andreaguarracino / chain2paf

convert CHAIN format to PAF format

chain2paf

convert CHAIN format to PAF format

citation

installation

chain2paf is built with rust, and so we install using cargo:

git clone https://github.com/AndreaGuarracino/chain2paf
cd chain2paf
cargo install --force --path .

usage

With alignments in data/hg18ToHg19.over.chain, we would convert it into a PAF format file using this call:

chain2paf -i data/hg18ToHg19.over.chain > hg18ToHg19.over.chain.paf

If full CIGAR strings (with =/X operators) are required, we can specify two FASTA files (uncompressed or bgzipped), the 1-st for the targets and the 2-nd for the queries. For example, if the sequences of the human genome versions hg18 and hg19 are available in the hg18.fa.gz and hg19.fa.gz files, you can execute

chain2paf -i data/hg18ToHg19.over.chain -f hg18.fa.gz hg19.fa.gz > hg18ToHg19.over.chain.paf

If the CHAIN file is the result of a pairwise alignment, you can specify the same FASTA file for both targets and queries:

chain2paf -i input.chain -f input.fa.gz input.fa.gz > input.chain.paf

info

chain2paf performs the reverse operation of paf2chain.

chain2paf's Issues

Some proposals about genome-alignment format conversion

Hi!

I am currently working on the coordinate transformation by using chain file : https://github.com/wjwei-handsome/crussmap

The results of whole-genome alignment are available in a variety of formats, such as MAF, PAF, CHAIN, SAM, delta, etc.

In fact, these files can be converted to each other and integrated with downstream pipeline analysis.

I'm also interested in rust, so I have some naive ideas:

• Write efficient parsers for different file types (mainly for chain and delta files) using nom
• Define reasonable alignment structure objects to ensure consistency
• Develop a kit of tools

Have a nice day!

Error in chain2paf

Hello, I have a problem when using chain2maf. I converted the chain file to the hal format. How should I solve this problem?

thread 'main' panicked at 'called Result::unwrap() on an Err value: ParseIntError { kind: InvalidDigit }', src/main.rs:277:77
stack backtrace:
0: rust_begin_unwind
at /rustc/90c541806f23a127002de5b4038be731ba1458ca/library/std/src/panicking.rs:578:5
1: core::panicking::panic_fmt
at /rustc/90c541806f23a127002de5b4038be731ba1458ca/library/core/src/panicking.rs:67:14
2: core::result::unwrap_failed
at /rustc/90c541806f23a127002de5b4038be731ba1458ca/library/core/src/result.rs:1687:5
3: chain2paf::main
note: Some details are omitted, run with RUST_BACKTRACE=full for a verbose backtrace.

paf2maf

Thank you very mush,i can get paf format file success,i want to maf format finally,but i use paftools.js view -f maf /media/zhf/ext2/26maizeData/B73-kill.Anchorwave.paf ,I get error WARNING: converting to MAF requires the 'cs' tag, which is absent on line 1 ....WARNING: converting to MAF requires the 'cs' tag, which is absent on line 12366，What should I do to get the maf file through this software.