Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Updated notebooks #295

Merged
merged 3 commits into from
Oct 7, 2024
Merged

Updated notebooks #295

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
e86fc3c
updated example_restriction (#285)
manulera Oct 4, 2024
26f36e2
small fixes (#294)
manulera Oct 7, 2024
fc72b03
allow run all on notebooks that have pip install for google colab
manulera Oct 7, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
12 changes: 8 additions & 4 deletions docs/notebooks/CRISPR.ipynb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -28,9 +28,14 @@
"metadata": {},
"outputs": [],
"source": [
"# Install pydna \n",
"%%capture\n",
"!pip install pydna"
"# Install pydna (only when running on Colab)\n",
"import sys\n",
"if 'google.colab' in sys.modules:\n",
" %%capture\n",
" # Install the current development version of pydna (comment to install pip version)\n",
" !pip install git+https://github.com/BjornFJohansson/pydna@dev_bjorn\n",
" # Install pip version instead (uncomment to install)\n",
" # !pip install pydna\n"
]
},
{
Expand All @@ -54,7 +59,6 @@
"cell_type": "code",
"execution_count": null,
"metadata": {},

"outputs": [
{
"name": "stdout",
Expand Down
11 changes: 8 additions & 3 deletions docs/notebooks/Dseq.ipynb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -23,9 +23,14 @@
"metadata": {},
"outputs": [],
"source": [
"# Install pydna \n",
"%%capture\n",
"!pip install pydna"
"# Install pydna (only when running on Colab)\n",
"import sys\n",
"if 'google.colab' in sys.modules:\n",
" %%capture\n",
" # Install the current development version of pydna (comment to install pip version)\n",
" !pip install git+https://github.com/BjornFJohansson/pydna@dev_bjorn\n",
" # Install pip version instead (uncomment to install)\n",
" # !pip install pydna\n"
]
},
{
Expand Down
11 changes: 8 additions & 3 deletions docs/notebooks/Dseq_Features.ipynb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -30,9 +30,14 @@
"metadata": {},
"outputs": [],
"source": [
"# Install pydna \n",
"%%capture\n",
"!pip install pydna"
"# Install pydna (only when running on Colab)\n",
"import sys\n",
"if 'google.colab' in sys.modules:\n",
" %%capture\n",
" # Install the current development version of pydna (comment to install pip version)\n",
" !pip install git+https://github.com/BjornFJohansson/pydna@dev_bjorn\n",
" # Install pip version instead (uncomment to install)\n",
" # !pip install pydna\n"
]
},
{
Expand Down
11 changes: 8 additions & 3 deletions docs/notebooks/Example_CRISPR.ipynb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -75,9 +75,14 @@
"metadata": {},
"outputs": [],
"source": [
"#Install pydna for colab.\n",
"%%capture\n",
"!pip install git+https://github.com/BjornFJohansson/pydna.git@dev_bjorn"
"# Install pydna (only when running on Colab)\n",
"import sys\n",
"if 'google.colab' in sys.modules:\n",
" %%capture\n",
" # Install the current development version of pydna (comment to install pip version)\n",
" !pip install git+https://github.com/BjornFJohansson/pydna@dev_bjorn\n",
" # Install pip version instead (uncomment to install)\n",
" # !pip install pydna\n"
]
},
{
Expand Down
11 changes: 8 additions & 3 deletions docs/notebooks/Example_Gibson.ipynb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -27,9 +27,14 @@
"metadata": {},
"outputs": [],
"source": [
"# Install pydna \n",
"%%capture\n",
"!pip install pydna"
"# Install pydna (only when running on Colab)\n",
"import sys\n",
"if 'google.colab' in sys.modules:\n",
" %%capture\n",
" # Install the current development version of pydna (comment to install pip version)\n",
" !pip install git+https://github.com/BjornFJohansson/pydna@dev_bjorn\n",
" # Install pip version instead (uncomment to install)\n",
" # !pip install pydna\n"
]
},
{
Expand Down
303 changes: 122 additions & 181 deletions docs/notebooks/Example_Restriction.ipynb
View file
Open in desktop

Large diffs are not rendered by default.

11 changes: 8 additions & 3 deletions docs/notebooks/Gibson.ipynb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -32,9 +32,14 @@
"metadata": {},
"outputs": [],
"source": [
"# Install pydna \n",
"%%capture\n",
"!pip install pydna"
"# Install pydna (only when running on Colab)\n",
"import sys\n",
"if 'google.colab' in sys.modules:\n",
" %%capture\n",
" # Install the current development version of pydna (comment to install pip version)\n",
" !pip install git+https://github.com/BjornFJohansson/pydna@dev_bjorn\n",
" # Install pip version instead (uncomment to install)\n",
" # !pip install pydna\n"
]
},
{
Expand Down
11 changes: 8 additions & 3 deletions docs/notebooks/Importing_Seqs.ipynb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -34,9 +34,14 @@
"metadata": {},
"outputs": [],
"source": [
"# Install pydna \n",
"%%capture\n",
"!pip install pydna"
"# Install pydna (only when running on Colab)\n",
"import sys\n",
"if 'google.colab' in sys.modules:\n",
" %%capture\n",
" # Install the current development version of pydna (comment to install pip version)\n",
" !pip install git+https://github.com/BjornFJohansson/pydna@dev_bjorn\n",
" # Install pip version instead (uncomment to install)\n",
" # !pip install pydna\n"
]
},
{
Expand Down
11 changes: 8 additions & 3 deletions docs/notebooks/PCR.ipynb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -32,9 +32,14 @@
"metadata": {},
"outputs": [],
"source": [
"# Install pydna \n",
"%%capture\n",
"!pip install pydna"
"# Install pydna (only when running on Colab)\n",
"import sys\n",
"if 'google.colab' in sys.modules:\n",
" %%capture\n",
" # Install the current development version of pydna (comment to install pip version)\n",
" !pip install git+https://github.com/BjornFJohansson/pydna@dev_bjorn\n",
" # Install pip version instead (uncomment to install)\n",
" # !pip install pydna\n"
]
},
{
Expand Down
11 changes: 8 additions & 3 deletions docs/notebooks/Restrict_Ligate_Cloning.ipynb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -29,9 +29,14 @@
"metadata": {},
"outputs": [],
"source": [
"# Install pydna \n",
"%%capture\n",
"!pip install pydna"
"# Install pydna (only when running on Colab)\n",
"import sys\n",
"if 'google.colab' in sys.modules:\n",
" %%capture\n",
" # Install the current development version of pydna (comment to install pip version)\n",
" !pip install git+https://github.com/BjornFJohansson/pydna@dev_bjorn\n",
" # Install pip version instead (uncomment to install)\n",
" # !pip install pydna\n"
]
},
{
Expand Down
Loading