{ "cells": [ { "cell_type": "markdown", "id": "08631867", "metadata": {}, "source": [ "# 01 Loading data into an AnnotatedGEM\n", "\n", "This notebook describes how to create and save an `AnnotatedGEM` object from separate count and label text files.\n", "\n", "***Download the demo data***\n", "\n", "An expression matrix and accompanying annotation text files are available in a public [OSF](https://osf.io) project.\n", "You can download them by:\n", "+ Navigating to the [data repository on osf](https://osf.io/t3xpw/) and manually download them.\n", "or\n", "+ Installing the [OSF CLI utility](https://osfclient.readthedocs.io/en/latest/index.html) and clone to a directory:\n", " \n", " **Linux**\n", " ```bash\n", " # Install the osfclient.\n", " pip install osfclient\n", " \n", " # To clone the entire osf project:\n", " osf -p rbhfz clone ~/GSForge_demo_data\n", " \n", " # To pull the minimum number of files to complete the examples:\n", " osf \n", " ```\n", "\n", "***Set up the notebook***" ] }, { "cell_type": "code", "execution_count": 1, "id": "013c3b81", "metadata": { "execution": { "iopub.execute_input": "2021-08-06T21:05:49.791345Z", "iopub.status.busy": "2021-08-06T21:05:49.790501Z", "iopub.status.idle": "2021-08-06T21:05:58.059572Z", "shell.execute_reply": "2021-08-06T21:05:58.060154Z" } }, "outputs": [], "source": [ "# OS-independent path management.\n", "from os import environ\n", "from pathlib import Path\n", "import pandas as pd\n", "import GSForge as gsf" ] }, { "cell_type": "markdown", "id": "8dc4c712", "metadata": {}, "source": [ "***Declare used paths***\n", "\n", "Declare the OSF project directory path. This is the root directory of the data files used in this notebook." ] }, { "cell_type": "code", "execution_count": 2, "id": "a204dd0b", "metadata": { "execution": { "iopub.execute_input": "2021-08-06T21:05:58.068374Z", "iopub.status.busy": "2021-08-06T21:05:58.067400Z", "iopub.status.idle": "2021-08-06T21:05:58.069609Z", "shell.execute_reply": "2021-08-06T21:05:58.070305Z" } }, "outputs": [], "source": [ "OSF_PATH = Path(environ.get(\"GSFORGE_DEMO_DATA\", default=\"~/GSForge_demo_data/\")).expanduser().joinpath(\"osfstorage\", \"oryza_sativa\")\n", "RAW_COUNT_PATH = OSF_PATH.joinpath(\"GEMmakerGEMs\", \"rice_heat_drought.GEM.raw.txt\")\n", "HYDRO_LABEL_PATH = OSF_PATH.joinpath(\"GEMmakerGEMs\", \"raw_annotation_data\", \"PRJNA301554.hydroponic.annotations.txt\")" ] }, { "cell_type": "markdown", "id": "3aa0f927", "metadata": {}, "source": [ "Ensure these files exist." ] }, { "cell_type": "code", "execution_count": 3, "id": "06ea372d", "metadata": { "execution": { "iopub.execute_input": "2021-08-06T21:05:58.076132Z", "iopub.status.busy": "2021-08-06T21:05:58.075241Z", "iopub.status.idle": "2021-08-06T21:05:58.078058Z", "shell.execute_reply": "2021-08-06T21:05:58.078764Z" } }, "outputs": [], "source": [ "assert RAW_COUNT_PATH.exists()\n", "assert HYDRO_LABEL_PATH.exists()" ] }, { "cell_type": "markdown", "id": "74af1f6b", "metadata": {}, "source": [ "Finally, declare a path to save the created `.nc` file." ] }, { "cell_type": "code", "execution_count": 4, "id": "e8671a53", "metadata": { "execution": { "iopub.execute_input": "2021-08-06T21:05:58.085257Z", "iopub.status.busy": "2021-08-06T21:05:58.084322Z", "iopub.status.idle": "2021-08-06T21:05:58.088426Z", "shell.execute_reply": "2021-08-06T21:05:58.087687Z" } }, "outputs": [], "source": [ "GEM_PATH = OSF_PATH.joinpath(\"AnnotatedGEMs\", \"oryza_sativa_hisat2_raw.nc\")" ] }, { "cell_type": "markdown", "id": "c7710e56", "metadata": {}, "source": [ "## Loading data with `pandas`\n", "\n", "***Loading the count matrix***" ] }, { "cell_type": "code", "execution_count": 5, "id": "ad9a8010", "metadata": { "execution": { "iopub.execute_input": "2021-08-06T21:05:58.096753Z", "iopub.status.busy": "2021-08-06T21:05:58.095957Z", "iopub.status.idle": "2021-08-06T21:06:00.548243Z", "shell.execute_reply": "2021-08-06T21:06:00.548789Z" } }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "CPU times: user 2.18 s, sys: 245 ms, total: 2.42 s\n", "Wall time: 2.45 s\n" ] } ], "source": [ "%%time\n", "count_df = pd.read_csv(RAW_COUNT_PATH, sep=\"\\t\", index_col=0)" ] }, { "cell_type": "code", "execution_count": 6, "id": "f0926b5e", "metadata": { "execution": { "iopub.execute_input": "2021-08-06T21:06:00.569618Z", "iopub.status.busy": "2021-08-06T21:06:00.568851Z", "iopub.status.idle": "2021-08-06T21:06:00.580494Z", "shell.execute_reply": "2021-08-06T21:06:00.581449Z" } }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "(55986, 475)\n" ] }, { "data": { "text/html": [ "
\n", " | SRX1423934 | \n", "SRX1423935 | \n", "SRX1423936 | \n", "SRX1423937 | \n", "SRX1423938 | \n", "SRX1423939 | \n", "SRX1423940 | \n", "SRX1423941 | \n", "SRX1423942 | \n", "SRX1423943 | \n", "... | \n", "SRX1424399 | \n", "SRX1424400 | \n", "SRX1424401 | \n", "SRX1424402 | \n", "SRX1424403 | \n", "SRX1424404 | \n", "SRX1424405 | \n", "SRX1424406 | \n", "SRX1424407 | \n", "SRX1424408 | \n", "
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
LOC_Os06g05820 | \n", "20 | \n", "2 | \n", "22 | \n", "11 | \n", "23 | \n", "39 | \n", "24 | \n", "34 | \n", "33 | \n", "20 | \n", "... | \n", "5 | \n", "20 | \n", "20 | \n", "38 | \n", "35 | \n", "43 | \n", "25 | \n", "8 | \n", "8 | \n", "21 | \n", "
LOC_Os10g27460 | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "... | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "
LOC_Os02g35980 | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "... | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "
LOC_Os09g23260 | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "... | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "
LOC_Os01g41670 | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "... | \n", "0 | \n", "0 | \n", "0 | \n", "2 | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "
5 rows × 475 columns
\n", "\n", " | BioSample | \n", "LoadDate | \n", "MBases | \n", "MBytes | \n", "Run | \n", "SRA_Sample | \n", "Sample_Name | \n", "genotype | \n", "time | \n", "treatment | \n", "... | \n", "Instrument | \n", "LibraryLayout | \n", "LibrarySelection | \n", "LibrarySource | \n", "Organism | \n", "Platform | \n", "ReleaseDate | \n", "SRA_Study | \n", "source_name | \n", "tissue | \n", "
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Experiment | \n", "\n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " |
SRX1423937 | \n", "SAMN04251851 | \n", "2015-11-20 | \n", "1166 | \n", "764 | \n", "SRR2931043 | \n", "SRS1156717 | \n", "GSM1933349 | \n", "Azuenca | \n", "30 | \n", "CONTROL | \n", "... | \n", "Illumina HiSeq 2000 | \n", "PAIRED | \n", "cDNA | \n", "TRANSCRIPTOMIC | \n", "Oryza sativa | \n", "ILLUMINA | \n", "2016-01-04 | \n", "SRP065945 | \n", "Rice leaf | \n", "leaf | \n", "
