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Update notebooks, alignment, and mapping code #64

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merged 18 commits into from
Oct 10, 2024
Merged

Update notebooks, alignment, and mapping code #64

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4b4c57b
Add updated notebooks, alignment, and mapping code
jarbesfeld Oct 1, 2024
cf8c554
Correct tests, add support for targets with underscores
jarbesfeld Oct 2, 2024
d0bf26d
Fix bug for mavedb_ids
jarbesfeld Oct 3, 2024
b24f919
Only select transcript for protein variants
jarbesfeld Oct 3, 2024
be93e1b
Remove extra annotation layer code
jarbesfeld Oct 3, 2024
fd2d642
Correct tests
jarbesfeld Oct 3, 2024
4f2baa3
Fix formatting of test_vrs_map.py
jarbesfeld Oct 3, 2024
8f1cc9f
Add support for checking previous hgnc gene symbols against UTA
jarbesfeld Oct 7, 2024
2d51ac2
Iterate through all possible words to extract gene symbol
jarbesfeld Oct 7, 2024
ba4ef6e
Minor changes to gene symbol selection
jarbesfeld Oct 8, 2024
d0bdc3b
Ensure that only variants covered by alignment are mapped
jarbesfeld Oct 9, 2024
e1af4c4
Fix failing tests
jarbesfeld Oct 9, 2024
e905dbe
Ruff format to fix actions
jarbesfeld Oct 9, 2024
7dd0a56
Fix gene location function
jarbesfeld Oct 9, 2024
a7d84ef
Update get_gene_symbol
jarbesfeld Oct 9, 2024
efc126a
Add flag to hide console output
jarbesfeld Oct 9, 2024
a478f1c
Correct flags
jarbesfeld Oct 9, 2024
12f82b5
Fix flag message
jarbesfeld Oct 9, 2024
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77 changes: 59 additions & 18 deletions notebooks/analysis/mapping_analysis.ipynb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -26,8 +26,10 @@
"outputs": [],
"source": [
"import json\n",
"\n",
"import pandas as pd\n",
"from Bio.Seq import Seq\n",
"import pandas as pd"
"from cool_seq_tool.schemas import Strand"
]
},
{
Expand All @@ -49,6 +51,26 @@
"score_sets = mave_metadata_dat[\"urn\"].to_list()[:-5]"
]
},
{
"cell_type": "code",
"execution_count": 3,
"id": "a69e4d2c",
"metadata": {},
"outputs": [],
"source": [
"import pickle\n",
"from pathlib import Path\n",
"\n",
"from dcd_mapping.schemas import AlignmentResult\n",
"\n",
"with Path.open(\"analysis_files/mave_blat_output.pickle\", \"rb\") as fn:\n",
" mave_blat_temp = pickle.load(fn)\n",
"align_results = {}\n",
"for scoreset in score_sets:\n",
" if scoreset != \"urn:mavedb:00000105-a-1\":\n",
" align_results[scoreset] = AlignmentResult(**mave_blat_temp[scoreset])"
]
},
{
"cell_type": "markdown",
"id": "4d037805",
Expand All @@ -60,7 +82,7 @@
},
{
"cell_type": "code",
"execution_count": 3,
"execution_count": 4,
"id": "3f5e44d2",
"metadata": {},
"outputs": [
Expand All @@ -70,23 +92,26 @@
"'The number of examined variant pairs is: 2499044'"
]
},
"execution_count": 3,
"execution_count": 4,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"diff_vars_dict = {}\n",
"var_count = 0\n",
"counter = 0\n",
"var_count_dict_new = {}\n",
"\n",
"for key in score_sets:\n",
" if key != \"urn:mavedb:00000072-a-1\" and key != \"urn:mavedb:00000105-a-1\": # No mapping for these score sets\n",
" f = open(f\"analysis_files/mappings/{key[11::]}.json\")\n",
" dat = json.load(f)\n",
" seq_type = dat[\"computed_reference_sequence\"][\"sequence_type\"]\n",
