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update notebook to pipeline changes
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@lisa-sousa
lisa-sousa committed Jul 17, 2024
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134 changes: 37 additions & 97 deletions docs/_tutorials/spapros_tutorial_end_to_end_selection_short.ipynb
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Expand Up @@ -216,25 +216,16 @@
"name": "stderr",
"output_type": "stream",
"text": [
"/Users/lisa.barros/anaconda3/envs/odt_test/lib/python3.10/site-packages/Bio/Application/__init__.py:40: BiopythonDeprecationWarning: The Bio.Application modules and modules relying on it have been deprecated.\n",
"\n",
"Due to the on going maintenance burden of keeping command line application\n",
"wrappers up to date, we have decided to deprecate and eventually remove these\n",
"modules.\n",
"\n",
"We instead now recommend building your command line and invoking it directly\n",
"with the subprocess module.\n",
" warnings.warn(\n",
"2024-06-19 21:20:21,234 [INFO] Parameters Load Annotations:\n",
"2024-06-19 21:20:21,235 [INFO] source = ncbi\n",
"2024-06-19 21:20:21,235 [INFO] source_params = {'taxon': 'vertebrate_mammalian', 'species': 'Homo_sapiens', 'annotation_release': 110}\n",
"2024-06-19 21:28:20,814 [WARNING] /Users/lisa.barros/Desktop/oligo-designer-toolsuite/oligo_designer_toolsuite/utils/_sequence_parser.py:104: DtypeWarning: Columns (0) have mixed types. Specify dtype option on import or set low_memory=False.\n",
"2024-07-16 17:15:53,511 [INFO] Parameters Load Annotations:\n",
"2024-07-16 17:15:53,511 [INFO] source = ncbi\n",
"2024-07-16 17:15:53,511 [INFO] source_params = {'taxon': 'vertebrate_mammalian', 'species': 'Homo_sapiens', 'annotation_release': 110}\n",
"2024-07-16 17:23:33,702 [WARNING] /Users/lisa.barros/Desktop/oligo-designer-toolsuite/oligo_designer_toolsuite/utils/_sequence_parser.py:104: DtypeWarning: Columns (0) have mixed types. Specify dtype option on import or set low_memory=False.\n",
" csv_df = pd.read_csv(csv_file, sep=\"\\t\", names=self.GFF_HEADER, header=None)\n",
"\n",
"2024-06-19 21:28:56,907 [INFO] The following annotation files are used for GTF annotation of regions: /Users/lisa.barros/Desktop/spapros/docs/_tutorials/output_genomic_region_generator_ncbi/annotation/GCF_000001405.40_GRCh38.p14_genomic.gtf and for fasta sequence file: /Users/lisa.barros/Desktop/spapros/docs/_tutorials/output_genomic_region_generator_ncbi/annotation/GCF_000001405.40_GRCh38.p14_genomic.fna .\n",
"2024-06-19 21:28:56,908 [INFO] The annotations are from NCBI source, for the species: Homo_sapiens, release number: 110 and genome assembly: GRCh38.p14\n",
"2024-06-19 21:32:27,987 [INFO] The genomic region 'exon' was stored in :/Users/lisa.barros/Desktop/spapros/docs/_tutorials/output_genomic_region_generator_ncbi/annotation/exon_annotation_source-NCBI_species-Homo_sapiens_annotation_release-110_genome_assemly-GRCh38.p14.fna.\n",
