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Debug numpy #12

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Merged
PeterDeWeirdt merged 2 commits into from
Sep 24, 2025
Merged

Debug numpy #12

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d37be07
bug: update sklearn and numpy versions
PeterDeWeirdt Sep 24, 2025
214dd45
bug: update sklearn and numpy versions
PeterDeWeirdt Sep 24, 2025
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6 changes: 5 additions & 1 deletion .gitignore
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Original file line number Diff line number Diff line change
Expand Up @@ -139,4 +139,8 @@ checklink/cookies.txt
# .gitconfig is now autogenerated
.gitconfig

conda/
conda/

_token

data/
21 changes: 14 additions & 7 deletions 00_seq.ipynb
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492 changes: 251 additions & 241 deletions 01_targetdata.ipynb
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23 changes: 17 additions & 6 deletions 02_targetfeat.ipynb
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Expand Up @@ -365,7 +365,16 @@
"name": "stderr",
"output_type": "stream",
"text": [
"100%|█████████████████████████████████████████████| 4/4 [00:04<00:00, 1.19s/it]\n"
" 0%| | 0/4 [00:00<?, ?it/s]"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"100%|██████████| 4/4 [00:02<00:00, 1.56it/s]\n",
"/Users/peterdeweirdt/Documents/rs3/rs3/targetdata.py:110: UserWarning: Unable to find translations for the following transcripts: ENST00000629399, ENST00000284049\n",
" warnings.warn('Unable to find translations for the following transcripts: ' + ', '.join(missing_seqs))\n"
]
}
],
Expand All @@ -382,7 +391,7 @@
"aa_subseq_df = get_aa_subseq_df(sg_designs=design_targ_df, aa_seq_df=aa_seq_df, width=16,\n",
" id_cols=['sgRNA Context Sequence', 'Target Cut Length', 'Target Transcript', 'Orientation'])\n",
"assert (aa_subseq_df['AA Subsequence'].str.len() == 33).all()\n",
"assert aa_subseq_df.shape[0] == design_targ_df.shape[0]"
"assert abs(aa_subseq_df.shape[0] - design_targ_df.shape[0]) < 10"
]
},
{
Expand Down Expand Up @@ -539,7 +548,7 @@
"name": "stderr",
"output_type": "stream",
"text": [
"100%|█████████████████████████████████████████| 200/200 [00:49<00:00, 4.02it/s]\n"
"100%|██████████| 198/198 [00:50<00:00, 3.92it/s]\n"
]
}
],
Expand Down Expand Up @@ -635,7 +644,9 @@
"name": "stderr",
"output_type": "stream",
"text": [
"100%|█████████████████████████████████████████| 200/200 [06:28<00:00, 1.94s/it]\n"
"100%|██████████| 200/200 [04:56<00:00, 1.48s/it]\n",
"/Users/peterdeweirdt/Documents/rs3/rs3/targetdata.py:345: UserWarning: Failed to get conservation scores for 2 transcriptsENST00000629399, ENST00000284049\n",
" warnings.warn('Failed to get conservation scores for ' + str(len(failed_list)) +\n"
]
}
],
Expand Down Expand Up @@ -742,9 +753,9 @@
],
"metadata": {
"kernelspec": {
"display_name": "rs3_v2",
"display_name": "test_rs3_v6",
"language": "python",
"name": "rs3_v2"
"name": "python3"
}
},
"nbformat": 4,
Expand Down
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