8000 Merge Dev-Master into Master by grabear · Pull Request #128 · datasnakes/OrthoEvolution · GitHub
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Merge Dev-Master into Master #128

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8000
Merged
merged 690 commits into from
Nov 17, 2017
Merged

Merge Dev-Master into Master #128

merged 690 commits into from
Nov 17, 2017

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grabear
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@grabear grabear commented Nov 17, 2017

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sdhutchins and others added 30 commits November 2, 2017 19:24
Deprecated gi functions. Added window_masker_taxid to blast parameter
cc5d2db
Added deprecation warnings for gi related functions
00f3494
@sdhutchins
Edited comments for consistency
9b4781a
@sdhutchins
Edited init for consistency
4eb81e3
@sdhutchins
Updated comments. Edited spacing in blastncommandline parameters
44b86a7
@sdhutchins
Updated utils.py to reflect gi deprecation
c48f699
@sdhutchins
Deprecated gi-related functions and edited docstrings
0d42ac2
@sdhutchins
Updated blastn_comparative_genetics to reflect deprecation of gi lists
927f46f
@sdhutchins
Updated database_management.py with new function for windowmakskerfiles
2739ede
@sdhutchins
Merge branch 'database-patch' of https://github.com/datasnakes/Datasn…
a81b4d6 
…akes-Scripts.git into GI-deprecation_patch
@sdhutchins
Updates to ncbiftp.py for codacy
0752556
@sdhutchins
Removed whitespace in blast init
1247658
@sdhutchins
Merge pull request #117 from datasnakes/gi-config-fix-patch
3527c4a 
Update create-sge-job-patch with edits to Blast and FTP
@sdhutchins
Updated Blast Readme
4ac1109
@sdhutchins
Merge branch 'gi-config-fix-patch' into create-sge-job-patch
d10bc2f
@grabear
Merge pull request #116 from datasnakes/GI-deprecation_patch
fdbb4df 
Update database-patch with windowmasker features
@sdhutchins
Added DatasnakesDeprecationWarning
82c6753
@sdhutchins
Implemented DatasnakesDeprecation Warning
fc7fd8b
@sdhutchins
Odobenus rosmarus divergens(9708) and Ceratotherium simum simum(73337…
aef842c 
…) not on NCBI
@sdhutchins
Update ftp readme
f530550
@sdhutchins
Added a warning for missing taxonomy ids. Updateed encoding.
4378e74
@sdhutchins
Edited ncbiftp.py for culling taxonomy ids not found
837306f
@sdhutchins
Added a line in other_utils.py
d696b36
Removed unused import from ncbiftp.py
84302d5
Added standalone ncbi-download.py script that has argparse incorporated
9b9ec43
@grabear
Created a functional/unfinished archive script.
f45b9fa
@grabear
Added db_config framework.
a733470
@grabear
Converted archive function to a Cookie utility.
2084e59
Changed name of file_gui folder to file-gui
336d210
gi-list multiprocessing folder name change
bc7f234
@grabear grabear added this to the Official project release milestone Nov 17, 2017
@grabear grabear requested a review from sdhutchins November 17, 2017 21:38
sdhutchins
sdhutchins approved these changes Nov 17, 2017
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Codacy angers me, but I'm happy with this.

@sdhutchins sdhutchins merged commit bde0ec8 into master Nov 17, 2017
This was referenced Nov 17, 2017
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@sdhutchins sdhutchins added 👁️ Status: Review Needed 👁️ 👍 Status: Accepted 👍 dependencies Pull requests that update a dependency file and removed 👁️ Status: Review Needed 👁️ dependencies Pull requests that update a dependency file labels Aug 21, 2020
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@sdhutchins sdhutchins sdhutchins approved these changes

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