"2024-06-19 21:44:45,118 [INFO] The genomic region 'exon_exon_junction' was stored in :/Users/lisa.barros/Desktop/spapros/docs/_tutorials/output_genomic_region_generator_ncbi/annotation/exon_exon_junction_annotation_source-NCBI_species-Homo_sapiens_annotation_release-110_genome_assemly-GRCh38.p14.fna.\n"
"2024-07-16 17:24:16,761 [INFO] The following annotation files are used for GTF annotation of regions: /Users/lisa.barros/Desktop/spapros/docs/_tutorials/output_genomic_region_generator_ncbi/annotation/GCF_000001405.40_GRCh38.p14_genomic.gtf and for fasta sequence file: /Users/lisa.barros/Desktop/spapros/docs/_tutorials/output_genomic_region_generator_ncbi/annotation/GCF_000001405.40_GRCh38.p14_genomic.fna .\n",
"2024-07-16 17:24:16,763 [INFO] The annotations are from NCBI source, for the species: Homo_sapiens, release number: 110 and genome assembly: GRCh38.p14\n",
"2024-07-16 17:28:18,217 [INFO] The genomic region 'exon' was stored in :/Users/lisa.barros/Desktop/spapros/docs/_tutorials/output_genomic_region_generator_ncbi/annotation/exon_annotation_source-NCBI_species-Homo_sapiens_annotation_release-110_genome_assemly-GRCh38.p14.fna.\n",
"2024-07-16 17:40:49,655 [INFO] The genomic region 'exon_exon_junction' was stored in :/Users/lisa.barros/Desktop/spapros/docs/_tutorials/output_genomic_region_generator_ncbi/annotation/exon_exon_junction_annotation_source-NCBI_species-Homo_sapiens_annotation_release-110_genome_assemly-GRCh38.p14.fna.\n"
]
}
],
Expand All @@ -248,68 +239,17 @@
"execution_count": 7,
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"/Users/lisa.barros/anaconda3/envs/odt_test/lib/python3.10/site-packages/Bio/Application/__init__.py:40: BiopythonDeprecationWarning: The Bio.Application modules and modules relying on it have been deprecated.\n",
"\n",
"Due to the on going maintenance burden of keeping command line application\n",
"wrappers up to date, we have decided to deprecate and eventually remove these\n",
"modules.\n",
"\n",
"We instead now recommend building your command line and invoking it directly\n",
"with the subprocess module.\n",
" warnings.warn(\n",
"/Users/lisa.barros/anaconda3/envs/odt_test/lib/python3.10/site-packages/Bio/Application/__init__.py:40: BiopythonDeprecationWarning: The Bio.Application modules and modules relying on it have been deprecated.\n",
"\n",
"Due to the on going maintenance burden of keeping command line application\n",
"wrappers up to date, we have decided to deprecate and eventually remove these\n",
"modules.\n",
"\n",
"We instead now recommend building your command line and invoking it directly\n",
"with the subprocess module.\n",
" warnings.warn(\n",
"/Users/lisa.barros/anaconda3/envs/odt_test/lib/python3.10/site-packages/Bio/Application/__init__.py:40: BiopythonDeprecationWarning: The Bio.Application modules and modules relying on it have been deprecated.\n",
"\n",
"Due to the on going maintenance burden of keeping command line application\n",
"wrappers up to date, we have decided to deprecate and eventually remove these\n",
"modules.\n",
"\n",
