rust-samtools-genomeview

• rust samtools genome-view
• rust-samtools-genome-view: takes a genome alignment files, a reference fasta file, the upstream and the downstream regions and the path to the prank aligner and then aligns the extracted regions and also outputs a unaligned file.The aligned region will also be visualized into the terminal using the embedded approach.
• This feature is not present in samtools and specific to rust-samtools and allows for the direct estimation of the reads to alignments approach for desining capture assay.
• targetd capture assay development for taking reads from HybSeq.
• general note: Incase of Golang and RUST, please see the last commit message and if it says compiled binary then it is completed or else still in development version.

cargo build 

λ gauravsablok rust-samtools-genomeview → λ git main* → \
./target/debug/rust-samtools-genome-view -h
Usage: rust-samtools-genome-view <ALIGNMENT_ARG> <IDLIST_ARG> <FASTA_ARG> <UPSTREAM_ARG> <DOWNSTREAM_ARG> <PRANK_ALIGNER_ARG>

Arguments:
  <ALIGNMENT_ARG>      please provide the path to the alignment file
  <IDLIST_ARG>         please provide the id list for the specific region
  <FASTA_ARG>          please provide the fasta file used for the reference alignment
  <UPSTREAM_ARG>       please provide the upstream add from the sam alignments to be extracted
  <DOWNSTREAM_ARG>     please provide the downstream add from the sam alignments to be extracted
  <PRANK_ALIGNER_ARG>  please provide the path to the prank aligner

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

• how to run the binary

./rust-samtools-genome-view ./sample-files/Col0_C1.100k_selected.sam ./sample-files/idlist.txt ./sample-files/sample-fasta.fasta 5 10 ./prank

• it will output following additional files

- selected-ids-downstream-aligned.fasta.best.fas - best alignment for the downstream region
- selected-ids-reads-aligned.fasta.best.fas - best alignment for the reads
- selected-ids-upstream-aligned.fasta.best.fas - best alignment for the upstream region.
- selected-ids-upstream-region-downstream-aliged.fasta.best.fas - best alignment for the upstream+region+downstream.
Gaurav Sablok