acorg/light-matter issues and pull requests

#46 - Database should write a line of JSON with parameters

Issue - State: closed - Opened by bamueh about 10 years ago

#46 - Database should write a line of JSON with parameters

Issue - State: closed - Opened by bamueh about 10 years ago

#45 - ScannedReadDatabaseResult.save should write one line of JSON

Issue - State: closed - Opened by bamueh about 10 years ago
Labels: enhancement

#45 - ScannedReadDatabaseResult.save should write one line of JSON

Issue - State: closed - Opened by bamueh about 10 years ago
Labels: enhancement

#44 - Added requirements file

Pull Request - State: closed - Opened by bamueh about 10 years ago

#44 - Added requirements file

Pull Request - State: closed - Opened by bamueh about 10 years ago

#43 - Add a requirements.txt

Issue - State: closed - Opened by terrycojones about 10 years ago
Labels: enhancement

#43 - Add a requirements.txt

Issue - State: closed - Opened by terrycojones about 10 years ago
Labels: enhancement

#42 - Create database now writes the database to stdout.

Pull Request - State: closed - Opened by terrycojones about 10 years ago

#42 - Create database now writes the database to stdout.

Pull Request - State: closed - Opened by terrycojones about 10 years ago

#41 - Change create-database.py so it writes out the newly created database.

Issue - State: closed - Opened by terrycojones about 10 years ago
Labels: enhancement

#41 - Change create-database.py so it writes out the newly created database.

Issue - State: closed - Opened by terrycojones about 10 years ago
Labels: enhancement

#40 - Added trivial pickle-based save and load methods for ScannedReadDatabase

Pull Request - State: closed - Opened by terrycojones about 10 years ago

#40 - Added trivial pickle-based save and load methods for ScannedReadDatabase

Pull Request - State: closed - Opened by terrycojones about 10 years ago

#39 - Added a find function and a bin script

Pull Request - State: closed - Opened by bamueh about 10 years ago

#38 - Add JSON save and load methods to ScannedReadDatabase

Issue - State: closed - Opened by terrycojones about 10 years ago
Labels: enhancement

#38 - Add JSON save and load methods to ScannedReadDatabase

Issue - State: closed - Opened by terrycojones about 10 years ago
Labels: enhancement

#37 - Add a bin script for the find method in ScannedReadDatabase

Issue - State: closed - Opened by bamueh about 10 years ago - 2 comments

#37 - Add a bin script for the find method in ScannedReadDatabase

Issue - State: closed - Opened by bamueh about 10 years ago - 2 comments

#36 - Added trig point finder that finds trig points based on specific amino acids

Pull Request - State: closed - Opened by bamueh about 10 years ago - 3 comments

#36 - Added trig point finder that finds trig points based on specific amino acids

Pull Request - State: closed - Opened by bamueh about 10 years ago - 3 comments

#35 - Implement a trig point finder using Cys

Issue - State: closed - Opened by bamueh about 10 years ago

#34 - Add a find method to scannedReadDatabase

Issue - State: closed - Opened by bamueh about 10 years ago

#33 - Add script to build db

Pull Request - State: closed - Opened by terrycojones about 10 years ago

#33 - Add script to build db

Pull Request - State: closed - Opened by terrycojones about 10 years ago

#32 - Fixed finder name listing and another small bug.

Pull Request - State: closed - Opened by terrycojones about 10 years ago

#32 - Fixed finder name listing and another small bug.

Pull Request - State: closed - Opened by terrycojones about 10 years ago

#31 - The list of landmark and trig point names printed by find-features is wrong

Issue - State: closed - Opened by terrycojones about 10 years ago
Labels: bug

#31 - The list of landmark and trig point names printed by find-features is wrong

Issue - State: closed - Opened by terrycojones about 10 years ago
Labels: bug

#30 - Added files to make a dictionary for look up

Pull Request - State: closed - Opened by bamueh about 10 years ago - 1 comment

#29 - Fix tests in ScannedReadDatabase

Issue - State: closed - Opened by bamueh about 10 years ago

#29 - Fix tests in ScannedReadDatabase

Issue - State: closed - Opened by bamueh about 10 years ago

#28 - Added getPairs method to ScannedRead class.

Pull Request - State: closed - Opened by terrycojones about 10 years ago - 1 comment

#28 - Added getPairs method to ScannedRead class.

Pull Request - State: closed - Opened by terrycojones about 10 years ago - 1 comment

#27 - Added ScannedReadDatabase class

Pull Request - State: closed - Opened by bamueh about 10 years ago - 1 comment

#27 - Added ScannedReadDatabase class

Pull Request - State: closed - Opened by bamueh about 10 years ago - 1 comment

#26 - Add bin script that builds a dictionary for lookup.

Issue - State: closed - Opened by bamueh about 10 years ago

#26 - Add bin script that builds a dictionary for lookup.

Issue - State: closed - Opened by bamueh about 10 years ago

#25 - Add class that builds a dictionary for lookup.

Issue - State: closed - Opened by bamueh about 10 years ago

#25 - Add class that builds a dictionary for lookup.