"We instead now recommend building your command line and invoking it directly\n",
"with the subprocess module.\n",
" warnings.warn(\n",
"/Users/lisa.barros/anaconda3/envs/odt_test/lib/python3.10/site-packages/Bio/Application/__init__.py:40: BiopythonDeprecationWarning: The Bio.Application modules and modules relying on it have been deprecated.\n",
"\n",
"Due to the on going maintenance burden of keeping command line application\n",
"wrappers up to date, we have decided to deprecate and eventually remove these\n",
"modules.\n",
"\n",
"We instead now recommend building your command line and invoking it directly\n",
"with the subprocess module.\n",
" warnings.warn(\n",
"/Users/lisa.barros/anaconda3/envs/odt_test/lib/python3.10/site-packages/Bio/Application/__init__.py:40: BiopythonDeprecationWarning: The Bio.Application modules and modules relying on it have been deprecated.\n",
"\n",
"Due to the on going maintenance burden of keeping command line application\n",
"wrappers up to date, we have decided to deprecate and eventually remove these\n",
"modules.\n",
"\n",
"We instead now recommend building your command line and invoking it directly\n",
"with the subprocess module.\n",
" warnings.warn(\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"\u001b[2K \u001b[35m100%\u001b[0m \u001b[36mDatabase Loading\u001b[0m \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m887/887\u001b[0m \u001b[33m1:09:27\u001b[0m < \u001b[36m0:00:00\u001b[0m< \u001b[36m0:00:04\u001b[0m03:37\u001b[0m\n",
"\u001b[2K \u001b[35m100%\u001b[0m \u001b[36mProperty Filter\u001b[0m \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m887/887\u001b[0m \u001b[33m1:00:48\u001b[0m < \u001b[36m0:00:00\u001b[0m< \u001b[36m0:00:04\u001b[0m01:38\u001b[0m\n",
"\u001b[2K \u001b[35m100%\u001b[0m \u001b[36mSpecificity Filter: Exact Matches\u001b[0m \u001b[90m━━━━━━━━━━━━━\u001b[0m \u001b[32m887/887\u001b[0m \u001b[33m0:04:27\u001b[0m < \u001b[36m0:00:00\u001b[0m< \u001b[36m0:00:01\u001b[0m00:21\u001b[0m\n",
"\u001b[2K \u001b[35m100%\u001b[0m \u001b[36mSpecificity Filter: Blastn Specificity\u001b[0m \u001b[90m━━━━━━━━\u001b[0m \u001b[32m887/887\u001b[0m \u001b[33m1:13:44\u001b[0m < \u001b[36m0:00:00\u001b[0m< \u001b[36m0:00:05\u001b[0m06:41\u001b[0m\n",
"\u001b[2K \u001b[35m100%\u001b[0m \u001b[36mSpecificity Filter: Blastn Crosshybridization\u001b[0m \u001b[90m━━━━━\u001b[0m \u001b[32m887/…\u001b[0m \u001b[33m0:02:…\u001b[0m < \u001b[36m0:00:…\u001b[0m < \u001b[36m0:00:…\u001b[0m:00:…\u001b[0m\n",
"\u001b[2K \u001b[35m100%\u001b[0m \u001b[36mFind Oligosets\u001b[0m \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m810/810\u001b[0m \u001b[33m2:42:58\u001b[0m < \u001b[36m0:00:00\u001b[0m< \u001b[36m0:00:04\u001b[0m02:54\u001b[0m\n",
"\u001b[2K \u001b[35m100%\u001b[0m \u001b[36mDesign Final Padlock Sequence\u001b[0m \u001b[90m━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m741/741\u001b[0m \u001b[33m0:11:26\u001b[0m < \u001b[36m0:00:00\u001b[0m< \u001b[36m0:00:01\u001b[0m00:38\u001b[0m\n",
