Python example program and README update

[a-slide]

Hi Mengyao I wrote a python script to test the python wrapper (pyssw) and added example illumina files to test it. The readme file was also updated as a markdown document and the documentation for the wrapper and pyssw was included. Sincerely.

Adrien

[mengyao]

Dear Adrien,

Thank you sincerely for your test and updates.

I have merged your contributions and changed the title to “C/C++/Python Library”, so that people who search for the Python SW may find it more easily.

It’s a pleasure to have conversation with you through this program. Thanks again for your encouragement.

Best wishes,

Mengyao

On Jan 28, 2014, at 7:52 AM, Slide notifications@github.com wrote:

Hi Mengyao I wrote a python script to test the python wrapper (pyssw) and added example illumina files to test it. The readme file was also updated as a markdown document and the documentation for the wrapper and pyssw was included. Sincerely.

Adrien

You can merge this Pull Request by running

git pull https://github.com/a-slide/Complete-Striped-Smith-Waterman-Library master Or view, comment on, or merge it at:

https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library/pull/13

Commit Summary

Start to fill readme.md and correct typo in ssw.wrap Update readme Minor modifications Standalone python test program added Update readme Benchmark added New functionality in pyssw and update readme Update README.md Update README.md Update README.md New demo gzipped Update README.md with new tests Modify sam file format output File Changes

D README (111) A README.md (195) A demo/100k_illumina1.fastq.gz (0) A demo/Virus_genome.fa.gz (0) A src/pyssw.py (275) M src/ssw_wrap.py (31) Patch Links:

https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library/pull/13.patch https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library/pull/13.diff — Reply to this email directly or view it on GitHub.

[a-slide]

You are welcome. I'm really not familiar with SIMD instructions, but would it be possible to parallelize further the algorithm by using separate processes when aligning multiple queries ?

Adrien

[mengyao]

Dear Adrien,

Yes, you can parallelize it further when you align multiple queries.

For example, you can use multiple thread approach to paralyze the alignments. Mosaik aligner (http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0090581) calls SSW in a multiple thread way.

Best wishes,

Mengyao

On Jan 28, 2014, at 11:16 AM, Slide notifications@github.com wrote:

You are welcome. I'm really not familiar with SIMD instructions, but would it be possible to parallelize further the algorithm by using separate processes when aligning multiple queries ?

Adrien

— Reply to this email directly or view it on GitHub.

[mengyao]

Dear Adrien,

May I ask your full name, so that I can acknowledge you formally.

Sorry, I forgot to ask before.

Best wishes,

Mengyao

On Jan 28, 2014, at 11:16 AM, Slide notifications@github.com wrote:

You are welcome. I'm really not familiar with SIMD instructions, but would it be possible to parallelize further the algorithm by using separate processes when aligning multiple queries ?

Adrien

— Reply to this email directly or view it on GitHub.

[a-slide]

Hi Mengyao,

Thanks for the answer. I'll update pyssw to parallelize the alignment when I'll have a little free time. My full name is Adrien Leger. Good luck for your PhD manuscript and defence

Regards

Adrien

[mengyao]

Dear Adrien,

Thanks a lot for letting me know your name and your good wish to my graduation.

I appreciate your contribution sincerely.

Best wishes,

Mengyao

On Jan 29, 2014, at 4:02 AM, Slide notifications@github.com wrote:

Hi Mengyao,

Thanks for the answer. I'll update pyssw to parallelize the alignment when I'll have a little free time. My full name is Adrien Leger. Good luck for your PhD manuscript and defence

Regards

Adrien

— Reply to this email directly or view it on GitHub.