command.finalize(),
description=description,
dependencies=parameters.dependencies)
def __init__(self, parameters):
commands = [parameters.commands['merge'].finalize()]
description = "<Variant Merge Node"
CommandNode.__init__(self,
description = description,
command = ParallelCmds(commands),
dependencies = parameters.dependencies)
def __init__(self, parameters):
description = "<MarkDuplicates: %s>" % (describe_files(
parameters.input_bams), )
CommandNode.__init__(self,
command=parameters.command.finalize(),
description=description,
dependencies=parameters.dependencies)
def __init__(self, parameters):
commands = [parameters.commands[key].finalize() for key in ('pileup','bcftools')]
description = "<Samtools VariantCaller : {}".format(os.path.basename(parameters.outfile))
CommandNode.__init__(self,
description = description,
command = ParallelCmds(commands),
dependencies = parameters.dependencies)
def __init__(self, config, reference, input_files, output_directory,
dependencies):
cat_cmds, cat_obj = concatenate_input_bams(config, input_files)
cmd_map = AtomicCmd(
[
"mapDamage", "--no-stats", "-n", _MAPDAMAGE_MAX_READS, "-i",
"-", "-d", "%(TEMP_DIR)s", "-r", reference
],
IN_STDIN=cat_obj,
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"),
CHECK_VERSION=MAPDAMAGE_VERSION)
description = "<mapDamage: %i file(s) -> '%s'>" % (len(input_files),
output_directory)
CommandNode.__init__(self,
command=ParallelCmds(cat_cmds + [cmd_map]),
description=description,
dependencies=dependencies)
def __init__(self, config, reference, input_files, output_file,
dependencies):
cat_cmds, cat_obj = concatenate_input_bams(config, input_files)
cmd_map = AtomicCmd([
"mapDamage", "-n", _MAPDAMAGE_MAX_READS, "-i", "-", "-d",
"%(TEMP_DIR)s", "-r", reference
],
IN_STDIN=cat_obj,
CHECK_VERSION=MAPDAMAGE_VERSION)
train_cmds = ParallelCmds(cat_cmds + [cmd_map])
cat_cmds, cat_obj = concatenate_input_bams(config, input_files)
cmd_scale = AtomicCmd([
"mapDamage", "--rescale-only", "-n", _MAPDAMAGE_MAX_READS, "-i",
"-", "-d", "%(TEMP_DIR)s", "-r", reference, "--rescale-out",
"%(OUT_BAM)s"
],
IN_STDIN=cat_obj,
OUT_BAM=output_file,
CHECK_VERSION=MAPDAMAGE_VERSION)
rescale_cmds = ParallelCmds(cat_cmds + [cmd_scale])
description = "<mapDamageRescale: %i file(s) -> '%s'>" % (
len(input_files), output_file)
CommandNode.__init__(self,
command=SequentialCmds([train_cmds,
rescale_cmds]),
description=description,
dependencies=dependencies)
def __init__(self, parameters):
self._directory = parameters.directory
description = "<mapDamage (model): %r>" % (parameters.directory, )
CommandNode.__init__(self,
command=parameters.command.finalize(),
description=description,
dependencies=parameters.dependencies)
def __init__(self, parameters):
command = parameters.command.finalize()
description = "<Bowtie2 Index '%s' -> '%s.*'>" % (
parameters.input_file, parameters.prefix)
CommandNode.__init__(self,
command=command,
description=description,
dependencies=parameters.dependencies)
def __init__(self, parameters):
command = parameters.command.finalize()
description = "<BuildRegions: '%s' -> '%s'>" % (parameters.infile,
parameters.outfile)
CommandNode.__init__(self,
description=description,
command=command,
dependencies=parameters.dependencies)
def __init__(self, parameters):
commands = [parameters.commands['Snp'].finalize()]
description = "<SNP List Generator Node>"
CommandNode.__init__(self,
description = description,
command = ParallelCmds(commands),
dependencies = parameters.dependencies
)
def __init__(self, parameters):
commands = [parameters.commands[key].finalize() for key in ("pileup", "genotype", "bgzip")]
description = "<Genotyper: '%s' -> '%s'>" % (parameters.infile,
parameters.outfile)
CommandNode.__init__(self,
description = description,
command = ParallelCmds(commands),
dependencies = parameters.dependencies)
def __init__(self, parameters):
self._version = parameters.version
self._basename = parameters.basename
if len(parameters.input_files_1) != len(parameters.input_files_2):
raise CmdError("Number of mate 1 files differ from mate 2 files: %i != %i" \
% (len(parameters.input_files_1),
len(parameters.input_files_2)))
zcat_pair_1 = _build_unicat_command(parameters.input_files_1,
"uncompressed_input_1")
zcat_pair_2 = _build_unicat_command(parameters.input_files_2,
"uncompressed_input_2")
zip_pair_1 = _build_zip_command(parameters.output_format,
parameters.output_prefix,
".pair1.truncated")
zip_pair_2 = _build_zip_command(parameters.output_format,
parameters.output_prefix,
".pair2.truncated")
zip_discarded = _build_zip_command(parameters.output_format,
parameters.output_prefix,
".discarded")
adapterrm = parameters.command.finalize()
commands = [adapterrm, zip_pair_1, zip_pair_2]
if parameters.version == VERSION_15:
zip_aln = _build_zip_command(parameters.output_format,
parameters.output_prefix,
".collapsed")
zip_aln_trunc = _build_zip_command(parameters.output_format,
parameters.output_prefix,
".collapsed.truncated")
zip_unaligned = _build_zip_command(parameters.output_format,
parameters.output_prefix,
".singleton.truncated")
commands += [zip_aln, zip_aln_trunc, zip_unaligned]
else:
zip_aln = _build_zip_command(parameters.output_format,
parameters.output_prefix,
".singleton.aln.truncated")
zip_unaligned = _build_zip_command(parameters.output_format,
parameters.output_prefix,
".singleton.unaln.truncated")
commands += [zip_aln, zip_unaligned]
commands += [zip_discarded, zcat_pair_1, zcat_pair_2]
# Opening of pipes block, so the order of these commands is dependent upon
# the order of file-opens in atomiccmd and the the programs themselves.
commands = ParallelCmds(commands)
description = "<PE_AdapterRM: %s -> '%s.*'>" \
% (fileutils.describe_files(parameters.input_files_1).replace("file", "pair"),
parameters.output_prefix)
CommandNode.__init__(self,
command=commands,
description=description,
dependencies=parameters.dependencies)
def __init__(self, parameters):
self._input_alignment = parameters.input_alignment
self._input_partitions = parameters.input_partitions
self._output_tree = parameters.output_tree
CommandNode.__init__(self,
command = parameters.command.finalize(),
description = "<RAxMLParsimonyTree: '%s' -> '%s'>" \
% (parameters.input_alignment, parameters.output_tree),
dependencies = parameters.dependencies)
def __init__(self, parameters):
commands = [
parameters.commands[key].finalize() for key in ("unicat", "pileup")
]
description = "<VCFPileup: '%s' -> '%s'>" % (parameters.in_bam,
parameters.outfile)
CommandNode.__init__(self,
description=description,
command=ParallelCmds(commands),
dependencies=parameters.dependencies)
def __init__(self, infile, dependencies = ()):
cmd_index = AtomicCmd(["samtools", "index", "%(IN_BAM)s", "%(OUT_BAI)s"],
IN_BAM = infile,
OUT_BAI = swap_ext(infile, ".bai"),
CHECK_SAM = SAMTOOLS_VERSION)
CommandNode.__init__(self,
description = "<BAMIndex: '%s'>" % (infile,),
command = cmd_index,
dependencies = dependencies)
def __init__(self, parameters):
self._symlinks = [os.path.realpath(parameters.input_alignment)]
self._output_tree = os.path.basename(parameters.output_tree)
CommandNode.__init__(self,
command = parameters.command.finalize(),
description = "<Parsimonator: '%s' -> '%s'>" \
% (parameters.input_alignment, parameters.output_tree),
dependencies = parameters.dependencies)
def __init__(self, parameters):
self._input_alignment = parameters.input_alignment
self._input_partition = parameters.input_partition
self._output_alignment = os.path.basename(parameters.output_alignment)
CommandNode.__init__(self,
command = parameters.command.finalize(),
description = "<RAxMLBootstrap: '%s' -> '%s'>" \
% (parameters.input_alignment, parameters.output_alignment),
dependencies = parameters.dependencies)
def __init__(self, parameters):
self._output_file = parameters.output_file
description = "<MAFFTNode (%s): '%s' -> '%s'>" \
% (parameters.algorithm,
parameters.input_file,
parameters.output_file)
CommandNode.__init__(self,
command = parameters.command.finalize(),
description = description,
dependencies = parameters.dependencies)
def __init__(self, parameters):
self._template = os.path.basename(parameters.output_template)
CommandNode.__init__(self,
command = parameters.command.finalize(),
description = "<EXaML (%i thread(s)): '%s' -> '%s'>" \
% (parameters.threads,
parameters.input_binary,
parameters.output_template),
threads = parameters.threads,
dependencies = parameters.dependencies)
def __init__(self, parameters):
self._in_vcf = parameters.infile_vcf
command = parameters.command.finalize()
description = "<VCFPileup: '%s' -> '%s'>" \
% (parameters.infile_vcf,
parameters.outfile)
CommandNode.__init__(self,
description=description,
command=command,
dependencies=parameters.dependencies)
def __init__(self, parameters):
_check_bwa_prefix(parameters.prefix)
command = ParallelCmds(
[parameters.commands[key].finalize() for key in parameters.order])
description = "<PE_BWA (%i threads): '%s'>" % (parameters.threads,
parameters.input_file_1)
CommandNode.__init__(self,
command=command,
description=description,
threads=parameters.threads,
dependencies=parameters.dependencies)
def __init__(self, infile, dependencies=()):
self._infile = infile
cmd_faidx = AtomicCmd(["samtools", "faidx", "%(TEMP_IN_FASTA)s"],
TEMP_IN_FASTA=os.path.basename(infile),
IN_FASTA=infile,
OUT_TBI=infile + ".fai",
CHECK_SAM=SAMTOOLS_VERSION)
CommandNode.__init__(self,
description="<FastaIndex: '%s'>" % (infile,),
command=cmd_faidx,
dependencies=dependencies)
def __init__(self, parameters):
self._symlinks = [
os.path.realpath(parameters.input_alignment),
os.path.realpath(parameters.input_partition)
]
self._output_file = os.path.basename(parameters.output_file)
CommandNode.__init__(self,
command = parameters.command.finalize(),
description = "<EXaMLParser: '%s' -> '%s'>" \
% (parameters.input_alignment, parameters.output_file),
dependencies = parameters.dependencies)
def __init__(self, config, input_bams, output_bam, dependencies=()):
cat_cmds, cat_obj = concatenate_input_bams(config, input_bams)
filteruniq = AtomicCmd(["bam_rmdup_collapsed", "--remove-duplicates"],
IN_STDIN=cat_obj,
OUT_STDOUT=output_bam)
command = ParallelCmds(cat_cmds + [filteruniq])
description = "<FilterCollapsedBAM: %s>" % (
describe_files(input_bams), )
CommandNode.__init__(self,
command=command,
description=description,
dependencies=dependencies)