"\u001b[2K \u001b[35m100%\u001b[0m \u001b[36mDatabase Loading\u001b[0m \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m887/887\u001b[0m \u001b[33m1:09:20\u001b[0m < \u001b[36m0:00:00\u001b[0m< \u001b[36m0:00:05\u001b[0m04:28\u001b[0m\n",
"\u001b[2K \u001b[35m100%\u001b[0m \u001b[36mProperty Filter\u001b[0m \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m887/887\u001b[0m \u001b[33m1:00:18\u001b[0m < \u001b[36m0:00:00\u001b[0m< \u001b[36m0:00:04\u001b[0m04:50\u001b[0m\n",
"\u001b[2K \u001b[35m100%\u001b[0m \u001b[36mSpecificity Filter: Exact Match\u001b[0m \u001b[90m━━━━━━━━━━━━━━━\u001b[0m \u001b[32m887/887\u001b[0m \u001b[33m0:04:31\u001b[0m < \u001b[36m0:00:00\u001b[0m< \u001b[36m0:00:01\u001b[0m00:26\u001b[0m\n",
"\u001b[2K \u001b[35m100%\u001b[0m \u001b[36mSpecificity Filter: Blastn Specificity\u001b[0m \u001b[90m━━━━━━━━\u001b[0m \u001b[32m887/887\u001b[0m \u001b[33m1:09:06\u001b[0m < \u001b[36m0:00:00\u001b[0m< \u001b[36m0:00:11\u001b[0m15:04\u001b[0m\n",
"\u001b[2K \u001b[35m100%\u001b[0m \u001b[36mSpecificity Filter: Blastn Crosshybridization\u001b[0m \u001b[90m━━━━━\u001b[0m \u001b[32m810/…\u001b[0m \u001b[33m0:02:…\u001b[0m < \u001b[36m0:00:…\u001b[0m < \u001b[36m0:00:…\u001b[0m:00:…\u001b[0m\n",
"\u001b[2K \u001b[35m100%\u001b[0m \u001b[36mFind Oligosets\u001b[0m \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m810/810\u001b[0m \u001b[33m2:44:14\u001b[0m < \u001b[36m0:00:00\u001b[0m< \u001b[36m0:00:04\u001b[0m01:51\u001b[0m\n",
"\u001b[2K \u001b[35m100%\u001b[0m \u001b[36mDesign Final Padlock Sequence\u001b[0m \u001b[90m━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m741/741\u001b[0m \u001b[33m0:11:25\u001b[0m < \u001b[36m0:00:00\u001b[0m< \u001b[36m0:00:01\u001b[0m00:49\u001b[0m\n",
"\u001b[?25h"
]
}
Expand All @@ -335,7 +275,7 @@
"##### Load probe design filter #####\n",
"genes_without_enough_probes = pd.read_csv('output_scrinshot_probe_designer/db_probes/regions_with_insufficient_oligos_for_db_probes.txt', index_col=0, sep=\"\\t\").index.tolist()\n",
"adata.var[\"has_enough_probes\"] = [g not in genes_without_enough_probes for g in adata.var_names]\n",
"adata.var[\"pass_constraints\"] = adata.var[\"has_enough_probes\"] & adata.var[\"highly_variable\"]\n"
"adata.var[\"pass_constraints\"] = adata.var[\"has_enough_probes\"] & adata.var[\"highly_variable\"]"
]
},
{
Expand All @@ -346,7 +286,7 @@
{
"data": {
"application/vnd.jupyter.widget-view+json": {
"model_id": "856cfa65e91446989bda6ed9bffa59e2",
"model_id": "5b1ed0e8aaaa4bd2a046ec85e95e1562",
"version_major": 2,
"version_minor": 0
},
Expand Down Expand Up @@ -511,35 +451,35 @@
{
"data": {
"text/plain": [
"{'oligoset_1': {'CTSS::21801': {'sequence_padlock_probe': 'CAGCAGTTGCTCCCACAGTTCCTCTATGATTACTGACTGCGTCTATTTAGTGGAGCCTGAATCTATCTTCTTTACCAGCCGTTTCATTGTGATAGAAC',\n",
"{'oligoset_1': {'CTSS::21801': {'sequence_padlock_probe': 'CAGCAGTTGCTCCCACAGTTCCTCTATGATTACTGACTGCGTCTATTTAGTGGAGCCTTCTCCTATCTTCTTTACCAGCCGTTTCATTGTGATAGAAC',\n",
" 'sequence_detection_oligo': 'CCGTTTCATTGTGATAGAACCAGCAGTTGCUCCCACAGU[fluorophore]'},\n",
