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Update deprecated functions #1

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a8d3365
Update deprecated functions
larsborm Dec 19, 2023
f585c47
Update README.md
larsborm May 16, 2024
6a34b36
Prep for Drosophila
larsborm Aug 7, 2024
520614c
Drosophila prep
larsborm Aug 7, 2024
43d59d3
Update Readme
larsborm Aug 7, 2024
dcbdf5b
update readme
larsborm Aug 7, 2024
7b8c74a
Add RepeatMasker instructions
larsborm Aug 8, 2024
4917b05
Merge updates Ale with brach Lars
larsborm Aug 8, 2024
6557f41
Update dependencies instructions
larsborm Aug 9, 2024
2202e14
Drosophila support
larsborm Aug 9, 2024
9d705cb
Drosophila support
larsborm Aug 9, 2024
eed1304
Drosophila support
larsborm Aug 9, 2024
2a84933
Small update
larsborm Aug 13, 2024
215b9f0
Fix input
larsborm Aug 13, 2024
2c0705f
Logging, Drosophila, Species agnostic
larsborm Aug 20, 2024
7f24f09
bug fix
larsborm Aug 20, 2024
886688d
Add masked Drosophila canonical transcripts
larsborm Aug 21, 2024
1d2cccd
Bug fix
larsborm Aug 21, 2024
d30926a
Fix for arbritrary number of tails
larsborm Aug 21, 2024
971ac4b
Randomize spacers between tails, CSV bug fix
larsborm Aug 22, 2024
96f6162
FlyBase gene names
larsborm Aug 26, 2024
6c7aa30
Clean unused files
larsborm Aug 27, 2024
5383386
Readme typo
larsborm Aug 28, 2024
844040a
Blast threads fix
larsborm Aug 28, 2024
2486530
temp debugging
larsborm Sep 6, 2024
e64b8e0
Made Blast2Dict3
larsborm Sep 6, 2024
730bb4b
Add Blast2Dict3
larsborm Sep 6, 2024
ec4c1ec
Add Blast2Dic3
larsborm Sep 6, 2024
ae7fb43
updated obtainBooleanlist2 and added input logging
larsborm Sep 13, 2024
10a98ed
minor fixes
larsborm Sep 23, 2024
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Binary file added .DS_Store
Binary file not shown.
9 changes: 6 additions & 3 deletions .gitignore
Original file line number Diff line number Diff line change
@@ -1,3 +1,6 @@
HUMAN_NCBI_GENES_retrieved.fasta.masked
MOUSE_NCBI_GENES_retrieved.fasta.masked
__pycache__
__pycache__
Results
Results*
codebook_*
.ipynb_checkpoints
.ipynb*
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