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jaxcs / Seqnature

Seqnature: incorporate SNPs and Indels into a reference genome
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Reference class Fasta parsing is really inefficient and error-prone #1

Open mdshw5 opened 10 years ago

mdshw5 commented 10 years ago

You might consider just using something like this: https://github.com/mdshw5/pyfaidx. If you are planning to keep developing this project I'd be glad to help clean this part up.

Disclaimer: I am the author of pyfaidx.

AlSimonsJax commented 10 years ago

Hi, Matt.

Thanks for the pointer to your project. I was unaware of it. I do plan another release toward the end of the summer, and will replace my code for accessing reference sequence with yours. Thanks.

At this point, I think I'm all set with staffing, but may come back to you. Thanks, -Al

From: Matt Shirley [notifications@github.com] Sent: Tuesday, June 24, 2014 2:50 PM To: jaxcs/Seqnature Subject: [Seqnature] Reference class Fasta parsing is really inefficient and error-prone (#1)

You might consider just using something like this: https://github.com/mdshw5/pyfaidx. If you are planning to keep developing this project I'd be glad to help clean this part up.

Disclaimer: I am the author of pyfaidx.

— Reply to this email directly or view it on GitHubhttps://github.com/jaxcs/Seqnature/issues/1.

The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.

mdshw5 commented 10 years ago

Cool.

On Jul 8, 2014, at 1:01 PM, Al Simons notifications@github.com wrote:

Hi, Matt.

Thanks for the pointer to your project. I was unaware of it. I do plan another release toward the end of the summer, and will replace my code for accessing reference sequence with yours. Thanks.

At this point, I think I'm all set with staffing, but may come back to you. Thanks, -Al

From: Matt Shirley [notifications@github.com] Sent: Tuesday, June 24, 2014 2:50 PM To: jaxcs/Seqnature Subject: [Seqnature] Reference class Fasta parsing is really inefficient and error-prone (#1)

You might consider just using something like this: https://github.com/mdshw5/pyfaidx. If you are planning to keep developing this project I'd be glad to help clean this part up.

Disclaimer: I am the author of pyfaidx.

— Reply to this email directly or view it on GitHubhttps://github.com/jaxcs/Seqnature/issues/1.

The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible. — Reply to this email directly or view it on GitHub.