Issue - State: closed - Opened by bamueh about 10 years ago

#24 - Add getPairs method in ScannedReads

Issue - State: closed - Opened by bamueh about 10 years ago

#24 - Add getPairs method in ScannedReads

Issue - State: closed - Opened by bamueh about 10 years ago

#23 - Added tests to test that landmark and trig point symbols don't collide.

Pull Request - State: closed - Opened by bamueh about 10 years ago - 1 comment

#23 - Added tests to test that landmark and trig point symbols don't collide.

Pull Request - State: closed - Opened by bamueh about 10 years ago - 1 comment

#22 - Add a test to make sure symbols in landmarks and trig points do not collide

Issue - State: closed - Opened by terrycojones about 10 years ago
Labels: enhancement

#22 - Add a test to make sure symbols in landmarks and trig points do not collide

Issue - State: closed - Opened by terrycojones about 10 years ago
Labels: enhancement

#21 - Add triangulation point

Pull Request - State: closed - Opened by bamueh about 10 years ago

#20 - Add landmark finders for other helices

Pull Request - State: closed - Opened by terrycojones about 10 years ago

#20 - Add landmark finders for other helices

Pull Request - State: closed - Opened by terrycojones about 10 years ago

#19 - Add the 3-10 helix and the π helix

Issue - State: closed - Opened by terrycojones about 10 years ago
Labels: enhancement

#19 - Add the 3-10 helix and the π helix

Issue - State: closed - Opened by terrycojones about 10 years ago
Labels: enhancement

#18 - Allow multiple landmarks from command line with find-landmarks.py

Pull Request - State: closed - Opened by terrycojones about 10 years ago - 1 comment

#18 - Allow multiple landmarks from command line with find-landmarks.py

Pull Request - State: closed - Opened by terrycojones about 10 years ago - 1 comment

#17 - Make it possible to run multiple landmark finders from the command line

Issue - State: closed - Opened by terrycojones about 10 years ago
Labels: enhancement

#17 - Make it possible to run multiple landmark finders from the command line

Issue - State: closed - Opened by terrycojones about 10 years ago
Labels: enhancement

#16 - Lots of changes to rename statistics to landmarks and to make the AlphaHelix landmark find all non-overlapping helices.

Pull Request - State: closed - Opened by terrycojones about 10 years ago - 1 comment

#16 - Lots of changes to rename statistics to landmarks and to make the AlphaHelix landmark find all non-overlapping helices.

Pull Request - State: closed - Opened by terrycojones about 10 years ago - 1 comment

#15 - Fix failing type tests

Pull Request - State: closed - Opened by bamueh over 10 years ago - 1 comment

#14 - Make it so that tests pass after type argument is no longer present

Issue - State: closed - Opened by bamueh over 10 years ago
Labels: bug

#14 - Make it so that tests pass after type argument is no longer present

Issue - State: closed - Opened by bamueh over 10 years ago
Labels: bug

#13 - Add statistic specific to Bunyaviridae

Pull Request - State: closed - Opened by bamueh over 10 years ago

#12 - Add statistic that checks for sequences specific to Bunyaviridae

Issue - State: closed - Opened by bamueh over 10 years ago

#12 - Add statistic that checks for sequences specific to Bunyaviridae

Issue - State: closed - Opened by bamueh over 10 years ago

#11 - Added functions to add table with statistics to database, and to query database with a precomputed statistic

Pull Request - State: closed - Opened by bamueh over 10 years ago - 2 comments

#11 - Added functions to add table with statistics to database, and to query database with a precomputed statistic

Pull Request - State: closed - Opened by bamueh over 10 years ago - 2 comments

#10 - Add functions to add statistics computed on the virus database to a mySQL database and to query that database

Issue - State: closed - Opened by bamueh over 10 years ago

#9 - Added statistics with alpha helix

Pull Request - State: closed - Opened by bamueh over 10 years ago - 2 comments

#8 - Add statistic function using alpha helices

Issue - State: closed - Opened by bamueh over 10 years ago

#8 - Add statistic function using alpha helices

Issue - State: closed - Opened by bamueh over 10 years ago

#7 - Add a statistic that checks whether a read is in an open reading frame or not

Issue - State: closed - Opened by bamueh over 10 years ago

#7 - Add a statistic that checks whether a read is in an open reading frame or not

Issue - State: closed - Opened by bamueh over 10 years ago

#6 - Find function 1

Pull Request - State: closed - Opened by bamueh over 10 years ago - 1 comment

#5 - Rearranged to add statistics sub-dirs in light and test dirs.

Pull Request - State: closed - Opened by terrycojones over 10 years ago

#5 - Rearranged to add statistics sub-dirs in light and test dirs.

Pull Request - State: closed - Opened by terrycojones over 10 years ago

#4 - Small rearrangements

Issue - State: closed - Opened by terrycojones over 10 years ago
Labels: enhancement

#4 - Small rearrangements

Issue - State: closed - Opened by terrycojones over 10 years ago
Labels: enhancement

#3 - moved runStatistic function, test

Pull Request - State: closed - Opened by bamueh over 10 years ago

#2 - move runStatistic in bin/calculate-statistics to light/utils, write tests

Issue - State: closed - Opened by bamueh over 10 years ago

#1 - Add a filter function to iterate over statistics classes

Issue - State: closed - Opened by bamueh over 10 years ago

GitHub / acorg/light-matter issues and pull requests