Command-Line Interfaces#
yasim#
yasim art#
art.py -- LLRG adapter for ART, a NGS DNA-Seq simulator
SYNOPSIS: python -m yasim art [-h] -F [FASTAS] [-j [JOBS]] [--simulator_name [SIMULATOR_NAME]] [-e [LLRG_EXECUTABLE_PATH]] -d [DEPTH] -o [OUT] [--not_perform_assemble]
[--sequencer_name [{GA1,GA2,HS10,HS20,HS25,HSXn,HSXt,MinS,MSv1,MSv3,NS50}]] [--read_length [READ_LENGTH]]
[--pair_end_fragment_length_mean [PAIR_END_FRAGMENT_LENGTH_MEAN]] [--pair_end_fragment_length_std [PAIR_END_FRAGMENT_LENGTH_STD]] [--is_pair_end]
[--preserve_intermediate_files]
OPTIONS:
-h, --help
[OPTIONAL]
show this help message and exit
-F [FASTAS], --fastas [FASTAS]
[REQUIRED] Type: str; No defaults
Directory of transcribed cDNA sequences in FASTA format from `transcribe` step
-j [JOBS], --jobs [JOBS]
[OPTIONAL] Type: int; Default: 20
Number of LLRGs to be executed in parallel
--simulator_name [SIMULATOR_NAME]
[OPTIONAL] Type: str; Default: None
Custom simulator name. Used in FASTQ tags
This step is done in assemble, so if --not_perform_assemble is set, this option would be useless.
-e [LLRG_EXECUTABLE_PATH], --llrg_executable_path [LLRG_EXECUTABLE_PATH]
[OPTIONAL] Type: str; Default: art_illumina
Executable name or absolute path of art
-d [DEPTH], --depth [DEPTH]
[REQUIRED] Type: str; No defaults
Path to input Isoform-Level Depth TSV generated by `generate_depth_v2` or `generate_isoform_depth` step
-o [OUT], --out [OUT]
[REQUIRED] Type: str; No defaults
Output transcript prefix. The output file would be {out}.fq for single-end and {out}_1.fq, {out}_2.fq for pair end.
If --not_perform_assemble is set, would NOT generate FASTQ files but a {out}.d unassembled directory
--not_perform_assemble
[OPTIONAL] Default: False
Do NOT assemble the output of each isoforms into one file.
--sequencer_name [{GA1,GA2,HS10,HS20,HS25,HSXn,HSXt,MinS,MSv1,MSv3,NS50}]
[OPTIONAL] Type: str; Default: HS25
Name of Illumina Sequencer to Simulate: GA1 -- GenomeAnalyzer I, GA2 -- GenomeAnalyzer II, HS10 -- HiSeq 1000, HS20 -- HiSeq 2000, HS25 -- HiSeq 2500, HSXn -- HiSeqX PCR free, HSXt -- HiSeqX TruSeq, MinS -- MiniSeq TruSeq, MSv1 -- MiSeq v1, MSv3 -- MSv3 - MiSeq v3, NS50 -- NextSeq500 v2
CHOICES:
GA1
GA2
HS10
HS20
HS25
HSXn
HSXt
MinS
MSv1
MSv3
NS50
--read_length [READ_LENGTH]
[OPTIONAL] Type: int; Default: 0
Read length. Sequencer -- Read Length Table: GenomeAnalyzer I -- [36, 44], GenomeAnalyzer II -- [50, 75], HiSeq 1000 -- [100], HiSeq 2000 -- [100], HiSeq 2500 -- [125, 150], HiSeqX PCR free -- [150], HiSeqX TruSeq -- [150], MiniSeq TruSeq -- [50], MiSeq v1 -- [250], MSv3 - MiSeq v3 -- [250], NextSeq500 v2 -- [75]
--pair_end_fragment_length_mean [PAIR_END_FRAGMENT_LENGTH_MEAN]
[OPTIONAL] Type: int; Default: 0
[PE Only] The mean size of DNA/RNA fragments for paired-end simulations
--pair_end_fragment_length_std [PAIR_END_FRAGMENT_LENGTH_STD]
[OPTIONAL] Type: int; Default: 0
[PE Only] The standard deviation of DNA/RNA fragment size for paired-end simulations.
--is_pair_end
[OPTIONAL] Default: False
Whether to use Pair End (PE) Simulation
--preserve_intermediate_files
[OPTIONAL] Default: False
Do not remove intermediate files.
yasim assemble#
assemble.py -- Assemble unassembled outputs.
SYNOPSIS: python -m yasim assemble [-h] -F [FASTAS] --simulator_name [SIMULATOR_NAME] -d [DEPTH] -o [OUT] -i [INPUT_FASTQ_DIR] [--is_pair_end]
[--truncate_ratio_3p [TRUNCATE_RATIO_3P]] [--truncate_ratio_5p [TRUNCATE_RATIO_5P]]
OPTIONS:
-h, --help
[OPTIONAL]
show this help message and exit
-F [FASTAS], --fastas [FASTAS]
[REQUIRED] Type: str; No defaults
Directory of transcribed cDNA sequences in FASTA format from `transcribe` step
--simulator_name [SIMULATOR_NAME]
[REQUIRED] Type: str; No defaults
Custom simulator name. Used in FASTQ tags.
-d [DEPTH], --depth [DEPTH]
[REQUIRED] Type: str; No defaults
Path to input Isoform-Level Depth TSV generated by `generate_depth_v2` or `generate_isoform_depth` step
-o [OUT], --out [OUT]
[REQUIRED] Type: str; No defaults
Output transcript prefix. Should be prefix path to {out}.d directory.
-i [INPUT_FASTQ_DIR], --input_fastq_dir [INPUT_FASTQ_DIR]
[REQUIRED] Type: str; No defaults
Input transcript prefix. Should be prefix path to {out}.d directory.
--is_pair_end
[OPTIONAL] Default: False
Whether to use Pair End (PE) Simulation
--truncate_ratio_3p [TRUNCATE_RATIO_3P]
[OPTIONAL] Type: float; Default: 0.0
[Single End TGS Only] Ratio of 3 prime truncation, range from 0 (no truncation) to 1 (truncate all).
This step is done in assemble, so if --not_perform_assemble is set, this option would be useless.
--truncate_ratio_5p [TRUNCATE_RATIO_5P]
[OPTIONAL] Type: float; Default: 0.0
[Single End TGS Only] Ratio of 5 prime truncation, range from 0 (no truncation) to 1 (truncate all).
This step is done in assemble, so if --not_perform_assemble is set, this option would be useless.
yasim badread#
badread.py -- LLRG adapter for BadRead, a TGS DNA-Seq simulator
SYNOPSIS: python -m yasim badread [-h] -F [FASTAS] [-j [JOBS]] [--simulator_name [SIMULATOR_NAME]] [-e [LLRG_EXECUTABLE_PATH]] -d [DEPTH] -o [OUT] [--not_perform_assemble]
[--truncate_ratio_3p [TRUNCATE_RATIO_3P]] [--truncate_ratio_5p [TRUNCATE_RATIO_5P]] -m [{nanopore2018,nanopore2020,pacbio2016,verybad,verynice}]
OPTIONS:
-h, --help
[OPTIONAL]
show this help message and exit
-F [FASTAS], --fastas [FASTAS]
[REQUIRED] Type: str; No defaults
Directory of transcribed cDNA sequences in FASTA format from `transcribe` step
-j [JOBS], --jobs [JOBS]
[OPTIONAL] Type: int; Default: 20
Number of LLRGs to be executed in parallel
--simulator_name [SIMULATOR_NAME]
[OPTIONAL] Type: str; Default: None
Custom simulator name. Used in FASTQ tags
This step is done in assemble, so if --not_perform_assemble is set, this option would be useless.
-e [LLRG_EXECUTABLE_PATH], --llrg_executable_path [LLRG_EXECUTABLE_PATH]
[OPTIONAL] Type: str; Default: badread
Executable name or absolute path of badread
-d [DEPTH], --depth [DEPTH]
[REQUIRED] Type: str; No defaults
Path to input Isoform-Level Depth TSV generated by `generate_depth_v2` or `generate_isoform_depth` step
-o [OUT], --out [OUT]
[REQUIRED] Type: str; No defaults
Output transcript prefix. The output file would be {out}.fq for single-end and {out}_1.fq, {out}_2.fq for pair end.
If --not_perform_assemble is set, would NOT generate FASTQ files but a {out}.d unassembled directory
--not_perform_assemble
[OPTIONAL] Default: False
Do NOT assemble the output of each isoforms into one file.
