3.4. Command-line tool¶
Even though SnakeMake-based approach is the prefered way to use RNFtools, we provide also a command-line tool
rnftools with most of functionality. Here you can find help messages for its subcommands.
Contents
3.4.1. General¶
3.4.1.1. rnftools (list of subcommands)¶
$ rnftools -h usage: rnftools [-h] {,check,publication,validate,liftover,sam2rnf,art2rnf,curesim2rnf,dwgsim2rnf,mason2rnf,wgsim2rnf,merge,sam2es,es2et,et2roc,sam2roc} ... ================================================== RNFtools - http://karel-brinda.github.io/rnftools -------------------------------------------------- version: 0.3.1.1 contact: Karel Brinda (karel.brinda@univ-mlv.fr) ================================================== positional arguments: {,check,publication,validate,liftover,sam2rnf,art2rnf,curesim2rnf,dwgsim2rnf,mason2rnf,wgsim2rnf,merge,sam2es,es2et,et2roc,sam2roc} check Check for the latest version. publication Print information about the associated publication. validate Validate RNF names in a FASTQ file. liftover Liftover genomic coordinates in RNF names. ---------------------[MIShmash]--------------------- sam2rnf Convert a SAM/BAM file to RNF-FASTQ. art2rnf Convert output of Art to RNF-FASTQ. curesim2rnf Convert output of CuReSim to RNF-FASTQ. dwgsim2rnf Convert output of DwgSim to RNF-FASTQ. mason2rnf Convert output of Mason to RNF-FASTQ. wgsim2rnf Convert output of WgSim to RNF-FASTQ. merge Merge RNF-FASTQ files and convert the output to 'traditional' FASTQ. ---------------------[LAVEnder]--------------------- sam2es Convert SAM/BAM with reads in RNF to ES (evaluation of segments). es2et Convert ES to ET (evaluation of read tuples). et2roc Convert ET to ROC (final statistics). sam2roc Previous three steps in a single command. optional arguments: -h, --help show this help message and exit
3.4.1.2. rnftools check¶
$ rnftools check -h usage: rnftools check [-h] Check if RNFtools are up-to-date. optional arguments: -h, --help show this help message and exit
3.4.1.3. rnftools publication¶
$ rnftools publication -h usage: rnftools publication [-h] Print information about the associated publication. optional arguments: -h, --help show this help message and exit
3.4.1.4. rnftools validate¶
$ rnftools validate -h usage: rnftools validate [-h] -i file [-w] [-a] Validate RNF names in a FASTQ file. optional arguments: -h, --help show this help message and exit -i file, --fastq file FASTQ file to be validated. -w, --warnings-as-errors Treat warnings as errors. -a, --all-occurrences Report all occurrences of warnings and errors.
3.4.1.5. rnftools liftover¶
$ rnftools liftover -h usage: rnftools liftover [-h] [-c file] -g int [-x file] [--invert] [--input-format str] [--output-format str] input output Liftover genomic coordinates in RNF names in a SAM/BAM files or in a FASTQ file. positional arguments: input Input file to be transformed (- for standard input). output Output file to be transformed (- for standard output). optional arguments: -h, --help show this help message and exit -c file, --chain file Chain liftover file for coordinates transformation. [no transformation] -g int, --genome-id int ID of genome to be transformed. -x file, --faidx file Fasta index of the reference sequence. [extract from chain file] --invert Invert chain file (transformation in the other direction). --input-format str Input format (SAM/BAM/FASTQ). [autodetect] --output-format str Output format (SAM/BAM/FASTQ). [autodetect]
3.4.2. MIShmash¶
3.4.2.1. rnftools sam2rnf¶
$ rnftools sam2rnf -h usage: rnftools sam2rnf [-h] -s file -o file -x file [-g int] [-u] Convert a SAM/BAM file to RNF-FASTQ. optional arguments: -h, --help show this help message and exit -s file, --sam file Input SAM/BAM with true (expected) alignments of the reads (- for standard input). -o file, --rnf-fastq file Output FASTQ file (- for standard output). -x file, --faidx file FAI index of the reference FASTA file (- for standard input). It can be created using 'samtools faidx'. -g int, --genome-id int Genome ID in RNF (default: 1). -u, --allow-unmapped Allow unmapped reads.
3.4.2.2. rnftools art2rnf¶
$ rnftools art2rnf -h usage: rnftools art2rnf [-h] -s file -o file -x file [-g int] [-u] [-n str] Convert an Art SAM file to RNF-FASTQ. Note that Art produces non-standard SAM files and manual editation might be necessary. In particular, when a FASTA file contains comments, Art left them in the sequence name. Comments must be removed in their corresponding @SQ headers in the SAM file, otherwise all reads are considered to be unmapped by this script. optional arguments: -h, --help show this help message and exit -s file, --sam file Input SAM/BAM with true (expected) alignments of the reads (- for standard input). -o file, --rnf-fastq file Output FASTQ file (- for standard output). -x file, --faidx file FAI index of the reference FASTA file (- for standard input). It can be created using 'samtools faidx'. -g int, --genome-id int Genome ID in RNF (default: 1). -u, --allow-unmapped Allow unmapped reads. -n str, --simulator-name str Name of the simulator (for RNF).
