From d9eb37799b6a261a120fba28fd66f695afdea83c Mon Sep 17 00:00:00 2001 From: Lisa Sousa Date: Wed, 17 Jul 2024 09:03:32 +0200 Subject: [PATCH] update notebook to pipeline changes --- ..._tutorial_end_to_end_selection_short.ipynb | 134 +++++------------- 1 file changed, 37 insertions(+), 97 deletions(-) diff --git a/docs/_tutorials/spapros_tutorial_end_to_end_selection_short.ipynb b/docs/_tutorials/spapros_tutorial_end_to_end_selection_short.ipynb index 20b9f8f..4a8537d 100644 --- a/docs/_tutorials/spapros_tutorial_end_to_end_selection_short.ipynb +++ b/docs/_tutorials/spapros_tutorial_end_to_end_selection_short.ipynb @@ -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" ] } ], @@ -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" ] } @@ -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\"]" ] }, { @@ -346,7 +286,7 @@ { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "856cfa65e91446989bda6ed9bffa59e2", + "model_id": "5b1ed0e8aaaa4bd2a046ec85e95e1562", "version_major": 2, "version_minor": 0 }, @@ -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]'}}}" ] },