--truncate_ratio_3p [TRUNCATE_RATIO_3P]
[OPTIONAL] Type: float; Default: 0.0
[Single End TGS Only] Ratio of 3 prime truncation, range from 0 (no truncation) to 1 (truncate all).
This step is done in assemble, so if --not_perform_assemble is set, this option would be useless.
--truncate_ratio_5p [TRUNCATE_RATIO_5P]
[OPTIONAL] Type: float; Default: 0.0
[Single End TGS Only] Ratio of 5 prime truncation, range from 0 (no truncation) to 1 (truncate all).
This step is done in assemble, so if --not_perform_assemble is set, this option would be useless.
-m [{nanopore2018,nanopore2020,pacbio2016,verybad,verynice}], --model_name [{nanopore2018,nanopore2020,pacbio2016,verybad,verynice}]
[REQUIRED] Type: str; No defaults
Badread model name
CHOICES:
nanopore2018
nanopore2020
pacbio2016
verybad
verynice
yasim dtgs#
dtgs.py -- LLRG adapter for dTGS simulator (Dumb Third-Generation Sequencing Simulator).
SYNOPSIS: python -m yasim dtgs [-h] -F [FASTAS] [-j [JOBS]] [--simulator_name [SIMULATOR_NAME]] -d [DEPTH] -o [OUT] [--not_perform_assemble] [--truncate_ratio_3p [TRUNCATE_RATIO_3P]]
[--truncate_ratio_5p [TRUNCATE_RATIO_5P]]
OPTIONS:
-h, --help
[OPTIONAL]
show this help message and exit
-F [FASTAS], --fastas [FASTAS]
[REQUIRED] Type: str; No defaults
Directory of transcribed cDNA sequences in FASTA format from `transcribe` step
-j [JOBS], --jobs [JOBS]
[OPTIONAL] Type: int; Default: 20
Number of LLRGs to be executed in parallel
--simulator_name [SIMULATOR_NAME]
[OPTIONAL] Type: str; Default: None
Custom simulator name. Used in FASTQ tags
This step is done in assemble, so if --not_perform_assemble is set, this option would be useless.
-d [DEPTH], --depth [DEPTH]
[REQUIRED] Type: str; No defaults
Path to input Isoform-Level Depth TSV generated by `generate_depth_v2` or `generate_isoform_depth` step
-o [OUT], --out [OUT]
[REQUIRED] Type: str; No defaults
Output transcript prefix. The output file would be {out}.fq for single-end and {out}_1.fq, {out}_2.fq for pair end.
If --not_perform_assemble is set, would NOT generate FASTQ files but a {out}.d unassembled directory
--not_perform_assemble
[OPTIONAL] Default: False
Do NOT assemble the output of each isoforms into one file.
--truncate_ratio_3p [TRUNCATE_RATIO_3P]
[OPTIONAL] Type: float; Default: 0.0
[Single End TGS Only] Ratio of 3 prime truncation, range from 0 (no truncation) to 1 (truncate all).
This step is done in assemble, so if --not_perform_assemble is set, this option would be useless.
--truncate_ratio_5p [TRUNCATE_RATIO_5P]
[OPTIONAL] Type: float; Default: 0.0
[Single End TGS Only] Ratio of 5 prime truncation, range from 0 (no truncation) to 1 (truncate all).
This step is done in assemble, so if --not_perform_assemble is set, this option would be useless.
yasim dwgsim#
dwgsim.py -- LLRG adapter for DWGSIM, a NGS DNA-Seq simulator
SYNOPSIS: python -m yasim dwgsim [-h] -F [FASTAS] [-j [JOBS]] [--simulator_name [SIMULATOR_NAME]] [-e [LLRG_EXECUTABLE_PATH]] -d [DEPTH] -o [OUT] [--not_perform_assemble]
[--preserve_intermediate_files]
OPTIONS:
-h, --help
[OPTIONAL]
show this help message and exit
-F [FASTAS], --fastas [FASTAS]
[REQUIRED] Type: str; No defaults
Directory of transcribed cDNA sequences in FASTA format from `transcribe` step
-j [JOBS], --jobs [JOBS]
[OPTIONAL] Type: int; Default: 20
Number of LLRGs to be executed in parallel
--simulator_name [SIMULATOR_NAME]
[OPTIONAL] Type: str; Default: None
Custom simulator name. Used in FASTQ tags
This step is done in assemble, so if --not_perform_assemble is set, this option would be useless.
