panutils

Some utils for pangenome construction

Installation

# The c_ffi feature need clang. You can install it with conda.
cargo install --path .

Subcommand

Usage: panutils <COMMAND>

Commands:
  fastixe  
  help     Print this message or the help of the given subcommand(s)

Options:
  -h, --help     Print help
  -V, --version  Print version

fastixe

This subcommand is like fastix, which can add prefixes to FASTA headers. It support pangenomic applications, following the PanSN hierarchical naming specification. The difference is to add more functions.

My idea for rewriting the code in Rust is that PGGB requires multiple genomes, each following the PanSN naming convention, to be merged into a single file, optionally compressed using bgzip. It also needs samtools faidx to build an index for the compressed genome file. I hope to implement these features more efficiently using Rust, rather than relying on a pipeline of shell commands involving fastix, bgzip, and samtools faidx. This would reduce dependency on conda-based tools. At the same time, it's also a rust practice project for me as a beginner.

Usage

Usage: panutils fastixe [OPTIONS]

Options:
  -t, --threads <THREADS>  Number of threads [default: 1]. [default: 1]
      --trace              Trace output (caution: very verbose).
      --debug              Debug output.
  -h, --help               Print help

INPUT FILE:
  -a, --stdin <INPUT_STDIN>             Input stream, use '-' for stdin
  -i, --input-genome <INPUT_GENOME>     Input genome.
  -s, --input-files <INPUT_FILES>...    Multiple input files.
  -l, --input-genome-list <INPUT_LIST>  Input genome list.
  -d, --input-dir <INPUT_DIRECTORY>     Input directory containing FASTA files.

OUTPUT:
  -o, --out-dir <OUT_DIRECTORY>  Output directory. [default: genomes]

SEPARATE OUTPUT:
      --stdout  Stdout.
  -g, --gz      Gzip output.

RENAME:
  -p, --prefix <PREFIX>  Prefix to add to headers.
  -r, --regex <REG>      File name regex [default: [^_]+_[^_]+]

Sequence:
  -u, --up  All bases are converted to uppercase letters.

MERGE OUTPUT:
  -e, --output-file-name <MERGE_OUTPUT_FILE_PATH>  Merge output file path. [default: merged.fa]
  -m, --merge                                      Merge output.
  -b, --bgz                                        Merge bgzip output.

INDEX:
  -f, --faidx  Build the index for fasta's bgzip file, just like samtools faidx.

COMPRESSION LEVEL:
      --level <COMPRESSION_LEVEL>  Compression (0-9).

Examples

# rename with default regex
panutils fastixe -i tests/GCF_002012065.1_ASM201206v1_genomic.fna --up 

# rename with specified prefix
panutils fastixe -i tests/GCF_002012065.1_ASM201206v1_genomic.fna --up -p GCF_002012065.1#0#

# multiple files input 
panutils fastixe -s tests/GCF_002012065.1_ASM201206v1_genomic.fna tests/GCF_006400955.1_ASM640095v1_genomic.fna --up
panutils fastixe -l tests/test_genome_list.txt --up
panutils fastixe -d tests/ --up

# gzip output
panutils fastixe -i tests/GCF_002012065.1_ASM201206v1_genomic.fna --up -g

# merge and bgzip output and faidx
panutils fastixe -d tests/ -m -b -f -e test_merged.fa --up