diff --git a/docs/af1/af1.0.ipynb b/docs/af1/af1.0.ipynb index 540a2c5..7492feb 100644 --- a/docs/af1/af1.0.ipynb +++ b/docs/af1/af1.0.ipynb @@ -14,7 +14,7 @@ "\n", "This page provides an introduction to open data resources released as part of the first phase of the Anopheles funestus Genomic Surveillance Project project, known as `Af1.0` for short. We hope the data from `Af1.0` will be a valuable resource for research and surveillance of malaria vectors. \n", "\n", - "The **[Af1.0](af1.0): _Anopheles gambiae_ data resource** contains single nucleotide polymorphism (SNP) calls, copy number variant (CNV) calls and SNP haplotypes from whole-genome sequencing of 656 mosquitoes.\n", + "The **[Af1.0](af1.0): _Anopheles funestus_ data resource** contains single nucleotide polymorphism (SNP) calls, copy number variant (CNV) calls and SNP haplotypes from whole-genome sequencing of 656 mosquitoes.\n", "\n", "More information about this release can be found in the [data resource website](https://www.malariagen.net/data_package/af10-anopheles-funestus-data-resource/). \n", "\n", @@ -469,23 +469,10 @@ "\n", "af1 = malariagen_data.Af1(pre=True)\n", "taxa = [\n", - " \"gambiae\",\n", - " \"melas\",\n", - " \"coluzzii\",\n", - " \"merus\",\n", - " \"arabiensis\",\n", - " \"quadriannulatus\",\n", - " \"funestus\", \n", - " \"fontenillei\",\n", - " \"gcx1\",\n", - " \"gcx2\",\n", - " \"gcx3\",\n", - " \"gcx4\",\n", - " \"vaneedeni\",\n", - " \"longipalpis\",\n", - " \"parensis\",\n", - " \"minimus\",\n", - " \"unassigned\",\n", + " 'funestus',\n", + " 'longipalpis',\n", + " 'parensis',\n", + " 'vaneedeni'\n", "]\n", "\n", "taxon_color = pd.Series(bkpal.Category20[len(taxa)], index=taxa)\n", @@ -1243,10 +1230,16 @@ "name": "Ag3.0-intro.ipynb", "provenance": [] }, + "environment": { + "kernel": "mgenv_7.2.0", + "name": "workbench-notebooks.m138", + "type": "gcloud", + "uri": "us-docker.pkg.dev/deeplearning-platform-release/gcr.io/workbench-notebooks:m138" + }, "kernelspec": { - "display_name": "global-global-mgenv-6.0.6", + "display_name": "Python (mgenv_7.2.0)", "language": "python", - "name": "conda-env-global-global-mgenv-6.0.6-py" + "name": "mgenv_7.2.0" }, "language_info": { "codemirror_mode": { @@ -1258,7 +1251,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.12.7" + "version": "3.12.11" } }, "nbformat": 4, diff --git a/docs/af1/af1.1.ipynb b/docs/af1/af1.1.ipynb index ff9091f..4326bb1 100644 --- a/docs/af1/af1.1.ipynb +++ b/docs/af1/af1.1.ipynb @@ -8,7 +8,7 @@ "source": [ "# Af1.1\n", "\n", - "The **[Af1.1](af1.1): _Anopheles gambiae_ data resource** contains single nucleotide polymorphism (SNP) calls, copy number variant (CNV) calls and SNP haplotypes from whole-genome sequencing of 1138 mosquitoes.\n", + "The **[Af1.1](af1.1): _Anopheles funestus_ data resource** contains single nucleotide polymorphism (SNP) calls, copy number variant (CNV) calls and SNP haplotypes from whole-genome sequencing of 1138 mosquitoes.\n", "\n", "More information about this release can be found in the [data resource website](https://www.malariagen.net/data_package/af11-anopheles-funestus-data-resource/). \n", "\n", @@ -1254,10 +1254,16 @@ "name": "Ag3.0-intro.ipynb", "provenance": [] }, + "environment": { + "kernel": "mgenv_7.2.0", + "name": "workbench-notebooks.m138", + "type": "gcloud", + "uri": "us-docker.pkg.dev/deeplearning-platform-release/gcr.io/workbench-notebooks:m138" + }, "kernelspec": { - "display_name": "global-global-mgenv-6.0.6", + "display_name": "Python (mgenv_7.2.0)", "language": "python", - "name": "conda-env-global-global-mgenv-6.0.6-py" + "name": "mgenv_7.2.0" }, "language_info": { "codemirror_mode": { @@ -1269,7 +1275,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.12.7" + "version": "3.12.11" } }, "nbformat": 4, diff --git a/docs/af1/af1.2.ipynb b/docs/af1/af1.2.ipynb index 3268070..a826001 100644 --- a/docs/af1/af1.2.ipynb +++ b/docs/af1/af1.2.ipynb @@ -8,7 +8,7 @@ "source": [ "# Af1.2\n", "\n", - "The **[Af1.2](af1.2): _Anopheles gambiae_ data resource** contains single nucleotide polymorphism (SNP) calls, copy number variant (CNV) calls and SNP haplotypes from whole-genome sequencing of 317 mosquitoes.