-e [LLRG_EXECUTABLE_PATH], --llrg_executable_path [LLRG_EXECUTABLE_PATH]
[OPTIONAL] Type: str; Default: dwgsim
Executable name or absolute path of dwgsim
-d [DEPTH], --depth [DEPTH]
[REQUIRED] Type: str; No defaults
Path to input Isoform-Level Depth TSV generated by `generate_depth_v2` or `generate_isoform_depth` step
-o [OUT], --out [OUT]
[REQUIRED] Type: str; No defaults
Output transcript prefix. The output file would be {out}.fq for single-end and {out}_1.fq, {out}_2.fq for pair end.
If --not_perform_assemble is set, would NOT generate FASTQ files but a {out}.d unassembled directory
--not_perform_assemble
[OPTIONAL] Default: False
Do NOT assemble the output of each isoforms into one file.
--preserve_intermediate_files
[OPTIONAL] Default: False
Do not remove intermediate files.
yasim generate_as_events#
generate_as_events.py -- Generate Alternative Splicing Events from Reference genome using YASIM V3 API.
SYNOPSIS: python -m yasim generate_as_events [-h] -g [GTF] -f [FASTA] -c [COMPLEXITY] -o [OUT]
OPTIONS:
-h, --help
[OPTIONAL]
show this help message and exit
-g [GTF], --gtf [GTF]
[REQUIRED] Type: str; No defaults
Path to input genomic annotation in GTF format. Can be compressed.
-f [FASTA], --fasta [FASTA]
[REQUIRED] Type: str; No defaults
Path to input reference genome sequence in FASTA format. Can be compressed.
-c [COMPLEXITY], --complexity [COMPLEXITY]
[REQUIRED] Type: int; No defaults
Transcriptome Complexity Index, should be an integer between 1 and 9.
-o [OUT], --out [OUT]
[REQUIRED] Type: str; No defaults
Path to output genome annotation with Ground-Truth AS Events in GTF.
yasim generate_gene_depth#
generate_gene_depth.py -- Generate Gene-Level Depth using YASIM V3 API.
SYNOPSIS: python -m yasim generate_gene_depth [-h] -g [GTF] -o [OUT] [-d [MU]] [--low_cutoff [LOW_CUTOFF]] [--high_cutoff_ratio [HIGH_CUTOFF_RATIO]]
OPTIONS:
-h, --help
[OPTIONAL]
show this help message and exit
-g [GTF], --gtf [GTF]
[REQUIRED] Type: str; No defaults
Path to input genomic annotation in GTF format. Can be compressed.
-o [OUT], --out [OUT]
[REQUIRED] Type: str; No defaults
Path to output Gene-Level depth TSV. Can be compressed.
-d [MU], --mu [MU]
[OPTIONAL] Type: float; Default: 100
Average depth.
--low_cutoff [LOW_CUTOFF]
[OPTIONAL] Type: float; Default: 0.01
Depth lower than this value would be this value.
--high_cutoff_ratio [HIGH_CUTOFF_RATIO]
[OPTIONAL] Type: float; Default: 200
Depth higher than `mu * high_cutoff_ratio` would be `mu * high_cutoff_ratio`
yasim generate_isoform_depth#
generate_isoform_depth.py -- Generate Isoform-Level Depth using YASIM V3 API.
SYNOPSIS: python -m yasim generate_isoform_depth [-h] -g [GTF] -o [OUT] -d [DEPTH] [--low_cutoff [LOW_CUTOFF]] [--high_cutoff_ratio [HIGH_CUTOFF_RATIO]] [--alpha [ALPHA]]
OPTIONS:
-h, --help
[OPTIONAL]
show this help message and exit
-g [GTF], --gtf [GTF]
[REQUIRED] Type: str; No defaults
Path to input genomic annotation in GTF format. Can be compressed.
-o [OUT], --out [OUT]
[REQUIRED] Type: str; No defaults
Path to output Isoform-Level Depth TSV. Can be compressed.
-d [DEPTH], --depth [DEPTH]
[REQUIRED] Type: str; No defaults
Path to input Gene-Level Depth TSV. Can be compressed.
--low_cutoff [LOW_CUTOFF]
[OPTIONAL] Type: float; Default: 0.01
Depth lower than this value would be this value.