SRX1423938 | \n", "SAMN04251852 | \n", "2015-11-20 | \n", "4005 | \n", "2500 | \n", "SRR2931044 | \n", "SRS1156720 | \n", "GSM1933350 | \n", "Azuenca | \n", "45 | \n", "CONTROL | \n", "... | \n", "Illumina HiSeq 2000 | \n", "PAIRED | \n", "cDNA | \n", "TRANSCRIPTOMIC | \n", "Oryza sativa | \n", "ILLUMINA | \n", "2016-01-04 | \n", "SRP065945 | \n", "Rice leaf | \n", "leaf | \n", "
2 rows × 28 columns
\n", "<xarray.Dataset>\n", "Dimensions: (Sample: 475, Gene: 55986)\n", "Coordinates:\n", " * Sample (Sample) object 'SRX1423934' ... 'SRX1424408'\n", " * Gene (Gene) object 'LOC_Os06g05820' ... 'LOC_Os07g03418'\n", "Data variables: (12/29)\n", " BioSample (Sample) object 'SAMN04251848' ... 'SAMN04251607'\n", " LoadDate (Sample) object '2015-11-20' ... '2015-11-19'\n", " MBases (Sample) int64 4016 5202 4053 1166 ... 3098 3529 2922\n", " MBytes (Sample) int64 2738 3652 2719 764 ... 1983 2370 1862\n", " Run (Sample) object 'SRR2931040' ... 'SRR2931514'\n", " SRA_Sample (Sample) object 'SRS1156722' ... 'SRS1156251'\n", " ... ...\n", " Platform (Sample) object 'ILLUMINA' 'ILLUMINA' ... 'ILLUMINA'\n", " ReleaseDate (Sample) object '2016-01-04' ... '2016-01-04'\n", " SRA_Study (Sample) object 'SRP065945' 'SRP065945' ... 'SRP065945'\n", " source_name (Sample) object 'Rice leaf' 'Rice leaf' ... 'Rice leaf'\n", " tissue (Sample) object 'leaf' 'leaf' 'leaf' ... 'leaf' 'leaf'\n", " counts (Sample, Gene) int64 20 0 0 0 0 0 ... 0 52 335 0 666 0
array(['SRX1423934', 'SRX1423935', 'SRX1423936', ..., 'SRX1424406',\n", " 'SRX1424407', 'SRX1424408'], dtype=object)
array(['LOC_Os06g05820', 'LOC_Os10g27460', 'LOC_Os02g35980', ...,\n", " 'LOC_Os03g50190', 'LOC_Os03g20020', 'LOC_Os07g03418'], dtype=object)
array(['SAMN04251848', 'SAMN04251849', 'SAMN04251850', 'SAMN04251851',\n", " 'SAMN04251852', 'SAMN04251853', 'SAMN04251854', 'SAMN04251855',\n", " 'SAMN04251856', 'SAMN04251857', 'SAMN04251858', 'SAMN04251859',\n", " 'SAMN04251860', 'SAMN04251861', 'SAMN04251862', 'SAMN04251863',\n", " 'SAMN04251864', 'SAMN04251865', 'SAMN04251866', 'SAMN04251867',\n", " 'SAMN04251868', 'SAMN04251869', 'SAMN04251870', 'SAMN04251871',\n", " 'SAMN04251872', 'SAMN04251873', 'SAMN04251874', 'SAMN04251875',\n", " 'SAMN04251876', 'SAMN04251877', 'SAMN04251878', 'SAMN04251879',\n", " 'SAMN04251880', 'SAMN04251881', 'SAMN04251882', 'SAMN04251883',\n", " 'SAMN04251884', 'SAMN04251885', 'SAMN04251886', 'SAMN04251887',\n", " 'SAMN04251888', 'SAMN04251889', 'SAMN04251890', 'SAMN04251891',\n", " 'SAMN04251892', 'SAMN04251893', 'SAMN04251894', 'SAMN04251895',\n", " 'SAMN04251896', 'SAMN04251897', 'SAMN04251898', 'SAMN04251899',\n", " 'SAMN04251900', 'SAMN04251901', 'SAMN04251902', 'SAMN04251903',\n", " 'SAMN04251964', 'SAMN04251965', 'SAMN04251966', 'SAMN04251967',\n", " 'SAMN04251968', 'SAMN04251969', 'SAMN04251970', 'SAMN04251971',\n", " 'SAMN04251972', 'SAMN04251973', 'SAMN04251974', 'SAMN04251975',\n", " 'SAMN04251976', 'SAMN04251977', 'SAMN04251978', 'SAMN04251979',\n", " 'SAMN04251980', 'SAMN04251981', 'SAMN04251982', 'SAMN04251983',\n", " 'SAMN04251984', 'SAMN04251985', 'SAMN04251986', 'SAMN04251987',\n", "...