" dat = dat[\"mapped_scores\"]\n",
"\n",
" diff_vars = []\n",
" strand = align_results[key].strand\n",
"\n",
" for j in range(len(dat)):\n",
" if \"members\" not in dat[j][\"pre_mapped\"]:\n",
Expand All @@ -95,8 +120,16 @@
" seq_post = dat[j][\"post_mapped\"][\"vrs_ref_allele_seq\"]\n",
" seq_pre_rv = str(Seq(seq_pre).reverse_complement())\n",
"\n",
" if seq_pre != seq_post and seq_post != seq_pre_rv:\n",
" diff_vars.append(j)\n",
" if seq_type == \"protein\":\n",
" if seq_pre != seq_post:\n",
" diff_vars.append(j)\n",
" else:\n",
" if strand == Strand.POSITIVE:\n",
" if seq_pre != seq_post:\n",
" diff_vars.append(j)\n",
" else:\n",
" if seq_post != seq_pre_rv:\n",
" diff_vars.append(j)\n",
"\n",
" else:\n",
" for k in range(len(dat[j][\"pre_mapped\"][\"members\"])):\n",
Expand All @@ -105,8 +138,16 @@
" seq_post = dat[j][\"post_mapped\"][\"members\"][k][\"vrs_ref_allele_seq\"]\n",
" seq_pre_rv = str(Seq(seq_pre).reverse_complement())\n",
"\n",
" if seq_pre != seq_post and seq_post != seq_pre_rv:\n",
" diff_vars.append(j)\n",
" if seq_type == \"protein\":\n",
" if seq_pre != seq_post:\n",
" diff_vars.append(j)\n",
" else:\n",
" if strand == Strand.POSITIVE:\n",
" if seq_pre != seq_post:\n",
" diff_vars.append(j)\n",
" else:\n",
" if seq_post != seq_pre_rv:\n",
" diff_vars.append(j)\n",
"\n",
" diff_vars_dict[key] = diff_vars\n",
" var_count_dict_new[key] = var_count\n",
Expand All @@ -123,7 +164,7 @@
},
{
"cell_type": "code",
"execution_count": 4,
"execution_count": 5,
"id": "240e02be",
"metadata": {},
"outputs": [],
Expand All @@ -142,7 +183,7 @@
},
{
"cell_type": "code",
"execution_count": 5,
"execution_count": 6,
"id": "1c5c6167",
"metadata": {},
"outputs": [
Expand Down Expand Up @@ -182,7 +223,7 @@
" 'score': 0.0836691871353702}"
]
},
"execution_count": 5,
"execution_count": 6,
"metadata": {},
"output_type": "execute_result"
}
Expand All @@ -205,17 +246,17 @@
},
{
"cell_type": "code",
"execution_count": 6,
"execution_count": 7,
"id": "de7a5de0",
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"'There are 24878 instances of reference mismatch. This corresponds to a percentage of 0.996 (24878/2499044)'"
"'There are 34832 instances of reference mismatch. This corresponds to a percentage of 1.394 (34832/2499044)'"
]
},
"execution_count": 6,
"execution_count": 7,
"metadata": {},
"output_type": "execute_result"
}
Expand All @@ -239,7 +280,7 @@
},
{
"cell_type": "code",
"execution_count": 7,
"execution_count": 8,
"id": "6a22205e",
"metadata": {},
"outputs": [
Expand All @@ -249,7 +290,7 @@
"'The number of unique pre-mapped MAVE variants is 363294. The number of unique post-mapped MAVE variants is 349972.'"
]
},
"execution_count": 7,
"execution_count": 8,
"metadata": {},
"output_type": "execute_result"
}
Expand Down Expand Up @@ -293,7 +334,7 @@
},
{
"cell_type": "code",
"execution_count": 8,
"execution_count": 9,
"id": "3eb301ed",
"metadata": {},
"outputs": [],
Expand Down Expand Up @@ -340,7 +381,7 @@
},
{
"cell_type": "code",
"execution_count": 9,
"execution_count": 10,
"id": "fc87cbbe",
"metadata": {},
"outputs": [
Expand All @@ -350,7 +391,7 @@
"'There are 349972 pre-mapped MAVE variants in the dictionary. 9553 post-mapped MAVE variants have 2 or more corresponding pre-mapped MAVE variants.'"