--high_cutoff_ratio [HIGH_CUTOFF_RATIO]
[OPTIONAL] Type: float; Default: 200
Depth higher than `mu * high_cutoff_ratio` would be `mu * high_cutoff_ratio`
--alpha [ALPHA]
[OPTIONAL] Type: int; Default: 4
Zipf's Coefficient, larger for larger differences
yasim generate_isoform_replicates#
generate_isoform_replicates.py -- Generate Technical Replicates using YASIM V3 API.
SYNOPSIS: python -m yasim generate_isoform_replicates [-h] -d [DEPTH] [-n [NUM_REPLICATES]] [-r [RANGE]]
OPTIONS:
-h, --help
[OPTIONAL]
show this help message and exit
-d [DEPTH], --depth [DEPTH]
[REQUIRED] Type: str; No defaults
Path to input Isoform-Level Depth TSV. Can be compressed.
-n [NUM_REPLICATES], --num_replicates [NUM_REPLICATES]
[OPTIONAL] Type: int; Default: 3
Number of Replicates to be generated
-r [RANGE], --range [RANGE]
[OPTIONAL] Type: float; Default: 0.1
Range of Generated Data
yasim pbsim#
pbsim.py -- LLRG adapter for PBSIM v1, a TGS DNA-Seq simulator
SYNOPSIS: python -m yasim pbsim [-h] -F [FASTAS] [-j [JOBS]] [--simulator_name [SIMULATOR_NAME]] [-e [LLRG_EXECUTABLE_PATH]] -d [DEPTH] -o [OUT] [--not_perform_assemble]
[--truncate_ratio_3p [TRUNCATE_RATIO_3P]] [--truncate_ratio_5p [TRUNCATE_RATIO_5P]] [-c] [--preserve_intermediate_files]
OPTIONS:
-h, --help
[OPTIONAL]
show this help message and exit
-F [FASTAS], --fastas [FASTAS]
[REQUIRED] Type: str; No defaults
Directory of transcribed cDNA sequences in FASTA format from `transcribe` step
-j [JOBS], --jobs [JOBS]
[OPTIONAL] Type: int; Default: 20
Number of LLRGs to be executed in parallel
--simulator_name [SIMULATOR_NAME]
[OPTIONAL] Type: str; Default: None
Custom simulator name. Used in FASTQ tags
This step is done in assemble, so if --not_perform_assemble is set, this option would be useless.
-e [LLRG_EXECUTABLE_PATH], --llrg_executable_path [LLRG_EXECUTABLE_PATH]
[OPTIONAL] Type: str; Default: pbsim
Executable name or absolute path of pbsim
-d [DEPTH], --depth [DEPTH]
[REQUIRED] Type: str; No defaults
Path to input Isoform-Level Depth TSV generated by `generate_depth_v2` or `generate_isoform_depth` step
-o [OUT], --out [OUT]
[REQUIRED] Type: str; No defaults
Output transcript prefix. The output file would be {out}.fq for single-end and {out}_1.fq, {out}_2.fq for pair end.
If --not_perform_assemble is set, would NOT generate FASTQ files but a {out}.d unassembled directory
--not_perform_assemble
[OPTIONAL] Default: False
Do NOT assemble the output of each isoforms into one file.
--truncate_ratio_3p [TRUNCATE_RATIO_3P]
[OPTIONAL] Type: float; Default: 0.0
[Single End TGS Only] Ratio of 3 prime truncation, range from 0 (no truncation) to 1 (truncate all).
This step is done in assemble, so if --not_perform_assemble is set, this option would be useless.
--truncate_ratio_5p [TRUNCATE_RATIO_5P]
[OPTIONAL] Type: float; Default: 0.0
[Single End TGS Only] Ratio of 5 prime truncation, range from 0 (no truncation) to 1 (truncate all).
This step is done in assemble, so if --not_perform_assemble is set, this option would be useless.
