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3ab6a3dbc1
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added untracked files in scripts and dynamut
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2022-01-04 12:26:54 +00:00 |
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00b84ccb1c
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handled rpob 5uhc position offset in mcsm_ppi2
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2022-01-04 10:45:29 +00:00 |
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c32de1bf0f
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Merge branch 'embb_dev'
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2021-11-12 14:37:10 +00:00 |
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4eaa0b5d2b
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saving work after running combining_dfs.py
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2021-11-12 14:16:48 +00:00 |
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873fd3a121
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added gene.lower to dynamut2 format result script
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2021-10-19 11:12:34 +01:00 |
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ba21188bd2
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added notes
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2021-10-18 13:58:06 +01:00 |
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675b222181
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added cmd option for dynamut2 formatting results
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2021-10-18 13:52:29 +01:00 |
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d443ecea6b
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added separate script for splitting csv after adding chain ID. saves lots of post processing
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2021-09-20 16:13:15 +01:00 |
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daa3556ede
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split csv for isoniazid
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2021-09-20 16:12:45 +01:00 |
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869fca7f94
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added function for generating lineage barplots and also test script along wiadding script for processing data and added it to get_plotting_dfs.R
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2021-09-06 19:50:50 +01:00 |
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605eb54526
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saving work for the day
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2021-09-02 17:40:24 +01:00 |
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f7aac58081
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adde format_results_dynamut2.py and ran shiny scripts for barplots
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2021-08-19 16:25:38 +01:00 |
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5529fbf63d
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added dynamut results formatting scripts, althouh needs to be rerun once b7 completes
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2021-08-13 13:24:22 +01:00 |
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5232731bc5
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saving work
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2021-08-12 17:37:56 +01:00 |
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8fbf5bcadd
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extracted results for dynamut gid bissection b10_21
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2021-08-12 17:35:12 +01:00 |
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efe5e0e391
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Merge branch 'master' into gidb_dev
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2021-08-12 15:35:28 +01:00 |
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fed8cd83a0
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minor tidy up for script submit_dynamut
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2021-08-12 15:33:57 +01:00 |
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93fae9e5f5
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reran b7 since previous run file output was 0 bytes
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2021-08-12 15:29:36 +01:00 |
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ca07351086
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ran b9 and b10 for gid after Dynamut team reran due to server issues
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2021-08-12 10:06:43 +01:00 |
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cf0db2a9c0
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saving dynamut and mcsm_na jobs submitted and retrieved
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2021-08-11 17:32:15 +01:00 |
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8975a4cedf
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retrieved results for gid b8 and b9
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2021-02-23 08:59:01 +00:00 |
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3ec42edc57
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retrieved gid b7 and submitted b8,b9 and b10
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2021-02-22 09:31:29 +00:00 |
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7925a408cd
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retrieved results for gid b6
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2021-02-21 16:23:22 +00:00 |
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e8644d7af5
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dynamut retrieved b5 and b6, submitted 6 and 7
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2021-02-20 13:05:30 +00:00 |
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d27b5898f7
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code to retrieve results from batch 4 and 5 once ready
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2021-02-19 12:09:26 +00:00 |
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8e68fb8f6a
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add files
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2021-02-18 11:50:46 +00:00 |
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ce5b545703
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running dynamut in batches
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2021-02-18 11:27:20 +00:00 |
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ff2bc78645
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renamed files in dynamut for consistency
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2021-02-18 10:52:51 +00:00 |
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84fccfbbb6
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renamed file in mcsm_na to be consistent
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2021-02-18 10:51:17 +00:00 |
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501492f9fb
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renaming file
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2021-02-18 10:48:06 +00:00 |
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96e101cf15
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renamed file run_submit to run_submit_dynamut
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2021-02-18 10:45:35 +00:00 |
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06df7369de
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renamed file run_results to run_get_results
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2021-02-18 10:43:45 +00:00 |
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4df1c54674
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saving work for mcsm_na
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2021-02-15 12:22:19 +00:00 |
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84970a667c
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added shell script to format muts for mcsm NA
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2021-02-12 17:38:42 +00:00 |
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7c84e8b044
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minor cody tidy up
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2021-02-12 16:50:34 +00:00 |
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26fe956d47
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tested and added note to reflect that tar.gz needs to be made into a cmd line option
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2021-02-12 15:32:16 +00:00 |
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2b6ffec100
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checked tar.gz downlaod from the script with example
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2021-02-12 15:25:32 +00:00 |
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a5f1878158
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added tar.gz download within get_results.py
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2021-02-12 15:24:51 +00:00 |
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deb0aa8e58
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separated defs and calls and added a separate script to test examples
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2021-02-12 14:15:55 +00:00 |
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6c458f8883
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updating and cleaning get_results script
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2021-02-12 12:04:49 +00:00 |
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db1c950c39
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updating get_results_def.py
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2021-02-12 11:38:21 +00:00 |
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c146ea0f43
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added example files to test dynamut results fetching for single and multiple urls
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2021-02-11 19:22:19 +00:00 |
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72426fd949
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updated with def for get_results.py for dynamut
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2021-02-11 19:21:26 +00:00 |
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9629d24169
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extracting single mut url from the batch processing step
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2021-02-11 17:19:04 +00:00 |
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e67a716d82
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added submit_def.py with example to run batch of 50
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2021-02-11 14:36:32 +00:00 |
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91f214f014
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added split_csv.sh
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2021-02-11 13:42:14 +00:00 |
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e302aafacf
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uncommented some debug output for mcsm, pandas and numpy conflict. So temporarily resolved it by running from base env
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2021-02-11 10:53:23 +00:00 |
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acd51ab3e4
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saving work in dynamut submit
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2021-02-11 09:46:11 +00:00 |
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e3189df74b
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dynamut scripts and minor change dir for rd_df.py
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2021-02-10 15:40:33 +00:00 |
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21451789e7
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renamed files
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2021-02-10 11:53:20 +00:00 |
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