def __init__(self, path="", max_threads=1): Tool.__init__(self, "repeatmasker", path=path, max_threads=max_threads) self.repeat_classes_used_for_gene_annotation = [ "DNA", "DNA\?", "LINE", "LINE\?", "LTR", "LTR\?", "RC", "RC\?", "Retroposon", "Retroposon\?", "SINE", "SINE\?", "Helitron", "Helitron\?" ]
def __init__(self, path="", max_threads=1): Tool.__init__(self, "repeatmasker", path=path, max_threads=max_threads) self.repeat_classes_used_for_gene_annotation = [ "DNA", "DNA\?", "LINE", "LINE\?", "LTR", "LTR\?", "RC", "RC\?", "Retroposon", "Retroposon\?", "SINE", "SINE\?", "Helitron", "Helitron\?" ] self.repeat_classes_used_for_gene_annotation_expanded_set = self.repeat_classes_used_for_gene_annotation + [ "Unknown", "Other", "ARTEFACT" ]
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, java_path="", max_threads=4, jar_path="", max_memory="1g"): jar = "GenomeAnalysisTK.jar" Tool.__init__(self, "java", path=java_path, max_threads=max_threads, jar_path=jar_path, jar=jar, max_memory=max_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=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, "jellyfish", path=path, max_threads=max_threads)
def __init__(self, path="", max_threads=1): Tool.__init__(self, "cookiecutter", path=path, max_threads=max_threads)
def __init__(self, path="", max_threads=4): Tool.__init__(self, "htseq-count", path=path, max_threads=max_threads)
def __init__(self, path="", max_threads=1): Tool.__init__(self, "facut", path=path, max_threads=max_threads)
def __init__(self, path="", max_threads=1): Tool.__init__(self, "guidance.pl", path=path, max_threads=max_threads)
def __init__(self, path="", max_threads=4): Tool.__init__(self, "blastdbcmd", path=path, max_threads=max_threads)
dest="prefix", help="Prefix of output files") parser.add_argument("-o", "--output_directory", action="store", dest="output_dir", help="Directory to write output files") parser.add_argument("-n", "--num_of_records_per_file", action="store", dest="num_of_records_per_file", type=int, help="Number of sequences per output file") parser.add_argument("-f", "--num_of_out_files", action="store", dest="num_of_out_files", type=int, help="Number of output files") args = parser.parse_args() if args.num_of_records_per_file and args.num_of_out_files: raise ValueError("Options -n and -f can't be set simultaneously") Tool.split_fasta(args.input, args.output_dir, num_of_recs_per_file=args.num_of_records_per_file, num_of_files=args.num_of_out_files, output_prefix=args.prefix)
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=1): Tool.__init__(self, "prank", path=path, max_threads=max_threads)
def __init__(self, path="", max_threads=4): Tool.__init__(self, "cufflinks", path=path, max_threads=max_threads)
def __init__(self, path="", max_threads=4): Tool.__init__(self, "gtf_to_sam", path=path, max_threads=max_threads)
def __init__(self, path="", max_threads=4): Tool.__init__(self, "cuffcompare", path=path, max_threads=max_threads)
def __init__(self, path="", max_threads=1): Tool.__init__(self, "nextclip", 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, "platanus", 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, max_memory=None): Tool.__init__(self, "longranger", path=path, max_threads=max_threads, max_memory=max_memory)
def __init__(self, path="", max_threads=4): """ USAGE makeblastdb [-h] [-help] [-in input_file] [-input_type type] -dbtype molecule_type [-title database_title] [-parse_seqids] [-hash_index] [-mask_data mask_data_files] [-mask_id mask_algo_ids] [-mask_desc mask_algo_descriptions] [-gi_mask] [-gi_mask_name gi_based_mask_names] [-out database_name] [-max_file_sz number_of_bytes] [-logfile File_Name] [-taxid TaxID] [-taxid_map TaxIDMapFile] [-version] DESCRIPTION Application to create BLAST databases, version 2.2.30+ REQUIRED ARGUMENTS -dbtype <String, `nucl', `prot'> Molecule type of target db OPTIONAL ARGUMENTS -h Print USAGE and DESCRIPTION; ignore all other parameters -help Print USAGE, DESCRIPTION and ARGUMENTS; ignore all other parameters -version Print version number; ignore other arguments *** Input options -in <File_In> Input file/database name Default = `-' -input_type <String, `asn1_bin', `asn1_txt', `blastdb', `fasta'> Type of the data specified in input_file Default = `fasta' *** Configuration options -title <String> Title for BLAST database Default = input file name provided to -in argument -parse_seqids Option to parse seqid for FASTA input if set, for all other input types seqids are parsed automatically -hash_index Create index of sequence hash values. *** Sequence masking options -mask_data <String> Comma-separated list of input files containing masking data as produced by NCBI masking applications (e.g. dustmasker, segmasker, windowmasker) -mask_id <String> Comma-separated list of strings to uniquely identify the masking algorithm * Requires: mask_data * Incompatible with: gi_mask -mask_desc <String> Comma-separated list of free form strings to describe the masking algorithm details * Requires: mask_id -gi_mask Create GI indexed masking data. * Requires: parse_seqids * Incompatible with: mask_id -gi_mask_name <String> Comma-separated list of masking data output files. * Requires: mask_data, gi_mask *** Output options -out <String> Name of BLAST database to be created Default = input file name provided to -in argumentRequired if multiple file(s)/database(s) are provided as input -max_file_sz <String> Maximum file size for BLAST database files Default = `1GB' -logfile <File_Out> File to which the program log should be redirected *** Taxonomy options -taxid <Integer, >=0> Taxonomy ID to assign to all sequences * Incompatible with: taxid_map -taxid_map <File_In> Text file mapping sequence IDs to taxonomy IDs. Format:<SequenceId> <TaxonomyId><newline> * Requires: parse_seqids * Incompatible with: taxid """ Tool.__init__(self, "makeblastdb", 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 = """
def __init__(self, path="", max_threads=4): Tool.__init__(self, "windowmasker", path=path, max_threads=max_threads)
def __init__(self, path="", max_threads=4): Tool.__init__(self, "primer3_core", path=path, max_threads=max_threads)
def __init__(self, path="", max_threads=4): Tool.__init__(self, "trf", path=path, max_threads=max_threads)
def __init__(self, path="", max_threads=4): Tool.__init__(self, "exonerate", path=path, max_threads=max_threads)