-c, --ccs
[OPTIONAL] Default: False
Simulate CCS instead of CLR
--preserve_intermediate_files
[OPTIONAL] Default: False
Do not remove intermediate files.
yasim pbsim2#
pbsim2.py -- LLRG adapter for PBSIM v2, a TGS DNA-Seq simulator
SYNOPSIS: python -m yasim pbsim2 [-h] -F [FASTAS] [-j [JOBS]] [--simulator_name [SIMULATOR_NAME]] [-e [LLRG_EXECUTABLE_PATH]] -d [DEPTH] -o [OUT] [--not_perform_assemble]
[--truncate_ratio_3p [TRUNCATE_RATIO_3P]] [--truncate_ratio_5p [TRUNCATE_RATIO_5P]] -m [{R103,P5C3,P4C2,P6C4,R95,R94}]
[--preserve_intermediate_files]
OPTIONS:
-h, --help
[OPTIONAL]
show this help message and exit
-F [FASTAS], --fastas [FASTAS]
[REQUIRED] Type: str; No defaults
Directory of transcribed cDNA sequences in FASTA format from `transcribe` step
-j [JOBS], --jobs [JOBS]
[OPTIONAL] Type: int; Default: 20
Number of LLRGs to be executed in parallel
--simulator_name [SIMULATOR_NAME]
[OPTIONAL] Type: str; Default: None
Custom simulator name. Used in FASTQ tags
This step is done in assemble, so if --not_perform_assemble is set, this option would be useless.
-e [LLRG_EXECUTABLE_PATH], --llrg_executable_path [LLRG_EXECUTABLE_PATH]
[OPTIONAL] Type: str; Default: pbsim2
Executable name or absolute path of pbsim2
-d [DEPTH], --depth [DEPTH]
[REQUIRED] Type: str; No defaults
Path to input Isoform-Level Depth TSV generated by `generate_depth_v2` or `generate_isoform_depth` step
-o [OUT], --out [OUT]
[REQUIRED] Type: str; No defaults
Output transcript prefix. The output file would be {out}.fq for single-end and {out}_1.fq, {out}_2.fq for pair end.
If --not_perform_assemble is set, would NOT generate FASTQ files but a {out}.d unassembled directory
--not_perform_assemble
[OPTIONAL] Default: False
Do NOT assemble the output of each isoforms into one file.
--truncate_ratio_3p [TRUNCATE_RATIO_3P]
[OPTIONAL] Type: float; Default: 0.0
[Single End TGS Only] Ratio of 3 prime truncation, range from 0 (no truncation) to 1 (truncate all).
This step is done in assemble, so if --not_perform_assemble is set, this option would be useless.
--truncate_ratio_5p [TRUNCATE_RATIO_5P]
[OPTIONAL] Type: float; Default: 0.0
[Single End TGS Only] Ratio of 5 prime truncation, range from 0 (no truncation) to 1 (truncate all).
This step is done in assemble, so if --not_perform_assemble is set, this option would be useless.
-m [{R103,P5C3,P4C2,P6C4,R95,R94}], --hmm_model [{R103,P5C3,P4C2,P6C4,R95,R94}]
[REQUIRED] Type: str; No defaults
Basename or absolute path of HMM file
CHOICES:
R103
P5C3
P4C2
P6C4
R95
R94
--preserve_intermediate_files
[OPTIONAL] Default: False
Do not remove intermediate files.
yasim pbsim3#
pbsim3.py -- LLRG adapter for PBSIM v3, a TGS DNA- and RNA-Seq simulator
SYNOPSIS: python -m yasim pbsim3 [-h] -F [FASTAS] [-j [JOBS]] [--simulator_name [SIMULATOR_NAME]] [-e [LLRG_EXECUTABLE_PATH]] -d [DEPTH] -o [OUT] [--not_perform_assemble]
[--truncate_ratio_3p [TRUNCATE_RATIO_3P]] [--truncate_ratio_5p [TRUNCATE_RATIO_5P]] -m [HMM_MODEL] -M [{errhmm,qshmm}] [--ccs_pass [CCS_PASS]]
[--ccs_path [CCS_PATH]] [--samtools_path [SAMTOOLS_PATH]] [--strategy {wgs,trans}] [--preserve_intermediate_files]
OPTIONS:
-h, --help
[OPTIONAL]
show this help message and exit
-F [FASTAS], --fastas [FASTAS]
[REQUIRED] Type: str; No defaults
Directory of transcribed cDNA sequences in FASTA format from `transcribe` step
-j [JOBS], --jobs [JOBS]
[OPTIONAL] Type: int; Default: 20
Number of LLRGs to be executed in parallel
--simulator_name [SIMULATOR_NAME]
[OPTIONAL] Type: str; Default: None
Custom simulator name. Used in FASTQ tags
This step is done in assemble, so if --not_perform_assemble is set, this option would be useless.