\n", + "The **[Af1.2](af1.2): _Anopheles funestus_ data resource** contains single nucleotide polymorphism (SNP) calls, copy number variant (CNV) calls and SNP haplotypes from whole-genome sequencing of 317 mosquitoes.\n", "\n", "More information about this release can be found in the [data resource website](https://www.malariagen.net/data_package/af12-anopheles-funestus-data-resource/). \n", "\n", @@ -683,10 +683,16 @@ "name": "Ag3.0-intro.ipynb", "provenance": [] }, + "environment": { + "kernel": "mgenv_7.2.0", + "name": "workbench-notebooks.m138", + "type": "gcloud", + "uri": "us-docker.pkg.dev/deeplearning-platform-release/gcr.io/workbench-notebooks:m138" + }, "kernelspec": { - "display_name": "global-global-mgenv-6.0.6", + "display_name": "Python (mgenv_7.2.0)", "language": "python", - "name": "conda-env-global-global-mgenv-6.0.6-py" + "name": "mgenv_7.2.0" }, "language_info": { "codemirror_mode": { @@ -698,7 +704,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.12.7" + "version": "3.12.11" } }, "nbformat": 4, diff --git a/docs/af1/af1.3.ipynb b/docs/af1/af1.3.ipynb index c460ece..a8132b6 100644 --- a/docs/af1/af1.3.ipynb +++ b/docs/af1/af1.3.ipynb @@ -8,7 +8,7 @@ "source": [ "# Af1.3\n", "\n", - "The **[Af1.3](af1.3): _Anopheles gambiae_ data resource** contains single nucleotide polymorphism (SNP) calls, copy number variant (CNV) calls and SNP haplotypes from whole-genome sequencing of 193 mosquitoes.\n", + "The **[Af1.3](af1.3): _Anopheles funestus_ data resource** contains single nucleotide polymorphism (SNP) calls, copy number variant (CNV) calls and SNP haplotypes from whole-genome sequencing of 193 mosquitoes.\n", "\n", "More information about this release can be found in the [data resource website](https://www.malariagen.net/data_package/af13-anopheles-funestus-data-resource/). \n", "\n", @@ -646,10 +646,16 @@ "name": "Ag3.0-intro.ipynb", "provenance": [] }, + "environment": { + "kernel": "mgenv_7.2.0", + "name": "workbench-notebooks.m138", + "type": "gcloud", + "uri": "us-docker.pkg.dev/deeplearning-platform-release/gcr.io/workbench-notebooks:m138" + }, "kernelspec": { - "display_name": "global-global-mgenv-6.0.6", + "display_name": "Python (mgenv_7.2.0)", "language": "python", - "name": "conda-env-global-global-mgenv-6.0.6-py" + "name": "mgenv_7.2.0" }, "language_info": { "codemirror_mode": { @@ -661,7 +667,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.12.7" + "version": "3.12.11" } }, "nbformat": 4, diff --git a/docs/af1/af1.4.ipynb b/docs/af1/af1.4.ipynb index 05fa9ca..6d26352 100644 --- a/docs/af1/af1.4.ipynb +++ b/docs/af1/af1.4.ipynb @@ -8,7 +8,7 @@ "source": [ "# Af1.4\n", "\n", - "The **[Af1.4](af1.4): _Anopheles gambiae_ data resource** contains single nucleotide polymorphism (SNP) calls, copy number variant (CNV) calls and SNP haplotypes from whole-genome sequencing of 733 mosquitoes.\n", + "The **[Af1.4](af1.4): _Anopheles funestus_ data resource** contains single nucleotide polymorphism (SNP) calls, copy number variant (CNV) calls and SNP haplotypes from whole-genome sequencing of 733 mosquitoes.\n", "\n", "More information about this release can be found in the [data resource website](https://www.malariagen.net/data_package/af14-anopheles-funestus-data-resource/). \n", "\n", @@ -683,10 +683,16 @@ "name": "Ag3.0-intro.ipynb", "provenance": [] }, + "environment": { + "kernel": "mgenv_7.2.0", + "name": "workbench-notebooks.m138", + "type": "gcloud", + "uri": "us-docker.pkg.dev/deeplearning-platform-release/gcr.io/workbench-notebooks:m138" + }, "kernelspec": { - "display_name": "global-global-mgenv-6.0.6", + "display_name": "Python (mgenv_7.2.0)", "language": "python", - "name": "conda-env-global-global-mgenv-6.0.6-py" + "name": "mgenv_7.2.0" }, "language_info": { "codemirror_mode": { @@ -698,7 +704,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.12.7" + "version": "3.12.11" } }, "nbformat": 4,