\n", " 'SAMN04251618', 'SAMN04251619', 'SAMN04251620', 'SAMN04251621',\n", " 'SAMN04251622', 'SAMN04251623', 'SAMN04251624', 'SAMN04251625',\n", " 'SAMN04251626', 'SAMN04251627', 'SAMN04251628', 'SAMN04251629',\n", " 'SAMN04251630', 'SAMN04251631', 'SAMN04251632', 'SAMN04251633',\n", " 'SAMN04251634', 'SAMN04251635', 'SAMN04251636', 'SAMN04251637',\n", " 'SAMN04251549', 'SAMN04251550', 'SAMN04251551', 'SAMN04251552',\n", " 'SAMN04251553', 'SAMN04251554', 'SAMN04251555', 'SAMN04251556',\n", " 'SAMN04251557', 'SAMN04251558', 'SAMN04251559', 'SAMN04251560',\n", " 'SAMN04251561', 'SAMN04251562', 'SAMN04251563', 'SAMN04251564',\n", " 'SAMN04251565', 'SAMN04251566', 'SAMN04251567', 'SAMN04251568',\n", " 'SAMN04251569', 'SAMN04251570', 'SAMN04251571', 'SAMN04251572',\n", " 'SAMN04251573', 'SAMN04251574', 'SAMN04251575', 'SAMN04251576',\n", " 'SAMN04251577', 'SAMN04251578', 'SAMN04251579', 'SAMN04251580',\n", " 'SAMN04251581', 'SAMN04251582', 'SAMN04251583', 'SAMN04251584',\n", " 'SAMN04251585', 'SAMN04251586', 'SAMN04251587', 'SAMN04251588',\n", " 'SAMN04251589', 'SAMN04251590', 'SAMN04251591', 'SAMN04251592',\n", " 'SAMN04251593', 'SAMN04251594', 'SAMN04251595', 'SAMN04251596',\n", " 'SAMN04251597', 'SAMN04251598', 'SAMN04251599', 'SAMN04251600',\n", " 'SAMN04251601', 'SAMN04251602', 'SAMN04251603', 'SAMN04251604',\n", " 'SAMN04251605', 'SAMN04251606', 'SAMN04251607'], dtype=object)
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array(['SRS1156722', 'SRS1156721', 'SRS1156718', 'SRS1156717',\n", " 'SRS1156720', 'SRS1156719', 'SRS1156716', 'SRS1156714',\n", " 'SRS1156715', 'SRS1156713', 'SRS1156711', 'SRS1156712',\n", " 'SRS1156710', 'SRS1156709', 'SRS1156708', 'SRS1156707',\n", " 'SRS1156706', 'SRS1156705', 'SRS1156703', 'SRS1156704',\n", " 'SRS1156702', 'SRS1156700', 'SRS1156698', 'SRS1156699',\n", " 'SRS1156701', 'SRS1156696', 'SRS1156697', 'SRS1156695',\n", " 'SRS1156694', 'SRS1156693', 'SRS1156691', 'SRS1156692',\n", " 'SRS1156690', 'SRS1156688', 'SRS1156689', 'SRS1156687',\n", " 'SRS1156686', 'SRS1156684', 'SRS1156685', 'SRS1156683',\n", " 'SRS1156682', 'SRS1156681', 'SRS1156680', 'SRS1156678',\n", " 'SRS1156679', 'SRS1156677', 'SRS1156676', 'SRS1156675',\n", " 'SRS1156674', 'SRS1156673', 'SRS1156672', 'SRS1156671',\n", " 'SRS1156668', 'SRS1156669', 'SRS1156670', 'SRS1156667',\n", " 'SRS1156666', 'SRS1156664', 'SRS1156665', 'SRS1156663',\n", " 'SRS1156662', 'SRS1156659', 'SRS1156660', 'SRS1156661',\n", " 'SRS1156658', 'SRS1156657', 'SRS1156656', 'SRS1156655',\n", " 'SRS1156654', 'SRS1156653', 'SRS1156652', 'SRS1156651',\n", " 'SRS1156650', 'SRS1156649', 'SRS1156648', 'SRS1156647',\n", " 'SRS1156646', 'SRS1156645', 'SRS1156644', 'SRS1156643',\n", "...\n", " 'SRS1156328', 'SRS1156327', 'SRS1156326', 'SRS1156325',\n", " 'SRS1156324', 'SRS1156323', 'SRS1156321', 'SRS1156322',\n", " 'SRS1156320', 'SRS1156319', 'SRS1156318', 'SRS1156317',\n", " 'SRS1156316', 'SRS1156315', 'SRS1156314', 'SRS1156313',\n", " 'SRS1156312', 'SRS1156311', 'SRS1156309', 'SRS1156310',\n", " 'SRS1156308', 'SRS1156307', 'SRS1156306', 'SRS1156305',\n", " 'SRS1156304', 'SRS1156303', 'SRS1156302', 'SRS1156301',\n", " 'SRS1156299', 'SRS1156300', 'SRS1156298', 'SRS1156297',\n", " 'SRS1156296', 'SRS1156295', 'SRS1156294', 'SRS1156292',\n", " 'SRS1156293', 'SRS1156249', 'SRS1156291', 'SRS1156290',\n", " 'SRS1156289', 'SRS1156288', 'SRS1156287', 'SRS1156286',\n", " 'SRS1156285', 'SRS1156284', 'SRS1156282', 'SRS1156283',\n", " 'SRS1156281', 'SRS1156280', 'SRS1156279', 'SRS1156277',\n", " 'SRS1156278', 'SRS1156276', 'SRS1156275', 'SRS1156274',\n", " 'SRS1156273', 'SRS1156272', 'SRS1156271', 'SRS1156270',\n", " 'SRS1156269', 'SRS1156268', 'SRS1156267', 'SRS1156266',\n", " 'SRS1156250', 'SRS1156265', 'SRS1156264', 'SRS1156263',\n", " 'SRS1156262', 'SRS1156261', 'SRS1156260', 'SRS1156258',\n", " 'SRS1156259', 'SRS1156257', 'SRS1156256', 'SRS1156255',\n", " 'SRS1156254', 'SRS1156252', 'SRS1156251'], dtype=object)