3.4.2.3. rnftools curesim2rnf¶
$ rnftools curesim2rnf -h usage: rnftools curesim2rnf [-h] -c file -o file -x file [-g int] Convert a CuReSim FASTQ file to RNF-FASTQ. optional arguments: -h, --help show this help message and exit -c file, --curesim-fastq file CuReSim FASTQ file (- for standard input). -o file, --rnf-fastq file Output FASTQ file (- for standard output). -x file, --faidx file FAI index of the reference FASTA file (- for standard input). It can be created using 'samtools faidx'. -g int, --genome-id int Genome ID in RNF (default: 1).
3.4.2.4. rnftools dwgsim2rnf¶
$ rnftools dwgsim2rnf -h usage: rnftools dwgsim2rnf [-h] -p str [-e] -o file -x file [-g int] Convert a DwgSim FASTQ file (dwgsim_prefix.bfast.fastq) to RNF-FASTQ. optional arguments: -h, --help show this help message and exit -p str, --dwgsim-prefix str Prefix for DwgSim. -e, --estimate-unknown Estimate unknown values. -o file, --rnf-fastq file Output FASTQ file (- for standard output). -x file, --faidx file FAI index of the reference FASTA file (- for standard input). It can be created using 'samtools faidx'. -g int, --genome-id int Genome ID in RNF (default: 1).
3.4.2.5. rnftools mason2rnf¶
$ rnftools mason2rnf -h usage: rnftools mason2rnf [-h] -s file -o file -x file [-g int] [-u] [-n str] Convert a Mason SAM file to RNF-FASTQ. optional arguments: -h, --help show this help message and exit -s file, --sam file Input SAM/BAM with true (expected) alignments of the reads (- for standard input). -o file, --rnf-fastq file Output FASTQ file (- for standard output). -x file, --faidx file FAI index of the reference FASTA file (- for standard input). It can be created using 'samtools faidx'. -g int, --genome-id int Genome ID in RNF (default: 1). -u, --allow-unmapped Allow unmapped reads. -n str, --simulator-name str Name of the simulator (for RNF).
3.4.2.6. rnftools wgsim2rnf¶
$ rnftools wgsim2rnf -h usage: rnftools wgsim2rnf [-h] -1 file [-2 file] -o file -x file [-g int] [-u] Convert WgSim FASTQ files to RNF-FASTQ. optional arguments: -h, --help show this help message and exit -1 file, --wgsim-fastq-1 file First WgSim FASTQ file (- for standard input) -2 file, --wgsim-fastq-2 file Second WgSim FASTQ file (in case of paired-end reads, default: none). -o file, --rnf-fastq file Output FASTQ file (- for standard output). -x file, --faidx file FAI index of the reference FASTA file (- for standard input). It can be created using 'samtools faidx'. -g int, --genome-id int Genome ID in RNF (default: 1). -u, --allow-unmapped Allow unmapped reads.
3.4.2.7. rnftools merge¶
$ rnftools merge -h usage: rnftools merge [-h] -i inp [inp ...] -m mode -o out todo optional arguments: -h, --help show this help message and exit -i inp [inp ...] input FASTQ files -m mode mode for mergeing files (single-end / paired-end-bwa / paired-end-bfast) -o out output prefix Source RNF-FASTQ files should satisfy the following conditions: 1) Each file contains only reads corresponding to one genome (with the same genome id). 2) All files contain reads of the same type (single-end / paired-end). 3) Reads with more reads per tuple (e.g., paired-end) have '/1', etc. in suffix (for identification of nb of read).
3.4.3. LAVEnder¶
3.4.3.1. rnftools sam2es¶
$ rnftools sam2es -h usage: rnftools sam2es [-h] -i file -o file [-d int] todo optional arguments: -h, --help show this help message and exit -i file, --sam file SAM/BAM with aligned RNF reads(- for standard input). -o file, --es file Output ES file (evaluated segments, - for standard output). -d int, --allowed-delta int Tolerance of difference of coordinates between true (i.e., expected) alignment and real alignment (very important parameter!) (default: 5).
3.4.3.2. rnftools es2et¶
$ rnftools es2et -h usage: rnftools es2et [-h] -i file -o file todo optional arguments: -h, --help show this help message and exit -i file, --es file Input ES file (evaluated segments, - for standard input). -o file, --et file Output ET file (evaluated read tuples, - for standard output).
3.4.3.3. rnftools et2roc¶
$ rnftools et2roc -h usage: rnftools et2roc [-h] -i file -o file todo optional arguments: -h, --help show this help message and exit -i file, --et file Input ET file (evaluated read tuples, - for standard input). -o file, --roc file Output ROC file (evaluated reads, - for standard output).
3.4.3.4. rnftools sam2roc¶
$ rnftools sam2roc -h usage: rnftools sam2roc [-h] -i file -o file [-d int] todo optional arguments: -h, --help show this help message and exit -i file, --sam file SAM/BAM with aligned RNF reads(- for standard input). -o file, --roc file Output ROC file (- for standard output). -d int, --allowed-delta int Tolerance of difference of coordinates between true (i.e., expected) alignment and real alignment (very important parameter!) (default: 5).