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ahernank merged 1 commit into from
Jan 23, 2026
Merged

Incorrect taxa in funestus VUGs #123

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35 changes: 14 additions & 21 deletions docs/af1/af1.0.ipynb
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Expand Up @@ -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",
Expand Down Expand Up @@ -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",
Expand Down Expand Up @@ -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": {
Expand All @@ -1258,7 +1251,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.12.7"
"version": "3.12.11"
}
},
"nbformat": 4,
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14 changes: 10 additions & 4 deletions docs/af1/af1.1.ipynb
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Expand Up @@ -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",
Expand Down Expand Up @@ -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": {
Expand All @@ -1269,7 +1275,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.12.7"
"version": "3.12.11"
}
},
"nbformat": 4,
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14 changes: 10 additions & 4 deletions docs/af1/af1.2.ipynb
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Expand Up @@ -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",
Expand Down Expand Up @@ -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": {
Expand All @@ -698,7 +704,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.12.7"
"version": "3.12.11"
}
},
"nbformat": 4,
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14 changes: 10 additions & 4 deletions docs/af1/af1.3.ipynb
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Expand Up @@ -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",
Expand Down Expand Up @@ -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": {
Expand All @@ -661,7 +667,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.12.7"
"version": "3.12.11"
}
},
"nbformat": 4,
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14 changes: 10 additions & 4 deletions docs/af1/af1.4.ipynb
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Expand Up @@ -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",
Expand Down Expand Up @@ -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": {
Expand All @@ -698,7 +704,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.12.7"
"version": "3.12.11"
}
},
"nbformat": 4,
Expand Down