array(['GSM1933346', 'GSM1933347', 'GSM1933348', 'GSM1933349',\n", " 'GSM1933350', 'GSM1933351', 'GSM1933352', 'GSM1933353',\n", " 'GSM1933354', 'GSM1933355', 'GSM1933356', 'GSM1933357',\n", " 'GSM1933358', 'GSM1933359', 'GSM1933360', 'GSM1933361',\n", " 'GSM1933362', 'GSM1933363', 'GSM1933364', 'GSM1933365',\n", " 'GSM1933366', 'GSM1933367', 'GSM1933368', 'GSM1933369',\n", " 'GSM1933370', 'GSM1933371', 'GSM1933372', 'GSM1933373',\n", " 'GSM1933374', 'GSM1933375', 'GSM1933376', 'GSM1933377',\n", " 'GSM1933378', 'GSM1933379', 'GSM1933380', 'GSM1933381',\n", " 'GSM1933382', 'GSM1933383', 'GSM1933384', 'GSM1933385',\n", " 'GSM1933386', 'GSM1933387', 'GSM1933388', 'GSM1933389',\n", " 'GSM1933390', 'GSM1933391', 'GSM1933392', 'GSM1933393',\n", " 'GSM1933394', 'GSM1933395', 'GSM1933396', 'GSM1933397',\n", " 'GSM1933398', 'GSM1933399', 'GSM1933400', 'GSM1933401',\n", " 'GSM1933402', 'GSM1933403', 'GSM1933404', 'GSM1933405',\n", " 'GSM1933406', 'GSM1933407', 'GSM1933408', 'GSM1933409',\n", " 'GSM1933410', 'GSM1933411', 'GSM1933412', 'GSM1933413',\n", " 'GSM1933414', 'GSM1933415', 'GSM1933416', 'GSM1933417',\n", " 'GSM1933418', 'GSM1933419', 'GSM1933420', 'GSM1933421',\n", " 'GSM1933422', 'GSM1933423', 'GSM1933424', 'GSM1933425',\n", "...\n", " 'GSM1933742', 'GSM1933743', 'GSM1933744', 'GSM1933745',\n", " 'GSM1933746', 'GSM1933747', 'GSM1933748', 'GSM1933749',\n", " 'GSM1933750', 'GSM1933751', 'GSM1933752', 'GSM1933753',\n", " 'GSM1933754', 'GSM1933755', 'GSM1933756', 'GSM1933757',\n", " 'GSM1933758', 'GSM1933759', 'GSM1933760', 'GSM1933761',\n", " 'GSM1933762', 'GSM1933763', 'GSM1933764', 'GSM1933765',\n", " 'GSM1933766', 'GSM1933767', 'GSM1933768', 'GSM1933769',\n", " 'GSM1933770', 'GSM1933771', 'GSM1933772', 'GSM1933773',\n", " 'GSM1933774', 'GSM1933775', 'GSM1933776', 'GSM1933777',\n", " 'GSM1933778', 'GSM1933779', 'GSM1933780', 'GSM1933781',\n", " 'GSM1933782', 'GSM1933783', 'GSM1933784', 'GSM1933785',\n", " 'GSM1933786', 'GSM1933787', 'GSM1933788', 'GSM1933789',\n", " 'GSM1933790', 'GSM1933791', 'GSM1933792', 'GSM1933793',\n", " 'GSM1933794', 'GSM1933795', 'GSM1933796', 'GSM1933797',\n", " 'GSM1933798', 'GSM1933799', 'GSM1933800', 'GSM1933801',\n", " 'GSM1933802', 'GSM1933803', 'GSM1933804', 'GSM1933805',\n", " 'GSM1933806', 'GSM1933807', 'GSM1933808', 'GSM1933809',\n", " 'GSM1933810', 'GSM1933811', 'GSM1933812', 'GSM1933813',\n", " 'GSM1933814', 'GSM1933815', 'GSM1933816', 'GSM1933817',\n", " 'GSM1933818', 'GSM1933819', 'GSM1933820'], dtype=object)
array(['Azuenca', 'Azuenca', 'Azuenca', 'Azuenca', 'Azuenca', 'Azuenca',\n", " 'Azuenca', 'Azuenca', 'Azuenca', 'Azuenca', 'Azuenca', 'Azuenca',\n", " 'Azuenca', 'Azuenca', 'Azuenca', 'Azuenca', 'Azuenca', 'Azuenca',\n", " 'Azuenca', 'Azuenca', 'Azuenca', 'Azuenca', 'Azuenca', 'Azuenca',\n", " 'Azuenca', 'Azuenca', 'Azuenca', 'Azuenca', 'Azuenca', 'Azuenca',\n", " 'Azuenca', 'Azuenca', 'Azuenca', 'Azuenca', 'Azuenca', 'Azuenca',\n", " 'Azuenca', 'Azuenca', 'Azuenca', 'Azuenca', 'Azuenca', 'Azuenca',\n", " 'Azuenca', 'Azuenca', 'Azuenca', 'Azuenca', 'Azuenca', 'Azuenca',\n", " 'Azuenca', 'Azuenca', 'Azuenca', 'Azuenca', 'Azuenca', 'Azuenca',\n", " 'Azuenca', 'Azuenca', 'Azuenca', 'Azuenca', 'Azuenca', 'Azuenca',\n", " 'Azuenca', 'Azuenca', 'Azuenca', 'Azuenca', 'Azuenca', 'Azuenca',\n", " 'Azuenca', 'Azuenca', 'Azuenca', 'Azuenca', 'Azuenca', 'Azuenca',\n", " 'Azuenca', 'Azuenca', 'Azuenca', 'Azuenca', 'Azuenca', 'Azuenca',\n", " 'Azuenca', 'Azuenca', 'Azuenca', 'Azuenca', 'Azuenca', 'Azuenca',\n", " 'Azuenca', 'Azuenca', 'Azuenca', 'Azuenca', 'Azuenca', 'Azuenca',\n", " 'Azuenca', 'Azuenca', 'Azuenca', 'Azuenca', 'Azuenca', 'Azuenca',\n", " 'Azuenca', 'Azuenca', 'Azuenca', 'Azuenca', 'Azuenca', 'Azuenca',\n", " 'Azuenca', 'Azuenca', 'Azuenca', 'Azuenca', 'Azuenca', 'Azuenca',\n", " 'Azuenca', 'Azuenca', 'Azuenca', 'Azuenca', 'Azuenca', 'Azuenca',\n", " 'Azuenca', 'Azuenca', 'Azuenca', 'Azuenca', 'Azuenca', 'Kinandang',\n", "...\n", " 'Tadukan', 'Tadukan', 'Tadukan', 'Tadukan', 'Tadukan', 'Tadukan',\n", " 'Tadukan', 'Tadukan', 'Tadukan', 'Tadukan', 'Tadukan', 'Tadukan',\n", " 'Tadukan', 'Tadukan', 'Tadukan', 'Tadukan', 'Tadukan', 'Tadukan',\n", " 'Tadukan', 'Tadukan', 'Tadukan', 'Tadukan', 'Tadukan', 'Tadukan',\n", " 'Tadukan', 'Tadukan', 'Tadukan', 'Tadukan', 'Tadukan', 'Tadukan',\n", " 'Tadukan', 'Tadukan', 'Tadukan', 'Tadukan', 'Tadukan', 'Tadukan',\n", " 'Tadukan', 'Tadukan', 'Tadukan', 'Tadukan', 'Tadukan', 'Tadukan',\n", " 'Tadukan', 'Tadukan', 'Tadukan', 'Tadukan', 'Tadukan', 'Tadukan',\n", " 'Tadukan', 'Tadukan', 'Tadukan', 'Tadukan', 'Tadukan', 'Tadukan',\n", " 'Tadukan', 'Tadukan', 'Tadukan', 'Tadukan', 'Tadukan', 'Tadukan',\n", " 'Tadukan', 'Tadukan', 'Tadukan', 'Tadukan', 'Tadukan', 'Tadukan',\n", " 'Tadukan', 'Tadukan', 'Tadukan', 'Tadukan', 'Tadukan', 'Tadukan',\n", " 'Tadukan', 'Tadukan', 'Tadukan', 'Tadukan', 'Tadukan', 'Tadukan',\n", " 'Tadukan', 'Tadukan', 'Tadukan', 'Tadukan', 'Tadukan', 'Tadukan',\n", " 'Tadukan', 'Tadukan', 'Tadukan', 'Tadukan', 'Tadukan', 'Tadukan',\n", " 'Tadukan', 'Tadukan', 'Tadukan', 'Tadukan', 'Tadukan', 'Tadukan',\n", " 'Tadukan', 'Tadukan', 'Tadukan', 'Tadukan', 'Tadukan', 'Tadukan',\n", " 'Tadukan', 'Tadukan', 'Tadukan', 'Tadukan', 'Tadukan', 'Tadukan',\n", " 'Tadukan', 'Tadukan', 'Tadukan', 'Tadukan', 'Tadukan', 'Tadukan'],\n", " dtype=object)
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array(['cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA',\n", " 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA',\n", " 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA',\n", " 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA',\n", " 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA',\n", " 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA',\n", " 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA',\n", " 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA',\n", " 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA',\n", " 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA',\n", " 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA',\n", " 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA',\n", " 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA',\n", " 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA',\n", " 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA',\n", " 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA',\n", " 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA',\n", " 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA',\n", " 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA',\n", " 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA',\n", "...