-e [LLRG_EXECUTABLE_PATH], --llrg_executable_path [LLRG_EXECUTABLE_PATH]
[OPTIONAL] Type: str; Default: pbsim3
Executable name or absolute path of pbsim3
-d [DEPTH], --depth [DEPTH]
[REQUIRED] Type: str; No defaults
Path to input Isoform-Level Depth TSV generated by `generate_depth_v2` or `generate_isoform_depth` step
-o [OUT], --out [OUT]
[REQUIRED] Type: str; No defaults
Output transcript prefix. The output file would be {out}.fq for single-end and {out}_1.fq, {out}_2.fq for pair end.
If --not_perform_assemble is set, would NOT generate FASTQ files but a {out}.d unassembled directory
--not_perform_assemble
[OPTIONAL] Default: False
Do NOT assemble the output of each isoforms into one file.
--truncate_ratio_3p [TRUNCATE_RATIO_3P]
[OPTIONAL] Type: float; Default: 0.0
[Single End TGS Only] Ratio of 3 prime truncation, range from 0 (no truncation) to 1 (truncate all).
This step is done in assemble, so if --not_perform_assemble is set, this option would be useless.
--truncate_ratio_5p [TRUNCATE_RATIO_5P]
[OPTIONAL] Type: float; Default: 0.0
[Single End TGS Only] Ratio of 5 prime truncation, range from 0 (no truncation) to 1 (truncate all).
This step is done in assemble, so if --not_perform_assemble is set, this option would be useless.
-m [HMM_MODEL], --hmm_model [HMM_MODEL]
[REQUIRED] Type: str; No defaults
Basename of HMM file. If you select errhmm in hmm_method, it would be ['ONT', 'SEQUEL', 'RSII']If you select qshmm in hmm_method, it would be ['ONT', 'RSII']
-M [{errhmm,qshmm}], --hmm_method [{errhmm,qshmm}]
[REQUIRED] Type: str; No defaults
Whether to simulate using quality score (as PBSIM2) or error profile (new)
CHOICES:
errhmm
qshmm
--ccs_pass [CCS_PASS]
[OPTIONAL] Type: int; Default: 1
CCS Multipass Settings. Use 1 for CLR and others for CCS.
--ccs_path [CCS_PATH]
[OPTIONAL] Type: str; Default: ccs
Executable name of ccs or pbccs. Omitted if ccs_pass == 1.
--samtools_path [SAMTOOLS_PATH]
[OPTIONAL] Type: str; Default: samtools
Executable name of samtools. Omitted if ccs_pass == 1.
--strategy {wgs,trans}
[OPTIONAL] Type: PBSIM3_STRATEGY; Default: wgs
Whether to use transcript (trans) mode or wgs (wgs) mode
CHOICES:
wgs -- WGS mode (as PBSIM2)
trans -- TRANS mode
--preserve_intermediate_files
[OPTIONAL] Default: False
Do not remove intermediate files.
yasim sample_transcript#
transcribe.py -- General-purposed stranded transcription, from reference genome to reference cDNA.
SYNOPSIS: python -m labw_utils.bioutils transcribe [-h] -f [FASTA] -g [GTF] -o [OUT] [--no_write_single_transcript]
OPTIONS:
-h, --help
[OPTIONAL]
show this help message and exit
-f [FASTA], --fasta [FASTA]
[REQUIRED] Type: str; No defaults
Path to input reference genome sequence in FASTA format. Can be compressed.
-g [GTF], --gtf [GTF]
[REQUIRED] Type: str; No defaults
Path to input genomic annotation in GTF format. Can be compressed.
-o [OUT], --out [OUT]
[REQUIRED] Type: str; No defaults
Path of Output cDNA FASTA
--no_write_single_transcript
[OPTIONAL] Default: False
Stop splitting cDNA of each isoform into separate file
yasim self_check#
self_check.py -- Check whether YASIM installation is complete.
.. versionadded:: 3.1.6
yasim transcribe#
transcribe.py -- General-purposed stranded transcription, from reference genome to reference cDNA.
SYNOPSIS: python -m labw_utils.bioutils transcribe [-h] -f [FASTA] -g [GTF] -o [OUT] [--no_write_single_transcript]
OPTIONS:
-h, --help
[OPTIONAL]
show this help message and exit
-f [FASTA], --fasta [FASTA]
[REQUIRED] Type: str; No defaults
Path to input reference genome sequence in FASTA format. Can be compressed.