]
},
"execution_count": 9,
"execution_count": 10,
"metadata": {},
"output_type": "execute_result"
}
Expand Down
99 changes: 95 additions & 4 deletions notebooks/analysis/mavedb_scoreset_breakdown.ipynb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -485,7 +485,7 @@
{
"data": {
"text/plain": [
"'The number of protein coding score sets with gene symbols/aliases is: 125'"
"'The number of protein coding score sets with gene symbols/aliases is: 126'"
]
},
"execution_count": 13,
Expand All @@ -495,7 +495,7 @@
],
"source": [
"td = list(coding_ss[\"target\"])\n",
"td = [x for x in td if \" \" not in x]\n",
"td = [x for x in td if \" \" not in x or x == \"Glycophorin A\"]\n",
"f\"The number of protein coding score sets with gene symbols/aliases is: {len(td)}\""
]
},
Expand All @@ -516,7 +516,7 @@
{
"data": {
"text/plain": [
"'The number of protein coding score sets with descriptive targets is: 43'"
"'The number of protein coding score sets with descriptive targets is: 42'"
]
},
"execution_count": 14,
Expand All @@ -526,7 +526,7 @@
],
"source": [
"td = list(coding_ss[\"target\"])\n",
"td = [x for x in td if \" \" in x]\n",
"td = [x for x in td if \" \" in x and x != \"Glycophorin A\"]\n",
"f\"The number of protein coding score sets with descriptive targets is: {len(td)}\""
]
},
Expand Down Expand Up @@ -606,6 +606,97 @@
" unique_genes.append(comp[0])\n",
"f\"The number of unique gene symbols across examined score set targets is: {len(set(unique_genes))}\""
]
},
{
"cell_type": "code",
"execution_count": 17,
"id": "4ef61ec4",
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"{'ACE2',\n",
" 'AICDA',\n",
" 'ALDOB',\n",
" 'Aβ42',\n",
" 'BCL11A',\n",
" 'BRAF',\n",
" 'BRCA1',\n",
" 'CALM1',\n",
" 'CBS',\n",
" 'CCR5',\n",
" 'CD86',\n",
" 'CXCR4',\n",
" 'CYP2C19',\n",
" 'CYP2C9',\n",
" 'DLG4',\n",
" 'ECR11',\n",
" 'ERBB2',\n",
" 'F9',\n",
" 'FOXE1',\n",
" 'GABBR1',\n",
" 'GCK',\n",
" 'GDI1',\n",
" 'GP1BB',\n",
" 'Glycophorin',\n",
" 'HBB',\n",
" 'HBG1',\n",
" 'HMBS',\n",
" 'HMGCR',\n",
" 'HNF4A',\n",
" 'IGHG1',\n",
" 'IRF4',\n",
" 'IRF6',\n",
" 'KCNQ1',\n",
" 'KCNQ4',\n",
" 'LDLR',\n",
" 'LDLRAP1',\n",
" 'MAPK1',\n",
" 'MPL',\n",
" 'MSH2',\n",
" 'MSMB',\n",
" 'MTHFR',\n",
" 'MYC',\n",
" 'NCS1',\n",
" 'NUDT15',\n",
" 'PARP1',\n",
" 'PKLR',\n",
" 'PSAT1',\n",
" 'PTEN',\n",
" 'RET',\n",
" 'RHO',\n",
" 'Ras',\n",
" 'SCN5A',\n",
" 'SORT1',\n",
" 'SRC',\n",
" 'SUMO1',\n",
" 'TARDBP',\n",
" 'TCF7L2',\n",
" 'TECR',\n",
" 'TERT',\n",
" 'TP53',\n",
" 'TPK1',\n",
" 'TPMT',\n",
" 'UBE2I',\n",
" 'UC88',\n",
" 'VKORC1',\n",
" 'WT1',\n",
" 'YAP1',\n",
" 'ZFAND3',\n",
" 'ZHX2',\n",
" 'ZRS',\n",
" 'alpha-synuclein'}"
]
},
"execution_count": 17,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"set(unique_genes)"
]
}
],
"metadata": {
Expand Down
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