def __init__(self, path="", max_threads=4, tmp_dir=None):
"""
Spliting sra into forward and reverse fastqs is default now.
Here are some important differences to fastq-dump:
The -Z|--stdout option does not work for split-3 and split-files. The tool will fall back to producing files in these cases.
There is no --gzip|--bizp2 option, you have to compress your files explicitly after they have been written.
There is no -A option for the accession; just specify the accession or the absolute path directly.
fasterq-dump does not take multiple accessions, just one.
There is no -N|--minSpotId and no -X|--maxSpotId option. fasterq-dump version 2.9.1 processes always the whole accession, although it may support partial access in future versions.
fasterq-dump.2.9.1 was released only on Linux platforms, and is intended primarily for use under larger installations. Our next release should be available for Windows and MacOS.
:param path:
:param max_threads:
"""
Tool.__init__(self,
"fasterq-dump",
path=path,
max_threads=max_threads,
tmp_dir=tmp_dir)
def __init__(self, max_threads=4, max_memory=None, timelog=None):
Tool.__init__(self,
"gatk --java-options -Xmx%s CombineVariants" %
max_memory if max_memory else "gatk CombineVariants",
max_threads=max_threads,
max_memory=max_memory,
timelog=timelog)
def __init__(self, max_threads=4, max_memory=None, timelog=None):
Tool.__init__(self,
"gatk --java-options -Xmx%s BaseRecalibrator" %
max_memory if max_memory else "gatk BaseRecalibrator",
max_threads=max_threads,
max_memory=max_memory,
timelog=timelog)
def __init__(self, path="", max_threads=4):
Tool.__init__(self, "run_BUSCO.py", path=path, max_threads=max_threads)
self.kingdoms = ["euk", "bac", "mito", "arc"]
self.status_list = ["Complete",
"Duplicated",
"Fragmented",
"Missing"]
def __init__(self, max_threads=1, max_memory=10, workdir="./"):
Tool.__init__(self,
cmd="",
max_threads=max_threads,
max_memory=max_memory)
self.workdir = workdir
self.dirs = None
def __init__(self, max_threads=4, max_memory=None, timelog=None):
Tool.__init__(
self,
"gatk --java-options -Xmx%s FastaAlternateReferenceMaker" %
max_memory if max_memory else "gatk FastaAlternateReferenceMaker",
max_threads=max_threads,
max_memory=max_memory,
timelog=timelog)
def __init__(self, path="", max_threads=4, max_memory="100G", max_per_thread_memory="5G"):
Tool.__init__(self, "plink", path=path, max_threads=max_threads, max_memory=max_memory, max_per_thread_memory=max_per_thread_memory)
# constants for PLINK bed file
self.samples_per_byte = 4
self.signature_byte_number = 3
# constans for PLINK bim file
self.allel_columns_in_bim_file = (4, 5)
def __init__(self, path="", max_threads=4):
Tool.__init__(self, "last", path=path, max_threads=max_threads)
self.sequence_order_dict = {
"input": "0",
"name": "1",
"length": "2",
"alignment": "3"
}
def __init__(self,
path="",
max_threads=4,
max_memory="100G",
max_per_thread_memory="5G"):
Tool.__init__(self,
"plink",
path=path,
max_threads=max_threads,
max_memory=max_memory,
max_per_thread_memory=max_per_thread_memory)
def __init__(self, path="", max_threads=4):
"""
USAGE
dustmasker [-h] [-help] [-xmlhelp] [-in input_file_name]
[-out output_file_name] [-window window_size] [-level level]
[-linker linker] [-infmt input_format] [-outfmt output_format]
[-parse_seqids] [-version-full]
DESCRIPTION
Low complexity region masker based on Symmetric DUST algorithm
OPTIONAL ARGUMENTS
-h
Print USAGE and DESCRIPTION; ignore all other parameters
-help
Print USAGE, DESCRIPTION and ARGUMENTS; ignore all other parameters
-xmlhelp
Print USAGE, DESCRIPTION and ARGUMENTS in XML format; ignore all other
parameters
-in <File_In>
input file name
Default = `-'
-out <File_Out>
output file name
Default = `-'
-window <Integer>
DUST window length
Default = `64'
-level <Integer>
DUST level (score threshold for subwindows)
Default = `20'
-linker <Integer>
DUST linker (how close masked intervals should be to get merged together).
Default = `1'
-infmt <String>
input format (possible values: fasta, blastdb)
Default = `fasta'
-outfmt <String, `acclist', `fasta', `interval', `maskinfo_asn1_bin',
`maskinfo_asn1_text', `maskinfo_xml', `seqloc_asn1_bin',
`seqloc_asn1_text', `seqloc_xml'>
output format
Default = `interval'
-parse_seqids
Parse Seq-ids in FASTA input
-version-full
Print extended version data; ignore other arguments
"""
Tool.__init__(self, "dustmasker", path=path, max_threads=max_threads)
def __init__(self, path="", max_threads=4):
Tool.__init__(self, "samtools", path=path, max_threads=max_threads)
# bam/sam flag values:
self.bam_flags = {
"read_paired": 1,
"read_mapped_in_proper_pair": 2,
"read_unmapped": 4,
"mate_unmapped": 8,
"read_reverse_strand": 16,
"mate_reverse_strand": 32,
"first_in_pair": 64,
"second_in_pair": 128,
"not_primary_alignment": 256,
"read_fails_platform/vendor_quality_checks": 512,
"read_is_PCR_or_optical_duplicate": 1024,
"supplementary_alignment": 2048
}
def __init__(self, path="", max_threads=1):
Tool.__init__(self, "RepeatModeler", path=path, max_threads=max_threads)
def __init__(self, path="", max_threads=4):
Tool.__init__(self,
"bedtools getfasta",
path=path,
max_threads=max_threads)
def __init__(self, path="", max_threads=4):
Tool.__init__(self, "TransDecoder", path=path, max_threads=max_threads)
def __init__(self, path="", max_threads=4):
Tool.__init__(self, "featureCounts", path=path, max_threads=max_threads)
def __init__(self, path="", max_threads=4):
Tool.__init__(self,
"bam clipOverlap",
path=path,
max_threads=max_threads)
def __init__(self, path="", max_threads=4):
Tool.__init__(self, "exonerate", path=path, max_threads=max_threads)
def __init__(self, path="", max_threads=4):
Tool.__init__(self,
"SSPACE_Standard_v3.0.pl",
path=path,
max_threads=max_threads)
def __init__(self, path="", max_threads=4):
Tool.__init__(self, "raxml", path=path, max_threads=max_threads)
def __init__(self, max_threads=4, max_memory=None, timelog=None):
Tool.__init__(self,
"gatk CombineGVCFs",
max_threads=max_threads,
max_memory=max_memory,
timelog=timelog)
def __init__(self, path="", max_threads=4):
Tool.__init__(self,
"bedtools bamtofastq",
path=path,
max_threads=max_threads)
def __init__(self, max_threads=4, max_memory=None, timelog=None):
Tool.__init__(self,
"GenomeAnalysisTK.jar -T ValidateVariants",
max_threads=max_threads,
max_memory=max_memory,
timelog=timelog)
def __init__(self, path="", max_threads=4):
Tool.__init__(self, "bowtie2", path=path, max_threads=max_threads)
def __init__(self, path="", max_threads=4):
Tool.__init__(self, "blastall", path=path, max_threads=max_threads)
def __init__(self, path="", max_threads=4):
Tool.__init__(self, "codeml", path=path, max_threads=max_threads)
self.example = """
def __init__(self, path="", max_threads=4):
Tool.__init__(self, "convert", path=path, max_threads=max_threads)
def __init__(self, path="", max_threads=1):
Tool.__init__(self, "V2_trim.exe", path=path, max_threads=max_threads)
def __init__(self, path="", max_threads=4):
Tool.__init__(self, "glistmaker", path=path, max_threads=max_threads)
def __init__(self, path="", max_threads=4):
Tool.__init__(self, "SWAMP.py", path=path, max_threads=max_threads)
def __init__(self, path="", max_threads=4):
Tool.__init__(self, "mcmctree", path=path, max_threads=max_threads)
self.example = """
