Skip to content
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

Multi contig implementation #9

Open
wants to merge 25 commits into
base: master
Choose a base branch
from
Open

Multi contig implementation #9

wants to merge 25 commits into from

Commits on Jan 11, 2019

  1. Remove test data

    Nolan Woods committed Jan 11, 2019
    Configuration menu
    Copy the full SHA
    94edd28 View commit details
    Browse the repository at this point in the history

Commits on Jan 17, 2019

  1. Add GFF output

    Nolan Woods committed Jan 17, 2019
    1 Configuration menu
    Copy the full SHA
    c81c1c6 View commit details
    Browse the repository at this point in the history

Commits on Jan 31, 2019

  1. Add input sequence and strand to GFF output

    Nolan Woods committed Jan 31, 2019
    Configuration menu
    Copy the full SHA
    f483e40 View commit details
    Browse the repository at this point in the history

  2. Fix bioperl not finding id() in embl files

    Nolan Woods committed Jan 31, 2019
    Configuration menu
    Copy the full SHA
    c8d1fe0 View commit details
    Browse the repository at this point in the history

Commits on Jun 5, 2019

  1. Add fix to ignore features with joins containing start > end that bre… 

    …ak the trunc() function
    @glwinsor
    glwinsor committed Jun 5, 2019
    Configuration menu
    Copy the full SHA
    7aa93b9 View commit details
    Browse the repository at this point in the history

Commits on Jun 6, 2019

  1. Merge remote-tracking branch 'origin/geoff' into gff 

    Incorporate fix for cross origin genes crashing islandpath.
    Nolan Woods committed Jun 6, 2019
    Configuration menu
    Copy the full SHA
    c24711b View commit details
    Browse the repository at this point in the history

Commits on Jun 25, 2019

  1. Suppress experimental smartmatch

    @JFsanchezherrero
    JFsanchezherrero committed Jun 25, 2019
    Configuration menu
    Copy the full SHA
    154f595 View commit details
    Browse the repository at this point in the history

  2. Let several contigs (def read_and_convert)

    @JFsanchezherrero
    JFsanchezherrero committed Jun 25, 2019
    Configuration menu
    Copy the full SHA
    52c7176 View commit details
    Browse the repository at this point in the history

  3. add csv outfile for dinuc bias

    @JFsanchezherrero
    JFsanchezherrero committed Jun 25, 2019
    Configuration menu
    Copy the full SHA
    7794abd View commit details
    Browse the repository at this point in the history

  4. Aesthetics, outfile to csv, loop bug fixed

    @JFsanchezherrero
    JFsanchezherrero committed Jun 25, 2019
    Configuration menu
    Copy the full SHA
    7455041 View commit details
    Browse the repository at this point in the history

  5. change header row

    @JFsanchezherrero
    JFsanchezherrero committed Jun 25, 2019
    Configuration menu
    Copy the full SHA
    9f7a0d1 View commit details
    Browse the repository at this point in the history

  6. Aesthetics, header row number

    @JFsanchezherrero
    JFsanchezherrero committed Jun 25, 2019
    Configuration menu
    Copy the full SHA
    ecbd4cf View commit details
    Browse the repository at this point in the history

  7. Add multi-contig analysis

    @JFsanchezherrero
    JFsanchezherrero committed Jun 25, 2019
    Configuration menu
    Copy the full SHA
    afbff58 View commit details
    Browse the repository at this point in the history

Commits on Jun 26, 2019

  1. remove debugging messages

    @JFsanchezherrero
    JFsanchezherrero committed Jun 26, 2019
    Configuration menu
    Copy the full SHA
    651d2a6 View commit details
    Browse the repository at this point in the history

Commits on Jun 27, 2019

  1. Add logging messages; GI min_length as variable

    @JFsanchezherrero
    JFsanchezherrero committed Jun 27, 2019
    Configuration menu
    Copy the full SHA
    7497c97 View commit details
    Browse the repository at this point in the history

  2. filter GI by min length

    @JFsanchezherrero
    JFsanchezherrero committed Jun 27, 2019
    Configuration menu
    Copy the full SHA
    02ec5a3 View commit details
    Browse the repository at this point in the history

  3. control for different contig sequences

    @JFsanchezherrero
    JFsanchezherrero committed Jun 27, 2019
    Configuration menu
    Copy the full SHA
    323d4c0 View commit details
    Browse the repository at this point in the history

  4. key as coordiantes_sequence

    @JFsanchezherrero
    JFsanchezherrero committed Jun 27, 2019
    Configuration menu
    Copy the full SHA
    1b56453 View commit details
    Browse the repository at this point in the history

  5. merge with gff branch

    @JFsanchezherrero
    JFsanchezherrero committed Jun 27, 2019
    Configuration menu
    Copy the full SHA
    7fe9c70 View commit details
    Browse the repository at this point in the history

  6. add credits

    @JFsanchezherrero
    JFsanchezherrero committed Jun 27, 2019
    Configuration menu
    Copy the full SHA
    b3e8ca2 View commit details
    Browse the repository at this point in the history

  7. add example embl format

    @JFsanchezherrero
    JFsanchezherrero committed Jun 27, 2019
    Configuration menu
    Copy the full SHA
    af28a7e View commit details
    Browse the repository at this point in the history

  8. add credits

    @JFsanchezherrero
    JFsanchezherrero committed Jun 27, 2019
    Configuration menu
    Copy the full SHA
    b008436 View commit details
    Browse the repository at this point in the history

  9. Update README.md

    @JFsanchezherrero
    JFsanchezherrero authored Jun 27, 2019
    Configuration menu
    Copy the full SHA
    9049154 View commit details
    Browse the repository at this point in the history

  10. Update README.md

    @JFsanchezherrero
    JFsanchezherrero authored Jun 27, 2019
    Configuration menu
    Copy the full SHA
    5ce24bf View commit details
    Browse the repository at this point in the history

  11. Add multi-contig example

    @JFsanchezherrero
    JFsanchezherrero committed Jun 27, 2019
    Configuration menu
    Copy the full SHA
    b4b2a03 View commit details
    Browse the repository at this point in the history