dishevelled.org bio
Install
- JDK 17 or later, https://openjdk.java.net
- Apache Maven 3.8.5 or later, https://maven.apache.org
To build
$ mvn install
In addition to APIs in various modules, dishevelled.org bio also provides a set of
command line tools, gathered together into a single top-level dsh-bio script
$ dsh-bio --help
usage:
dsh-bio [command] [args]
commands:
bin-fastq-quality-scores bin quality scores from files in FASTQ format
compress-bed compress features in BED format to splittable bgzf or bzip2 compression codecs
compress-fasta compress sequences in FASTA format to splittable bgzf or bzip2 compression codecs
compress-fastq compress sequences in FASTQ format to splittable bgzf or bzip2 compression codecs
compress-gaf compress alignments in GAF format to splittable bgzf or bzip2 compression codecs
compress-gfa1 compress assembly in GFA 1.0 format to splittable bgzf or bzip2 compression codecs
compress-gfa2 compress assembly in GFA 2.0 format to splittable bgzf or bzip2 compression codecs
compress-gff3 compress features in GFF3 format to splittable bgzf or bzip2 compression codecs
compress-paf compress alignments in PAF format to splittable bgzf or bzip2 compression codecs
compress-rgfa compress assembly in rGFA format to splittable bgzf or bzip2 compression codecs
compress-sam compress alignments in SAM format to splittable bgzf or bzip2 compression codecs
compress-vcf compress variants and genotypes in VCF format to splittable bgzf or bzip2 compression codecs
create-sequence-dictionary create a SequenceDictionary from DNA sequences in FASTA format
disinterleave-fastq convert interleaved FASTQ format into first and second DNA sequence files in FASTQ format
downsample-fastq downsample DNA sequences from files in FASTQ format
downsample-interleaved-fastq downsample DNA sequences from a file in interleaved FASTQ format
export-segments export assembly segment sequences in GFA 1.0 format to FASTA format
extract-fasta extract matching DNA or protein sequences in FASTA format
extract-fastq extract matching DNA sequences in FASTQ format
extract-fastq-by-length extract DNA sequences in FASTQ format with a range of lengths
fasta-to-fastq convert DNA sequences in FASTA format to FASTQ format
fasta-to-parquet (beta) convert DNA or protein sequences in FASTA format to Parquet format
fasta-to-parquet2 (beta) convert DNA or protein sequences in FASTA format to Parquet format, with transaction size
fasta-to-parquet3 (beta) convert DNA or protein sequences in FASTA format to Parquet format, with partition size
fasta-to-parquet4 (beta) convert DNA or protein sequences in FASTA format to Parquet format, with flush after
fasta-to-text convert DNA or protein sequences in FASTA format to tab-separated values (tsv) text format
fastq-description output description lines from DNA sequences in FASTQ format
fastq-sequence-length output sequence lengths from DNA sequences in FASTQ format
fastq-to-bam convert DNA sequences in FASTQ format to unaligned BAM format
fastq-to-fasta convert DNA sequences in FASTQ format to FASTA format
fastq-to-text convert DNA sequences in FASTQ format to tab-separated values (tsv) text format
filter-bed filter features in BED format
filter-fasta filter sequences in FASTA format
filter-fastq filter sequences in FASTQ format
filter-gaf filter alignments in GAF format
filter-gfa1 filter assembly in GFA 1.0 format
filter-gfa2 filter assembly in GFA 2.0 format
filter-gff3 filter features in GFF3 format
filter-paf filter alignments in PAF format
filter-rgfa filter assembly in rGFA format
filter-sam filter alignments in SAM format
filter-vcf filter variants in VCF format
gfa1-to-gfa2 convert GFA 1.0 format to GFA 2.0 format
identify-gfa1 add identifier annotation to records in GFA 1.0 format
interleave-fastq convert first and second DNA sequence files in FASTQ format to interleaved FASTQ format
interleaved-fastq-to-bam convert DNA sequences in interleaved FASTQ format to unaligned BAM format
links-to-cytoscape-edges convert links in GFA 1.0 format to edges.txt format for Cytoscape
links-to-property-graph convert links in GFA 1.0 format to property graph CSV format
list-filesystems list filesystem providers
reassemble-paths reassemble paths in GFA 1.0 format from traversal records
remap-dbsnp remap DB Type=String flags in VCF format to DB Type=Flag and dbsnp Type=String fields
remap-phase-set remap PS Type=String phase set ids in VCF format to PS Type=Integer
rename-bed-references rename references in BED files
rename-gff3-references rename references in GFF3 files
rename-vcf-references rename references in VCF files
segments-to-cytoscape-nodes convert segments in GFA 1.0 format to nodes.txt format for Cytoscape
segments-to-property-graph convert segments in GFA 1.0 format to property graph CSV format
split-bed split files in BED format
split-fasta split files in FASTA format
split-fastq split files in FASTQ format
split-gaf split files in GAF format
split-gff3 split files in GFF3 format
split-interleaved-fastq split files in interleaved FASTQ format
split-paf split files in PAF format
split-sam split files in SAM format
split-vcf split files in VCF format
text-to-fasta convert DNA or protein sequences in tab-separated values (tsv) text format to FASTA format
text-to-fastq convert DNA sequences in tab-separated values (tsv) text format to FASTQ format
traversals-to-cytoscape-edges convert traversals in GFA 1.0 format to edges.txt format for Cytoscape
traversals-to-property-graph convert traversals in GFA 1.0 format to property graph CSV format
traverse-paths traverse paths in GFA 1.0 format
truncate-fasta truncate DNA or protein sequences in FASTA format
truncate-paths truncate paths in GFA 1.0 format
variant-table-to-vcf convert Ensembl variant table to VCF format
vcf-pedigree extract a pedigree from VCF format
vcf-samples extract samples from VCF format
arguments:
-a, --about display about message [optional]
-v, --version display about message [optional]
-h, --help display help message [optional]
$ dsh-bio split-bed --help
usage:
dsh-split-bed -r 100 -i foo.bed.gz
arguments:
-a, --about display about message [optional]
-h, --help display help message [optional]
-i, --input-path [interface java.nio.file.Path] input BED path, default stdin [optional]
-b, --bytes [class java.lang.String] split input path at next record after each n bytes [optional]
-r, --records [class java.lang.Long] split input path after each n records [optional]
-p, --prefix [class java.lang.String] output file prefix [optional]
-d, --left-pad [class java.lang.Integer] left pad split index in output file name [optional]
-s, --suffix [class java.lang.String] output file suffix, e.g. .bed.gz [optional]Each command is also available as a separate script, e.g. dsh-split-bed
$ dsh-split-bed --help
usage:
dsh-split-bed -r 100 -i foo.bed.gz
arguments:
-a, --about display about message [optional]
-h, --help display help message [optional]
-i, --input-path [interface java.nio.file.Path] input BED path, default stdin [optional]
-b, --bytes [class java.lang.String] split input path at next record after each n bytes [optional]
-r, --records [class java.lang.Long] split input path after each n records [optional]
-p, --prefix [class java.lang.String] output file prefix [optional]
-d, --left-pad [class java.lang.Integer] left pad split index in output file name [optional]
-s, --suffix [class java.lang.String] output file suffix, e.g. .bed.gz [optional]Across the dishevelled.org bio command line tools, stdin and stdout should behave as expected,
and files and streams compressed with Zstandard (zstd), XZ, GZIP, BZip2, and block-compressed GZIP
(BGZF) are handled transparently. Use file extensions .zst, .xz, .gz, .bz2, and .bgz
respectively to force the issue, if necessary.
As of version 2.1, cloud storage file systems from Google Cloud Storage (via gs:// paths)
and Amazon Simple Storage Service (Amazon S3) (via s3:// paths) are supported for input paths.
$ dsh-bio list-filesystems
Installed filesystem providers:
file sun.nio.fs.MacOSXFileSystemProvider
jar jdk.nio.zipfs.ZipFileSystemProvider
jrt jdk.internal.jrtfs.JrtFileSystemProvider
gs com.google.cloud.storage.contrib.nio.CloudStorageFileSystemProvider
s3 software.amazon.nio.spi.s3.S3FileSystemProvider
s3x software.amazon.nio.spi.s3.S3XFileSystemProvider
Commands with a --script argument expect an expression written in JavaScript that evaluates
to boolean true or false against a record, provided in the context as variable r. For example,
with dsh-filter-bed, to filter BED records by chromosome and score
r.getChrom() == 1 && r.getScore() > 10specified on the command line as
$ dsh-bio filter-bed -i input.bed --script "r.getChrom() == 1 && r.getScore() > 10"The dishevelled.org bio command line tools are available in Conda via Bioconda, https://bioconda.github.io
$ conda install dsh-bioThe dishevelled.org bio command line tools are available in Homebrew via Brewsci/bio, https://github.com/brewsci/homebrew-bio
$ brew install brewsci/bio/dsh-bioThe dishevelled.org bio command line tools are available in Docker via BioContainers, https://biocontainers.pro
$ docker pull quay.io/biocontainers/dsh-bio:{tag}Find {tag} on the tag search page, https://quay.io/repository/biocontainers/dsh-bio?tab=tags