" 'CTSS::3064': {'sequence_padlock_probe': 'GCCACAGCTTCTTTCAGGACATCCTCTATGATTACTGACTGCGTCTATTTAGTGGAGCCTGAATCTATCTTCTTTCCAACAGACACTGGGCCTTTATTG',\n",
" 'CTSS::3064': {'sequence_padlock_probe': 'GCCACAGCTTCTTTCAGGACATCCTCTATGATTACTGACTGCGTCTATTTAGTGGAGCCTTCTCCTATCTTCTTTCCAACAGACACTGGGCCTTTATTG',\n",
" 'sequence_detection_oligo': 'CAGACACTGGGCCTTTATTGGCCACAGCUTCTTUCAGGAC[fluorophore]'},\n",
" 'CTSS::22579': {'sequence_padlock_probe': 'GCGTCTGAGTCGATGCCCTTTCCTCTATGATTACTGACTGCGTCTATTTAGTGGAGCCTGAATCTATCTTCTTTATCCATGGCTTTGTAGGGATAGGAA',\n",
" 'CTSS::22579': {'sequence_padlock_probe': 'GCGTCTGAGTCGATGCCCTTTCCTCTATGATTACTGACTGCGTCTATTTAGTGGAGCCTTCTCCTATCTTCTTTATCCATGGCTTTGTAGGGATAGGAA',\n",
" 'sequence_detection_oligo': 'TGGCTTTGTAGGGATAGGAAGCGTCTGAGTCGAUGCCCU[fluorophore]'},\n",
" 'CTSS::979': {'sequence_padlock_probe': 'TTCCCATTGAATGCTCCAGGTTCCTCTATGATTACTGACTGCGTCTATTTAGTGGAGCCTGAATCTATCTTCTTTTGCCCAGATCGTATGAGTGCA',\n",
" 'CTSS::979': {'sequence_padlock_probe': 'TTCCCATTGAATGCTCCAGGTTCCTCTATGATTACTGACTGCGTCTATTTAGTGGAGCCTTCTCCTATCTTCTTTTGCCCAGATCGTATGAGTGCA',\n",
" 'sequence_detection_oligo': 'GCCCAGATCGTATGAGTGCATTCCCATUGAATGCUCCAGG[fluorophore]'},\n",
" 'CTSS::22236': {'sequence_padlock_probe': 'AGCACCACAAGAACCCATGTCTTCCTCTATGATTACTGACTGCGTCTATTTAGTGGAGCCTGAATCTATCTTCTTTACAGCACTGAAAGCCCAGCA',\n",
" 'CTSS::22236': {'sequence_padlock_probe': 'AGCACCACAAGAACCCATGTCTTCCTCTATGATTACTGACTGCGTCTATTTAGTGGAGCCTTCTCCTATCTTCTTTACAGCACTGAAAGCCCAGCA',\n",
" 'sequence_detection_oligo': 'ACAGCACUGAAAGCCCAGCAAGCACCACAAGAACCCATGU[fluorophore]'}},\n",
" 'oligoset_2': {'CTSS::21801': {'sequence_padlock_probe': 'CAGCAGTTGCTCCCACAGTTCCTCTATGATTACTGACTGCGTCTATTTAGTGGAGCCTGAATCTATCTTCTTTACCAGCCGTTTCATTGTGATAGAAC',\n",
" 'oligoset_2': {'CTSS::21801': {'sequence_padlock_probe': 'CAGCAGTTGCTCCCACAGTTCCTCTATGATTACTGACTGCGTCTATTTAGTGGAGCCTTCTCCTATCTTCTTTACCAGCCGTTTCATTGTGATAGAAC',\n",
" 'sequence_detection_oligo': 'CCGTTTCATTGTGATAGAACCAGCAGTTGCUCCCACAGU[fluorophore]'},\n",
" 'CTSS::3064': {'sequence_padlock_probe': 'GCCACAGCTTCTTTCAGGACATCCTCTATGATTACTGACTGCGTCTATTTAGTGGAGCCTGAATCTATCTTCTTTCCAACAGACACTGGGCCTTTATTG',\n",
" 'sequence_detection_oligo': 'CAGACACTGGGCCTTTATTGGCCACAGCUTCTTUCAGGAC[fluorophore]'},\n",
" 'CTSS::2173': {'sequence_padlock_probe': 'GTCTGAGTCGATGCCCTTGTTTCCTCTATGATTACTGACTGCGTCTATTTAGTGGAGCCTGAATCTATCTTCTTTATGGCTTTGTAGGGATAGGAAGC',\n",
" 'sequence_detection_oligo': 'GCTTTGTAGGGATAGGAAGCGTCTGAGTCGAUGCCCTTGU[fluorophore]'},\n",
" 'CTSS::979': {'sequence_padlock_probe': 'TTCCCATTGAATGCTCCAGGTTCCTCTATGATTACTGACTGCGTCTATTTAGTGGAGCCTGAATCTATCTTCTTTTGCCCAGATCGTATGAGTGCA',\n",
" 'CTSS::22579': {'sequence_padlock_probe': 'GCGTCTGAGTCGATGCCCTTTCCTCTATGATTACTGACTGCGTCTATTTAGTGGAGCCTTCTCCTATCTTCTTTATCCATGGCTTTGTAGGGATAGGAA',\n",
" 'sequence_detection_oligo': 'TGGCTTTGTAGGGATAGGAAGCGTCTGAGTCGAUGCCCU[fluorophore]'},\n",
" 'CTSS::979': {'sequence_padlock_probe': 'TTCCCATTGAATGCTCCAGGTTCCTCTATGATTACTGACTGCGTCTATTTAGTGGAGCCTTCTCCTATCTTCTTTTGCCCAGATCGTATGAGTGCA',\n",
