New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Genome -> Reads #2

Closed

7 tasks done

HadrienG opened this issue Nov 17, 2016 · 1 comment

Assignees

Owner

HadrienG commented Nov 17, 2016 •

edited

Loading

Issue to track the progress on the Roadmap item "From a genome, output perfect reads in fastq format"

Test file: genome.fasta
Pattern: ATCG
Length: 2000bp

add Biopython to requirements.txt (aka let's not re-write a fasta parser)
add Numpy to requirements.txt (required by Biopython)
generate 100 (pseudo)random subsequences in fasta format
generate x subsequences covering the input genome 40x (or an arbitrary coverage level)
add quality information (fastq output)
get out of app.py, import module and write ArgumentParser
setup travis and write tests

Note: Biopython discards everything after a blank space (' ') in the sequence headers

HadrienG self-assigned this

HadrienG mentioned this issue

Open

20 tasks

Owner Author

HadrienG commented Nov 17, 2016

Closed with f064c98

HadrienG closed this as completed

HadrienG pushed a commit that referenced this issue


          Merge pull request #2 from ENPICOM/amplicon

47f16ed

Amplicon

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment