Skip to content

Instantly share code, notes, and snippets.

@prasad-kumkar

prasad-kumkar/genomics_project.ipynb

Created November 26, 2021 13:05
Show Gist options

  • Select an option

    Learn more about clone URLs
  • Save prasad-kumkar/3731dbed9eb2b850b50e4cbcc85041e4 to your computer and use it in GitHub Desktop.

Select an option

Learn more about clone URLs
Save prasad-kumkar/3731dbed9eb2b850b50e4cbcc85041e4 to your computer and use it in GitHub Desktop.
Download ZIP
Genomics_Project.ipynb
Display the source blob
Display the rendered blob
Raw
genomics_project.ipynb
{
"nbformat": 4,
"nbformat_minor": 0,
"metadata": {
"colab": {
"name": "Genomics_Project.ipynb",
"provenance": [],
"authorship_tag": "ABX9TyPkjt1RPFdmdtxujoQ4nC85",
"include_colab_link": true
},
"kernelspec": {
"name": "python3",
"display_name": "Python 3"
}
},
"cells": [
{
"cell_type": "markdown",
"metadata": {
"id": "view-in-github",
"colab_type": "text"
},
"source": [
"<a href=\"https://colab.research.google.com/gist/prasad-kumkar/3731dbed9eb2b850b50e4cbcc85041e4/genomics_project.ipynb\" target=\"_parent\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/></a>"
]
},
{
"cell_type": "code",
"metadata": {
"id": "gF5D5Rpxg659",
"colab": {
"base_uri": "https://localhost:8080/"
},
"outputId": "caa09c3a-82ec-420e-d11b-40a9e7409b39"
},
"source": [
"from google.colab import drive\n",
"drive.mount('/content/drive')"
],
"execution_count": null,
"outputs": [
{
"output_type": "stream",
"text": [
"Mounted at /content/drive\n"
],
"name": "stdout"
}
]
},
{
"cell_type": "code",
"metadata": {
"id": "UYo2H6S-h540",
"colab": {
"base_uri": "https://localhost:8080/"
},
"outputId": "cb4c3655-0622-4a26-97ce-3e19377afce2"
},
"source": [
"!ls \"/content/drive/My Drive/Colab Notebooks\""
],
"execution_count": null,
"outputs": [
{
"output_type": "stream",
"text": [
"baseline_on_sequence.py helper_with_N.py test_testing.txt\n",
"baselines_output\t helper_with_N.pyc Untitled\n",
"data\t\t\t merge_and_retrain.py Untitled0.ipynb\n",
"Deep_Q_Network_Solution.ipynb n-mer_freq.py\t Untitled1.ipynb\n",
"dqn\t\t\t output_folder\t Untitled2.ipynb\n",
"final_freq\t\t pattern_branch.py Untitled3.ipynb\n",
"final_pattern\t\t predict_only.py\t Untitled4.ipynb\n",
"final_ViraMiner\t\t README.md\t ViraMiner_end2end.py\n",
"frequency_branch.py\t test_output.txt\n"
],
"name": "stdout"
}
]
},
{
"cell_type": "code",
"metadata": {
"id": "yOeXBGWYh8_0",
"colab": {
"base_uri": "https://localhost:8080/"
},
"outputId": "37d3af3c-469d-4519-9d7c-ca502399e850"
},
"source": [
"!python2 /content/drive/My\\ Drive/Colab\\ Notebooks/frequency_branch.py /content/drive/My\\ Drive/Colab\\ Notebooks/output_folder/output_model_name --input_path /content/drive/My\\ Drive/Colab\\ Notebooks/data/DNA_data/fullset --epochs 10 --filter_size 8 --layer_sizes 800 --dropout 0.1 --learning_rate 0.001 --lr_decay None > /content/drive/My\\ Drive/Colab\\ Notebooks/output_folder/output_logfile.txt"
],
"execution_count": null,
"outputs": [
{
"output_type": "stream",
"text": [
"Using TensorFlow backend.\n",
"2020-11-01 22:43:26.426404: I tensorflow/stream_executor/platform/default/dso_loader.cc:44] Successfully opened dynamic library libcuda.so.1\n",
"2020-11-01 22:43:26.491492: E tensorflow/stream_executor/cuda/cuda_driver.cc:351] failed call to cuInit: CUDA_ERROR_NO_DEVICE: no CUDA-capable device is detected\n",
"2020-11-01 22:43:26.491550: I tensorflow/stream_executor/cuda/cuda_diagnostics.cc:156] kernel driver does not appear to be running on this host (5d69b9e2c8ea): /proc/driver/nvidia/version does not exist\n",
"2020-11-01 22:43:26.503360: I tensorflow/core/platform/profile_utils/cpu_utils.cc:94] CPU Frequency: 2200000000 Hz\n",
"2020-11-01 22:43:26.503650: I tensorflow/compiler/xla/service/service.cc:168] XLA service 0x56344ebfaa00 initialized for platform Host (this does not guarantee that XLA will be used). Devices:\n",
"2020-11-01 22:43:26.503693: I tensorflow/compiler/xla/service/service.cc:176] StreamExecutor device (0): Host, Default Version\n"
],
"name": "stdout"
}
]
},
{
"cell_type": "code",
"metadata": {
"id": "qYQhaETIo3SM",
"colab": {
"base_uri": "https://localhost:8080/"
},
"outputId": "df27ae06-d39f-45bc-ab0c-1ff203431778"
},
"source": [
"!python2 /content/drive/My\\ Drive/Colab\\ Notebooks/pattern_branch.py /content/drive/My\\ Drive/Colab\\ Notebooks/output_folder/output_model_name_pattern --input_path /content/drive/My\\ Drive/Colab\\ Notebooks/data/DNA_data/fullset --epochs 10 --filter_size 8 --layer_sizes 800 --dropout 0.1 --learning_rate 0.001 --lr_decay None > /content/drive/My\\ Drive/Colab\\ Notebooks/output_folder/output_logfile_pattern.txt"
],
"execution_count": null,
"outputs": [
{
"output_type": "stream",
"text": [
"Using TensorFlow backend.\n",
"2020-11-02 00:36:50.478848: I tensorflow/stream_executor/platform/default/dso_loader.cc:44] Successfully opened dynamic library libcuda.so.1\n",
"2020-11-02 00:36:50.488776: E tensorflow/stream_executor/cuda/cuda_driver.cc:351] failed call to cuInit: CUDA_ERROR_NO_DEVICE: no CUDA-capable device is detected\n",
"2020-11-02 00:36:50.488840: I tensorflow/stream_executor/cuda/cuda_diagnostics.cc:156] kernel driver does not appear to be running on this host (5d69b9e2c8ea): /proc/driver/nvidia/version does not exist\n",
"2020-11-02 00:36:50.494728: I tensorflow/core/platform/profile_utils/cpu_utils.cc:94] CPU Frequency: 2200000000 Hz\n",
"2020-11-02 00:36:50.495107: I tensorflow/compiler/xla/service/service.cc:168] XLA service 0x559307794a00 initialized for platform Host (this does not guarantee that XLA will be used). Devices:\n",
"2020-11-02 00:36:50.495148: I tensorflow/compiler/xla/service/service.cc:176] StreamExecutor device (0): Host, Default Version\n",
"Traceback (most recent call last):\n",
" File \"/content/drive/My Drive/Colab Notebooks/pattern_branch.py\", line 153, in <module>\n",
" pred_probas = model.predict_generator(generate_batches_from_file(args.input_path+\"_validation.csv\",args.batch_size), steps=val_steps_per_epoch+1,workers=1, use_multiprocessing=False)\n",
"NameError: name 'val_steps_per_epoch' is not defined\n"
],
"name": "stdout"
}
]
},
{
"cell_type": "code",
"metadata": {
"id": "-e_MUp44s0OR",
"colab": {
"base_uri": "https://localhost:8080/"
},
"outputId": "92b2cadc-2873-4bf8-bb1b-290612aa8179"
},
"source": [
