Command line options

Usage: pypaswasall [options] FILE_1 FILE_2

This program performs a Smith-Waterman alignment of all sequences in FILE_1 against all sequences in FILE_2. Both files should be in the fasta format.

Options:

-h, --help show this help message and exit

Options that affect the general operation of the program:

Short option	Long option	description
-L FILE	--logfile=FILE	log events to FILE*
	--loglevel=LOGLEVEL	log level. Valid options are DEBUG, INFO, WARNING, ERROR and CRITICAL
-o OUT_FILE	--out=OUT_FILE	The file in which the program stores the generated output. Defaults to ./output
	--outputformat=OUT_FORMAT	The format of the file in which the program stores the generated output. Available options are TXT and SAM.Defaults to txt
-p PROGRAM	--program=PROGRAM	The program to be executed. Valid options are "aligner", "trimmer", "indexed" and "mapper" (last two are experimental)
-1 FILETYPE1	--filetype1=FILETYPE1	File type of the first file. See bioPython IO for available options
-2 FILETYPE2	--filetype2=FILETYPE2	File type of the second file. See bioPython IO for available options
-O OVERRIDE_OUTPUT	--override_output=OVERRIDE_OUTPUT	When output file exists, override it (T/F)
-c CONFIG_FILE	--configfile=CONFIG_FILE	Give settings using configuration file

Options that affect the alignment.

Aligners include aligner and mapper.

Short option	Long option	description
-G GAP_SCORE		Float. Penalty for a gap
-M MATRIX_NAME	--matrixname=MATRIX_NAME	The scoring to be used. Valid options are "DNA-RNA", "BASIC" and "CUSTOM"
-q MISMATCH_SCORE	--mismatch_score=MISMATCH_SCORE	Float. Penalty for mismatch
-r MATCH_SCORE	--match_score=MATCH_SCORE	Float. Reward for match
	--any=ANY_SCORE	Float. Score for a character which is neither in the nucleotide list ("ACGTU"), nor equal to the anyNucleotide character ("N"). Only relevant for use with the DNA-RNA scoring type.
	--other=OTHER_SCORE	Float. Score if the anyNucleotide character ("N") is present in either query or subject. Only relevant for use with the DNA-RNA scoring type.
	--minimum=MINIMUM_SCORE	Float. Sets the minimal score that initiates a backtrace. Do not set this very low: output may be flooded by hits.
	--llimit=LOWER_LIMIT_SCORE	Float. Sets the lower limit for the maximum score which will be used to report a hit. pyPaSWAS will then also report hits with a score lowerLimitScore * highest hit score. Set to <= 1.0.
	--customMatrix=CUSTOM_MATRIX	The custom matrix that should be used

Options for filtering the output

Short option	Long option	description
	--filter_factor=FILTER_FACTOR	The filter factor to be used. Reports only hits within filterFactor * highest possible score * length shortest sequence (or: defines lowest value of the reported relative score). Set to <= 1.0
	--query_coverage=QUERY_COVERAGE	Minimum query coverage. Set to <= 1.0
	--query_identity=QUERY_IDENTITY	Minimum query identity. Set to <= 1.0
	--relative_score=RELATIVE_SCORE	Minimum relative score, defined by the alignment score divided by the length of the shortest of the two sequences. Set to <= highest possible score, for example 5.0 in case of DNA
	--base_score=BASE_SCORE	Minimum base score, defined by the alignment score divided by the length of the alignment (including gaps). Set to <= highest possible score, for example 5.0 in case of DNA

Options that affect the usage and settings of the parallel devices

Short option	Long option	description
	--device_type=[CPU,GPU,ACCELERATOR]	Selects basic device type. GPU is more fine grained than CPU version in the OpenCL implementation
	--platform_name=[Intel,NVIDIA]	Selects platform.
	--framework=[opencl,CUDA]	Selects either OpenCL or CUDA support. CUDA is only available for NVIDIA GPUs
	--device=DEVICE_NUMBER	The device on which the computations will be performed. This should be an integer.
	--maximum_memory_usage=MEM_USAGE	Fraction (<= 1.0) of available device memory to use. Useful when several pyPaSWAS applications are running.
	--number_of_compute_units	Number of compute units to use (openCL only). Will not work on every device, recommended for CPU only. Set this 1 to use a single core on the device for example. This should be an integer.
	--sub_device=DEVICE_NUMBER	The sub_device on which the computations will be performed (OpenCL only). Only used when number_of_compute_units > 0. This should be an integer.
	--limit_length=LIMIT_LENGTH	Length of the longest sequence in characters to be read from file. Lower this when memory of GPU is low.
	--max_genome_length=MAX_GENOME_LENGTH	Deprecated. Defaults to 200000
	--recompile=RECOMPILE	Recompile CUDA code? Set to F(alse) when sequences are of similar length: much faster.
	--sequence_step=SEQUENCE_STEP	Number of sequences read from file 2 before processing. Handy when processing NGS files.
	--query_step=QUERY_STEP	Number of sequences read from file 1 before processing. Handy when processing NGS files.
	--short_sequences=SHORT_SEQUENCES	Set to T(true) when aligning short sequences (trimming?) to maximize memory usage.