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🐛 fix #12 exercises and colab link #13

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🐛 fix #12 exercises and colab link #13

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51 changes: 24 additions & 27 deletions notebooks/seq_analysis.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -22,10 +22,7 @@
"metadata": {},
"source": [
"\n",
"[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/Multiomics-Analytics-Group/course_protein_language_modeling/blob/main/notebooks/model_training.ipynb)\n",
"\n",
"\n",
"This is a version of the notebook from [Matthew Carrigan](https://huggingface.co/Rocketknight1) --- [here](https://huggingface.co/blog/deep-learning-with-proteins)."
"[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/Multiomics-Analytics-Group/course_protein_language_modeling/blob/main/notebooks/seq_analysis.ipynb)"
]
},
{
Expand Down Expand Up @@ -111,7 +108,7 @@
},
{
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"execution_count": 3,
"execution_count": 1,
"id": "1334524b-898b-4276-9c44-9016a10227d4",
"metadata": {},
"outputs": [
Expand Down Expand Up @@ -152,7 +149,7 @@
},
{
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"execution_count": 2,
"id": "c4e19716-4e0b-4607-90c1-4c1f7deeeab1",
"metadata": {},
"outputs": [
Expand Down Expand Up @@ -186,7 +183,7 @@
},
{
"cell_type": "code",
"execution_count": 5,
"execution_count": 3,
"id": "a7f1c4e4-0f9e-45ac-bbe7-f72bdd116219",
"metadata": {},
"outputs": [
Expand Down Expand Up @@ -216,7 +213,7 @@
},
{
"cell_type": "code",
"execution_count": 6,
"execution_count": 4,
"id": "fc25307c-ea84-4ef3-aa2d-91c7ea5f8515",
"metadata": {},
"outputs": [
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},
{
"cell_type": "code",
"execution_count": 7,
"execution_count": 5,
"id": "6422e42d-4ead-46dc-810c-74ec9931b735",
"metadata": {},
"outputs": [
Expand All @@ -260,7 +257,7 @@
"0.46875"
]
},
"execution_count": 7,
"execution_count": 5,
"metadata": {},
"output_type": "execute_result"
}
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},
{
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"execution_count": 8,
"execution_count": 6,
"id": "af46ca6e-c4a3-4d21-be12-12e0ec252d62",
"metadata": {},
"outputs": [
Expand All @@ -302,7 +299,7 @@
"'GATCGATGGGCCTATATAGGATCGAAAATCGC'"
]
},
"execution_count": 8,
"execution_count": 6,
"metadata": {},
"output_type": "execute_result"
}
Expand All @@ -321,7 +318,7 @@
},
{
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"execution_count": 9,
"execution_count": 7,
"id": "e6e11edc-cd91-4012-8a37-5fa90959f375",
"metadata": {},
"outputs": [
Expand Down Expand Up @@ -378,7 +375,7 @@
},
{
"cell_type": "code",
"execution_count": 10,
"execution_count": 8,
"id": "95e01c9b-cb39-4c58-9f06-c782d890125c",
"metadata": {},
"outputs": [
Expand Down Expand Up @@ -650,7 +647,7 @@
},
{
"cell_type": "code",
"execution_count": 18,
"execution_count": 16,
"id": "a9aca611-085f-4864-9c8f-acc4e775c89b",
"metadata": {},
"outputs": [],
Expand All @@ -668,7 +665,7 @@
},
{
"cell_type": "code",
"execution_count": 19,
"execution_count": 15,
"id": "ce1b70bf-1a3c-4c32-84c4-38caaa6905d1",
"metadata": {},
"outputs": [],
Expand All @@ -681,12 +678,12 @@
"id": "8d3275b5-c7ce-463d-acd9-c332a87b0b1b",
"metadata": {},
"source": [
"(Extra) 3. Which is the most abundant protein?"
"(Extra) 3. Which is the most abundant amino acid?"
]
},
{
"cell_type": "code",
"execution_count": 20,
"execution_count": 14,
"id": "934a17ce-e409-4bd1-9c7f-5cd5166eade0",
"metadata": {},
"outputs": [],
Expand Down Expand Up @@ -756,16 +753,16 @@
" <summary><font color=\"green\"><b>(Optional) Solution 3</b></font></summary>\n",
" \n",
" ```python\n",
" from Bio.SeqUtils.ProtParam import ProteinAnalysis\n",
" from Bio.SeqUtils.ProtParam import ProteinAnalysis\n",
"\n",
" # instantiate\n",
" protein_sequence = ProteinAnalysis(pro)\n",
" \n",
" # get aa count\n",
" aa_count = protein_sequence.count_amino_acids()\n",
" \n",
" # most abdundant amino acid\n",
" print(max(aa_count)) # Y - Tyrosine\n",
" # instantiate\n",
" protein_sequence = ProteinAnalysis(pro)\n",
"\n",
" # get aa count\n",
" aa_count = protein_sequence.count_amino_acids()\n",
"\n",
" # most abdundant amino acid\n",
" print(max(aa_count, key=aa_count.get)) # L - Leucine\n",
" ```\n",
"</details>\n",
"\n",
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