bam2m5: Covert bam file to Pacbio m5 format

Description

Pacbio .m5 alignment format is used by several assembly software like pbdagcon, sparc, yet only blasr could output this format. sam/bam file is still the standard output format for alignment. Here provides a converter from sam/bam format to m5, connecting universal Pacbio alignment results with downstream analysis softwares need m5 format.

Usage

Usage: python3 bam2m5.py <in.bam> <ref.fa> [--score <score_scheme>] <out.m5>

in.bam

input bam file, should be sorted by coordinate for efficiency.

Note: as coordinate of read is used in m5 file, if bam is generated by blasr, -clipping (soft|hard) parameter should be used.

ref.fa

reference file

the <ref.fa>.fai is needed. either you already have one or the programm will build one for you, in which case the write permission to the dir which contains <ref.fa> is needed.

score_scheme

• scoring parameter used for alignment, in format match,mismatch,gap_open,gap_extend.
• eg: -5,6,10,0 means score -5 for a match, score 6 for a mismatch, 10 for gap open and 0 for one base gap extend.

• the default score schemes for these software:

  • blasr -sam: -5,6,10,0
  • blasr -m 5: -5,6,0,5
  • bwa mem -x pacbio: 1,-1,-1,-1

• notice the different sign of scores for blasr and bwa
• the default value is -5,6,0,5, equivalent to blasr -m 5 scheme
• if the score filed in m5 file is used by downstream analysis, one may choose use the blasr -m 5 scheme to get compatibility with blasr -m 5 result, no matter which score scheme is really used by the alignment software.

out.m5

output m5 file

example: python3 bam2m5.py align.sorted.bam ref.fa -5,6,0,5 align.sorted.m5

Dependency

Python >= 3.0:

this script is in python3, python2 support may be added later

BioUtil >= 0.2:

python package, handling bam file, fasta file reading. Use pip3 install BioUtil to install this pacakge.

cython >= 0.24:

used for speed up code

Install

1. download the file, unzip the file, into the dir
2. run python3 cython_build.py
3. (optional) cd test; bash run_test.sh for test. (blasr needed)
4. Now you can invoke bam2m5.py for use.

Authors

Yu XU, [email protected]

Lisense

These scripts are under GPL2 lisense.