" 'sequence_detection_oligo': 'GCCCAGATCGTATGAGTGCATTCCCATUGAATGCUCCAGG[fluorophore]'},\n",
" 'CTSS::22236': {'sequence_padlock_probe': 'AGCACCACAAGAACCCATGTCTTCCTCTATGATTACTGACTGCGTCTATTTAGTGGAGCCTGAATCTATCTTCTTTACAGCACTGAAAGCCCAGCA',\n",
" 'CTSS::2942': {'sequence_padlock_probe': 'GGCCACAGCTTCTTTCAGGACTCCTCTATGATTACTGACTGCGTCTATTTAGTGGAGCCTTCTCCTATCTTCTTTCCAACAGACACTGGGCCTTTATT',\n",
" 'sequence_detection_oligo': 'ACAGACACTGGGCCTTTATTGGCCACAGCUTCTTUCAGGA[fluorophore]'},\n",
" 'CTSS::22236': {'sequence_padlock_probe': 'AGCACCACAAGAACCCATGTCTTCCTCTATGATTACTGACTGCGTCTATTTAGTGGAGCCTTCTCCTATCTTCTTTACAGCACTGAAAGCCCAGCA',\n",
" 'sequence_detection_oligo': 'ACAGCACUGAAAGCCCAGCAAGCACCACAAGAACCCATGU[fluorophore]'}},\n",
" 'oligoset_3': {'CTSS::21801': {'sequence_padlock_probe': 'CAGCAGTTGCTCCCACAGTTCCTCTATGATTACTGACTGCGTCTATTTAGTGGAGCCTGAATCTATCTTCTTTACCAGCCGTTTCATTGTGATAGAAC',\n",
" 'oligoset_3': {'CTSS::21801': {'sequence_padlock_probe': 'CAGCAGTTGCTCCCACAGTTCCTCTATGATTACTGACTGCGTCTATTTAGTGGAGCCTTCTCCTATCTTCTTTACCAGCCGTTTCATTGTGATAGAAC',\n",
" 'sequence_detection_oligo': 'CCGTTTCATTGTGATAGAACCAGCAGTTGCUCCCACAGU[fluorophore]'},\n",
" 'CTSS::3064': {'sequence_padlock_probe': 'GCCACAGCTTCTTTCAGGACATCCTCTATGATTACTGACTGCGTCTATTTAGTGGAGCCTGAATCTATCTTCTTTCCAACAGACACTGGGCCTTTATTG',\n",
" 'sequence_detection_oligo': 'CAGACACTGGGCCTTTATTGGCCACAGCUTCTTUCAGGAC[fluorophore]'},\n",
" 'CTSS::22579': {'sequence_padlock_probe': 'GCGTCTGAGTCGATGCCCTTTCCTCTATGATTACTGACTGCGTCTATTTAGTGGAGCCTGAATCTATCTTCTTTATCCATGGCTTTGTAGGGATAGGAA',\n",
" 'sequence_detection_oligo': 'TGGCTTTGTAGGGATAGGAAGCGTCTGAGTCGAUGCCCU[fluorophore]'},\n",
" 'CTSS::1139': {'sequence_padlock_probe': 'CCCATTGAATGCTCCAGGTTGTTCCTCTATGATTACTGACTGCGTCTATTTAGTGGAGCCTGAATCTATCTTCTTTGCCCAGATCGTATGAGTGCATT',\n",
" 'sequence_detection_oligo': 'CCAGATCGTATGAGTGCATTCCCATTGAATGCUCCAGGU[fluorophore]'},\n",
" 'CTSS::22236': {'sequence_padlock_probe': 'AGCACCACAAGAACCCATGTCTTCCTCTATGATTACTGACTGCGTCTATTTAGTGGAGCCTGAATCTATCTTCTTTACAGCACTGAAAGCCCAGCA',\n",
" 'CTSS::2173': {'sequence_padlock_probe': 'GTCTGAGTCGATGCCCTTGTTTCCTCTATGATTACTGACTGCGTCTATTTAGTGGAGCCTTCTCCTATCTTCTTTATGGCTTTGTAGGGATAGGAAGC',\n",
" 'sequence_detection_oligo': 'GCTTTGTAGGGATAGGAAGCGTCTGAGTCGAUGCCCTTGU[fluorophore]'},\n",
" 'CTSS::979': {'sequence_padlock_probe': 'TTCCCATTGAATGCTCCAGGTTCCTCTATGATTACTGACTGCGTCTATTTAGTGGAGCCTTCTCCTATCTTCTTTTGCCCAGATCGTATGAGTGCA',\n",
" 'sequence_detection_oligo': 'GCCCAGATCGTATGAGTGCATTCCCATUGAATGCUCCAGG[fluorophore]'},\n",
" 'CTSS::2942': {'sequence_padlock_probe': 'GGCCACAGCTTCTTTCAGGACTCCTCTATGATTACTGACTGCGTCTATTTAGTGGAGCCTTCTCCTATCTTCTTTCCAACAGACACTGGGCCTTTATT',\n",
" 'sequence_detection_oligo': 'ACAGACACTGGGCCTTTATTGGCCACAGCUTCTTUCAGGA[fluorophore]'},\n",
" 'CTSS::22236': {'sequence_padlock_probe': 'AGCACCACAAGAACCCATGTCTTCCTCTATGATTACTGACTGCGTCTATTTAGTGGAGCCTTCTCCTATCTTCTTTACAGCACTGAAAGCCCAGCA',\n",
" 'sequence_detection_oligo': 'ACAGCACUGAAAGCCCAGCAAGCACCACAAGAACCCATGU[fluorophore]'}}}"
]
},
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