-g [GTF], --gtf [GTF]
[REQUIRED] Type: str; No defaults
Path to input genomic annotation in GTF format. Can be compressed.
-o [OUT], --out [OUT]
[REQUIRED] Type: str; No defaults
Path of Output cDNA FASTA
--no_write_single_transcript
[OPTIONAL] Default: False
Stop splitting cDNA of each isoform into separate file
yasim_scripts#
yasim_scripts extract_quality_from_maf#
extract_quality_from_maf.py -- Extract per-base alignment status from MAF files.
This script extracts per-base alignment status from MAF files into a TSV file of one line,
which have 4 fields for Insertion, Deletion, Match and Substitution.
Synopsis: python -m yasim_scrips extract_quality_from_maf [MAF1] [[MAF2]...]
Arguments:
[MAF1] [[MAF2]...] path to MAF files produced by PBSIM3 or LAST aligner.
.. versionadded:: 3.1.5
yasim_scripts extract_read_length_from_maf_gp#
extract_read_length_from_maf_gp.py -- Extraction of Read Length from MAF, General-Purposed
This script can be used to extract read length of all transcript ID from transcriptomically-aligned TGS RNA-Seq MAF
for assessing read completeness.
Synopsis: python -m yasim_scrips extract_quality_from_maf [MAF1] [[MAF2]...]
Arguments:
[MAF1] [[MAF2]...] path to MAF files produced by PBSIM3 or LAST aligner.
.. versionadded:: 3.1.5
yasim_scripts extract_read_length_from_maf_yasim#
extract_read_length_from_maf_gp.py -- Extraction of Read Length from MAF, YASIM
This script can be used to extract read length of all transcript ID from transcriptomically-aligned TGS RNA-Seq MAF
generated by YASIM for assessing read completeness.
Synopsis: python -m yasim_scrips extract_quality_from_maf [MAF1] [[MAF2]...]
Arguments:
[MAF1] [[MAF2]...] path to MAF files produced by PBSIM3 or LAST aligner.
.. versionadded:: 3.1.5
yasim_scripts featurecounts_to_depth#
featurecounts_to_depth.py -- Convert FeatureCounts Output for NGS and TGS to YASIM input depth.
SYNOPSIS: python -m yasim_scripts featurecounts_to_depth [-h] -i [INPUT] [--software [{featureCounts,Salmon}]] -o [OUT] [-f [{GENE_ID,TRANSCRIPT_ID}]] [--read_length [READ_LENGTH] |
--read_completeness [READ_COMPLETENESS]]
OPTIONS:
-h, --help
[OPTIONAL]
show this help message and exit
-i [INPUT], --input [INPUT]
[REQUIRED] Type: str; No defaults
Path to featureCounts/Salmon output TSV
--software [{featureCounts,Salmon}]
[OPTIONAL] Type: str; Default: featureCounts
name of quantification software
CHOICES:
featureCounts
Salmon
-o [OUT], --out [OUT]
[REQUIRED] Type: str; No defaults
Path to output TSV
-f [{GENE_ID,TRANSCRIPT_ID}], --feature_name [{GENE_ID,TRANSCRIPT_ID}]
[OPTIONAL] Type: str; Default: TRANSCRIPT_ID
Name of output feature
CHOICES:
GENE_ID
TRANSCRIPT_ID
--read_length [READ_LENGTH]
[OPTIONAL] Type: int; Default: None
[For NGS Only] Read length
--read_completeness [READ_COMPLETENESS]
[OPTIONAL] Type: float; Default: None
[For TGS Only] Mean read completeness
yasim_scripts merge_pbccs#
merge_pbccs.py -- Merge BAMs created by pbccs.
SYNOPSIS: python -m yasim_scripts merge_pbccs [-h] -o OUT [-e PBMERGE_PATH] --input_bam_glob INPUT_BAM_GLOB
OPTIONS:
-h, --help
[OPTIONAL]
show this help message and exit
-o OUT, --out OUT
[REQUIRED] Type: str; No defaults
Output BAM file
-e PBMERGE_PATH, --pbmerge_path PBMERGE_PATH
[OPTIONAL] Type: str; Default: None
Path to pbmerge
--input_bam_glob INPUT_BAM_GLOB
[REQUIRED] Type: str; No defaults
Glob expression for BAM files that will be merged.