"!python2 /content/drive/My\\ Drive/Colab\\ Notebooks/merge_and_retrain.py /content/drive/My\\ Drive/Colab\\ Notebooks/output_folder/output_model_name_final --input_path /content/drive/My\\ Drive/Colab\\ Notebooks/data/DNA_data/fullset --pattern_model /content/drive/My\\ Drive/Colab\\ Notebooks/final_freq/pattern_model.hdf5 --freq_model /content/drive/My\\ Drive/Colab\\ Notebooks/final_freq/frequency_model.hdf5 --finetuning True --epochs 10 --dropout 0.1 --learning_rate 0.001 --lr_decay None > /content/drive/My\\ Drive/Colab\\ Notebooks/output_folder/output_logfile_final.txt"
],
"execution_count": null,
"outputs": [
{
"output_type": "stream",
"text": [
"Using TensorFlow backend.\n",
"2020-11-02 03:03:08.079942: I tensorflow/stream_executor/platform/default/dso_loader.cc:44] Successfully opened dynamic library libcuda.so.1\n",
"2020-11-02 03:03:08.089492: E tensorflow/stream_executor/cuda/cuda_driver.cc:351] failed call to cuInit: CUDA_ERROR_NO_DEVICE: no CUDA-capable device is detected\n",
"2020-11-02 03:03:08.089546: I tensorflow/stream_executor/cuda/cuda_diagnostics.cc:156] kernel driver does not appear to be running on this host (5d69b9e2c8ea): /proc/driver/nvidia/version does not exist\n",
"2020-11-02 03:03:08.095511: I tensorflow/core/platform/profile_utils/cpu_utils.cc:94] CPU Frequency: 2200000000 Hz\n",
"2020-11-02 03:03:08.095787: I tensorflow/compiler/xla/service/service.cc:168] XLA service 0x55ea5d3a8840 initialized for platform Host (this does not guarantee that XLA will be used). Devices:\n",
"2020-11-02 03:03:08.095827: I tensorflow/compiler/xla/service/service.cc:176] StreamExecutor device (0): Host, Default Version\n"
],
"name": "stdout"
}
]
},
{
"cell_type": "code",
"metadata": {
"id": "Y2huCnHz5GUb",
"colab": {
"base_uri": "https://localhost:8080/"
},
"outputId": "58bd841d-48b5-4692-cb4f-abd8e1b7ac28"
},
"source": [
"!python2 /content/drive/My\\ Drive/Colab\\ Notebooks/predict_only.py --input_file /content/drive/My\\ Drive/Colab\\ Notebooks/data/DNA_data/fullset_test.csv --model_path /content/drive/My\\ Drive/Colab\\ Notebooks/output_folder/output_model_name_final_afterFT.hdf5 > /content/drive/My\\ Drive/Colab\\ Notebooks/test_testing.txt\n",
"\n"
],
"execution_count": null,
"outputs": [
{
"output_type": "stream",
"text": [
"Using TensorFlow backend.\n",
"2020-11-02 08:51:35.062835: I tensorflow/stream_executor/platform/default/dso_loader.cc:44] Successfully opened dynamic library libcuda.so.1\n",
"2020-11-02 08:51:35.072233: E tensorflow/stream_executor/cuda/cuda_driver.cc:351] failed call to cuInit: CUDA_ERROR_NO_DEVICE: no CUDA-capable device is detected\n",
"2020-11-02 08:51:35.072288: I tensorflow/stream_executor/cuda/cuda_diagnostics.cc:156] kernel driver does not appear to be running on this host (5d69b9e2c8ea): /proc/driver/nvidia/version does not exist\n",
"2020-11-02 08:51:35.078011: I tensorflow/core/platform/profile_utils/cpu_utils.cc:94] CPU Frequency: 2200000000 Hz\n",
"2020-11-02 08:51:35.078327: I tensorflow/compiler/xla/service/service.cc:168] XLA service 0x55e9e43a2840 initialized for platform Host (this does not guarantee that XLA will be used). Devices:\n",
"2020-11-02 08:51:35.078368: I tensorflow/compiler/xla/service/service.cc:176] StreamExecutor device (0): Host, Default Version\n"
],
"name": "stdout"
}
]
},
{
"cell_type": "code",
"metadata": {
"id": "GW2cCHDpJVgm"
},
"source": [
""
],
"execution_count": null,
"outputs": []
}
]
}
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment