Ecosyste.ms: Issues

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GitHub / widdowquinn/find_differential_primers issues and pull requests

#57 - Simple method for providing more params to blastn

Pull Request - State: open - Opened by nick-youngblut almost 4 years ago

#56 - added ArgumentDefaultsHelpFormatter to all parsers

Pull Request - State: closed - Opened by nick-youngblut almost 4 years ago - 3 comments

#55 - parameter defaults

Issue - State: closed - Opened by nick-youngblut almost 4 years ago - 13 comments
Labels: question, enhancement, unable to reproduce

#54 - conda commands

Issue - State: closed - Opened by maguileraf almost 4 years ago - 3 comments
Labels: question

#53 - Problems with use of pdp

Issue - State: open - Opened by aiqubo almost 4 years ago - 3 comments
Labels: bug, installation

#52 - Clarify documentation regarding pdp/find_differential_primer versions

Issue - State: open - Opened by widdowquinn almost 4 years ago
Labels: enhancement, documentation

#51 - Problems with installation of Find differential Primers on Ubuntu

Issue - State: closed - Opened by J123T almost 4 years ago - 6 comments
Labels: question, bug, documentation

#50 - Fix broken bioconda recipe

Issue - State: closed - Opened by widdowquinn almost 4 years ago - 2 comments
Labels: bug

#49 - conda install pdp not working

Issue - State: closed - Opened by rsiani about 4 years ago - 1 comment
Labels: question

#48 - is pdp still available?

Issue - State: closed - Opened by AlexGaithuma over 4 years ago - 1 comment
Labels: question

#47 - Use `mypy` to aid with type checking

Issue - State: open - Opened by widdowquinn almost 5 years ago
Labels: style clean

#46 - Add `pdp config` option to take `pyani download` output and create a config file.

Issue - State: open - Opened by widdowquinn almost 5 years ago
Labels: enhancement

#45 - Put user documentation on ReadTheDocs

Issue - State: open - Opened by widdowquinn almost 5 years ago
Labels: enhancement, documentation

#44 - Add option to multiplex primers

Issue - State: open - Opened by widdowquinn almost 5 years ago
Labels: enhancement

#43 - Update logging exception formats

Issue - State: open - Opened by widdowquinn almost 5 years ago
Labels: style clean, enhancement

#42 - Add option to use online Primer-BLAST for off-target screening

Issue - State: open - Opened by widdowquinn almost 5 years ago
Labels: enhancement

#41 - Supply Flask interface/API onto SQLite backend

Issue - State: open - Opened by widdowquinn almost 5 years ago
Labels: enhancement

#40 - Store primer design information in SQLite backend

Issue - State: open - Opened by widdowquinn almost 5 years ago
Labels: enhancement

#39 - Stage third-party tool output in a temp directory for checking

Issue - State: open - Opened by widdowquinn over 5 years ago
Labels: enhancement

#38 - Add `--recovery` option to schedulable subcommands

Pull Request - State: closed - Opened by widdowquinn over 5 years ago - 2 comments

#37 - Add `--recovery` option to subcommands

Issue - State: closed - Opened by widdowquinn over 5 years ago - 1 comment
Labels: enhancement

#36 - Primer3 v2

Pull Request - State: closed - Opened by widdowquinn over 5 years ago - 1 comment

#35 - refactor parsers for `pdp` subcommands into individual `.py` files

Pull Request - State: closed - Opened by widdowquinn almost 6 years ago

#34 - Fixes #32 and #33

Pull Request - State: closed - Opened by widdowquinn almost 6 years ago - 1 comment

#33 - Add diversity measure to output of `pdp extract`

Issue - State: closed - Opened by widdowquinn almost 6 years ago - 1 comment
Labels: enhancement

#32 - Add filter option that targets variable regions within a single class

Issue - State: closed - Opened by widdowquinn almost 6 years ago - 1 comment
Labels: enhancement

#31 - Add filter option that restricts primer design to regions specific to a target class

Issue - State: open - Opened by widdowquinn almost 6 years ago - 1 comment
Labels: enhancement

#30 - Replace `ePrimer3` with modern Primer3 (v2+)

Issue - State: closed - Opened by widdowquinn almost 6 years ago - 4 comments
Labels: enhancement

#29 - Use read mapper as alternative to `PrimerSearch`

Issue - State: open - Opened by widdowquinn almost 6 years ago - 8 comments
Labels: enhancement

#28 - Add primer location output for use with IGV

Issue - State: closed - Opened by widdowquinn almost 6 years ago - 1 comment
Labels: enhancement

#27 - Progress bar formatting in `pdp config` is not right

Issue - State: closed - Opened by widdowquinn almost 6 years ago - 2 comments
Labels: bug

#26 - Filter subcommand

Pull Request - State: closed - Opened by widdowquinn about 6 years ago - 1 comment

#25 - Filter subcommand

Pull Request - State: closed - Opened by widdowquinn about 6 years ago

#24 - Refactor extract

Pull Request - State: closed - Opened by widdowquinn about 6 years ago - 1 comment
Labels: enhancement

#23 - Some predicted primers have runs of `N` in the amplicons

Issue - State: open - Opened by widdowquinn over 6 years ago
Labels: enhancement

#22 - If ePrimer3 does not generate primers, the pipeline hangs

Issue - State: open - Opened by widdowquinn over 6 years ago
Labels: bug

#21 - Tag new release?

Issue - State: open - Opened by druvus over 6 years ago - 5 comments
Labels: enhancement

#20 - Docs

Pull Request - State: closed - Opened by widdowquinn over 6 years ago

#19 - Extend tests

Pull Request - State: closed - Opened by widdowquinn over 6 years ago

#18 - Tools test

Pull Request - State: closed - Opened by widdowquinn over 6 years ago - 1 comment

#17 - add primersearch code

Pull Request - State: closed - Opened by widdowquinn almost 7 years ago - 1 comment

#16 - Extend tests

Pull Request - State: closed - Opened by widdowquinn almost 7 years ago - 1 comment

#15 - modifications for config command

Pull Request - State: closed - Opened by widdowquinn almost 7 years ago - 1 comment
Labels: style clean, enhancement

#14 - ValueError: Your XML file did not start with <?xml... but instead '\n'

Issue - State: open - Opened by BioJNO about 7 years ago - 1 comment
Labels: bug

#13 - Eprimer3 test

Pull Request - State: closed - Opened by widdowquinn over 7 years ago - 1 comment
Labels: bugfix

#12 - Eprimer3 test

Pull Request - State: closed - Opened by widdowquinn over 7 years ago - 1 comment

#11 - Add ePrimer3 tests

Pull Request - State: closed - Opened by widdowquinn over 7 years ago - 1 comment
Labels: bugfix, tests

#10 - Add tests

Pull Request - State: closed - Opened by widdowquinn over 7 years ago - 1 comment
Labels: tests

#9 - Add blastscreen tests

Pull Request - State: closed - Opened by widdowquinn over 7 years ago - 1 comment

#8 - Fix cmdline tests

Pull Request - State: closed - Opened by widdowquinn over 7 years ago - 1 comment
Labels: refactor, tests

#7 - Config to json

Pull Request - State: closed - Opened by widdowquinn over 7 years ago - 1 comment
Labels: refactor, style clean, tests

#6 - Refactor script

Pull Request - State: closed - Opened by widdowquinn over 7 years ago - 3 comments
Labels: refactor, style clean

#5 - update test suite

Pull Request - State: closed - Opened by widdowquinn over 7 years ago - 1 comment
Labels: refactor, style clean, tests

#4 - Add debugging code explanantion

Issue - State: closed - Opened by wjidea about 11 years ago - 3 comments

#3 - Minor fixes

Pull Request - State: closed - Opened by mikerobeson over 11 years ago

#2 - Merged dev branch to master, mod to pull request.

Pull Request - State: closed - Opened by cometsong about 12 years ago

#1 - Dev update

Pull Request - State: closed - Opened by cometsong about 12 years ago