\n", " 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA',\n", " 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA',\n", " 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA',\n", " 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA',\n", " 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA',\n", " 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA',\n", " 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA',\n", " 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA',\n", " 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA',\n", " 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA',\n", " 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA',\n", " 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA',\n", " 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA',\n", " 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA',\n", " 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA',\n", " 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA',\n", " 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA',\n", " 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA',\n", " 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA', 'cDNA',\n", " 'cDNA', 'cDNA', 'cDNA'], dtype=object)
array(['TRANSCRIPTOMIC', 'TRANSCRIPTOMIC', 'TRANSCRIPTOMIC',\n", " 'TRANSCRIPTOMIC', 'TRANSCRIPTOMIC', 'TRANSCRIPTOMIC',\n", " 'TRANSCRIPTOMIC', 'TRANSCRIPTOMIC', 'TRANSCRIPTOMIC',\n", " 'TRANSCRIPTOMIC', 'TRANSCRIPTOMIC', 'TRANSCRIPTOMIC',\n", " 'TRANSCRIPTOMIC', 'TRANSCRIPTOMIC', 'TRANSCRIPTOMIC',\n", " 'TRANSCRIPTOMIC', 'TRANSCRIPTOMIC', 'TRANSCRIPTOMIC',\n", " 'TRANSCRIPTOMIC', 'TRANSCRIPTOMIC', 'TRANSCRIPTOMIC',\n", " 'TRANSCRIPTOMIC', 'TRANSCRIPTOMIC', 'TRANSCRIPTOMIC',\n", " 'TRANSCRIPTOMIC', 'TRANSCRIPTOMIC', 'TRANSCRIPTOMIC',\n", " 'TRANSCRIPTOMIC', 'TRANSCRIPTOMIC', 'TRANSCRIPTOMIC',\n", " 'TRANSCRIPTOMIC', 'TRANSCRIPTOMIC', 'TRANSCRIPTOMIC',\n", " 'TRANSCRIPTOMIC', 'TRANSCRIPTOMIC', 'TRANSCRIPTOMIC',\n", " 'TRANSCRIPTOMIC', 'TRANSCRIPTOMIC', 'TRANSCRIPTOMIC',\n", " 'TRANSCRIPTOMIC', 'TRANSCRIPTOMIC', 'TRANSCRIPTOMIC',\n", " 'TRANSCRIPTOMIC', 'TRANSCRIPTOMIC', 'TRANSCRIPTOMIC',\n", " 'TRANSCRIPTOMIC', 'TRANSCRIPTOMIC', 'TRANSCRIPTOMIC',\n", " 'TRANSCRIPTOMIC', 'TRANSCRIPTOMIC', 'TRANSCRIPTOMIC',\n", " 'TRANSCRIPTOMIC', 'TRANSCRIPTOMIC', 'TRANSCRIPTOMIC',\n", " 'TRANSCRIPTOMIC', 'TRANSCRIPTOMIC', 'TRANSCRIPTOMIC',\n", " 'TRANSCRIPTOMIC', 'TRANSCRIPTOMIC', 'TRANSCRIPTOMIC',\n", "...\n", " 'TRANSCRIPTOMIC', 'TRANSCRIPTOMIC', 'TRANSCRIPTOMIC',\n", " 'TRANSCRIPTOMIC', 'TRANSCRIPTOMIC', 'TRANSCRIPTOMIC',\n", " 'TRANSCRIPTOMIC', 'TRANSCRIPTOMIC', 'TRANSCRIPTOMIC',\n", " 'TRANSCRIPTOMIC', 'TRANSCRIPTOMIC', 'TRANSCRIPTOMIC',\n", " 'TRANSCRIPTOMIC', 'TRANSCRIPTOMIC', 'TRANSCRIPTOMIC',\n", " 'TRANSCRIPTOMIC', 'TRANSCRIPTOMIC', 'TRANSCRIPTOMIC',\n", " 'TRANSCRIPTOMIC', 'TRANSCRIPTOMIC', 'TRANSCRIPTOMIC',\n", " 'TRANSCRIPTOMIC', 'TRANSCRIPTOMIC', 'TRANSCRIPTOMIC',\n", " 'TRANSCRIPTOMIC', 'TRANSCRIPTOMIC', 'TRANSCRIPTOMIC',\n", " 'TRANSCRIPTOMIC', 'TRANSCRIPTOMIC', 'TRANSCRIPTOMIC',\n", " 'TRANSCRIPTOMIC', 'TRANSCRIPTOMIC', 'TRANSCRIPTOMIC',\n", " 'TRANSCRIPTOMIC', 'TRANSCRIPTOMIC', 'TRANSCRIPTOMIC',\n", " 'TRANSCRIPTOMIC', 'TRANSCRIPTOMIC', 'TRANSCRIPTOMIC',\n", " 'TRANSCRIPTOMIC', 'TRANSCRIPTOMIC', 'TRANSCRIPTOMIC',\n", " 'TRANSCRIPTOMIC', 'TRANSCRIPTOMIC', 'TRANSCRIPTOMIC',\n", " 'TRANSCRIPTOMIC', 'TRANSCRIPTOMIC', 'TRANSCRIPTOMIC',\n", " 'TRANSCRIPTOMIC', 'TRANSCRIPTOMIC', 'TRANSCRIPTOMIC',\n", " 'TRANSCRIPTOMIC', 'TRANSCRIPTOMIC', 'TRANSCRIPTOMIC',\n", " 'TRANSCRIPTOMIC', 'TRANSCRIPTOMIC', 'TRANSCRIPTOMIC',\n", " 'TRANSCRIPTOMIC'], dtype=object)
array(['Oryza sativa', 'Oryza sativa', 'Oryza sativa', 'Oryza sativa',\n", " 'Oryza sativa', 'Oryza sativa', 'Oryza sativa', 'Oryza sativa',\n", " 'Oryza sativa', 'Oryza sativa', 'Oryza sativa', 'Oryza sativa',\n", " 'Oryza sativa', 'Oryza sativa', 'Oryza sativa', 'Oryza sativa',\n", " 'Oryza sativa', 'Oryza sativa', 'Oryza sativa', 'Oryza sativa',\n", " 'Oryza sativa', 'Oryza sativa', 'Oryza sativa', 'Oryza sativa',\n", " 'Oryza sativa', 'Oryza sativa', 'Oryza sativa', 'Oryza sativa',\n", " 'Oryza sativa', 'Oryza sativa', 'Oryza sativa', 'Oryza sativa',\n", " 'Oryza sativa', 'Oryza sativa', 'Oryza sativa', 'Oryza sativa',\n", " 'Oryza sativa', 'Oryza sativa', 'Oryza sativa', 'Oryza sativa',\n", " 'Oryza sativa', 'Oryza sativa', 'Oryza sativa', 'Oryza sativa',\n", " 'Oryza sativa', 'Oryza sativa', 'Oryza sativa', 'Oryza sativa',\n", " 'Oryza sativa', 'Oryza sativa', 'Oryza sativa', 'Oryza sativa',\n", " 'Oryza sativa', 'Oryza sativa', 'Oryza sativa', 'Oryza sativa',\n", " 'Oryza sativa', 'Oryza sativa', 'Oryza sativa', 'Oryza sativa',\n", " 'Oryza sativa', 'Oryza sativa', 'Oryza sativa', 'Oryza sativa',\n", " 'Oryza sativa', 'Oryza sativa', 'Oryza sativa', 'Oryza sativa',\n", " 'Oryza sativa', 'Oryza sativa', 'Oryza sativa', 'Oryza sativa',\n", " 'Oryza sativa', 'Oryza sativa', 'Oryza sativa', 'Oryza sativa',\n", " 'Oryza sativa', 'Oryza sativa', 'Oryza sativa', 'Oryza sativa',\n", "...\n", " 'Oryza sativa', 'Oryza sativa', 'Oryza sativa', 'Oryza sativa',\n", " 'Oryza sativa', 'Oryza sativa', 'Oryza sativa', 'Oryza sativa',\n", " 'Oryza sativa', 'Oryza sativa', 'Oryza sativa', 'Oryza sativa',\n", " 'Oryza sativa', 'Oryza sativa', 'Oryza sativa', 'Oryza sativa',\n", " 'Oryza sativa', 'Oryza sativa', 'Oryza sativa', 'Oryza sativa',\n", " 'Oryza sativa', 'Oryza sativa', 'Oryza sativa', 'Oryza sativa',\n", " 'Oryza sativa', 'Oryza sativa', 'Oryza sativa', 'Oryza sativa',\n", " 'Oryza sativa', 'Oryza sativa', 'Oryza sativa', 'Oryza sativa',\n", " 'Oryza sativa', 'Oryza sativa', 'Oryza sativa', 'Oryza sativa',\n", " 'Oryza sativa', 'Oryza sativa', 'Oryza sativa', 'Oryza sativa',\n", " 'Oryza sativa', 'Oryza sativa', 'Oryza sativa', 'Oryza sativa',\n", " 'Oryza sativa', 'Oryza sativa', 'Oryza sativa', 'Oryza sativa',\n", " 'Oryza sativa', 'Oryza sativa', 'Oryza sativa', 'Oryza sativa',\n", " 'Oryza sativa', 'Oryza sativa', 'Oryza sativa', 'Oryza sativa',\n", " 'Oryza sativa', 'Oryza sativa', 'Oryza sativa', 'Oryza sativa',\n", " 'Oryza sativa', 'Oryza sativa', 'Oryza sativa', 'Oryza sativa',\n", " 'Oryza sativa', 'Oryza sativa', 'Oryza sativa', 'Oryza sativa',\n", " 'Oryza sativa', 'Oryza sativa', 'Oryza sativa', 'Oryza sativa',\n", " 'Oryza sativa', 'Oryza sativa', 'Oryza sativa', 'Oryza sativa',\n", " 'Oryza sativa', 'Oryza sativa', 'Oryza sativa'], dtype=object)
array(['ILLUMINA', 'ILLUMINA', 'ILLUMINA', 'ILLUMINA', 'ILLUMINA',\n", " 'ILLUMINA', 'ILLUMINA', 'ILLUMINA', 'ILLUMINA', 'ILLUMINA',\n", " 'ILLUMINA', 'ILLUMINA', 'ILLUMINA', 'ILLUMINA', 'ILLUMINA',\n", " 'ILLUMINA', 'ILLUMINA', 'ILLUMINA', 'ILLUMINA', 'ILLUMINA',\n", " 'ILLUMINA', 'ILLUMINA', 'ILLUMINA', 'ILLUMINA', 'ILLUMINA',\n", " 'ILLUMINA', 'ILLUMINA', 'ILLUMINA', 'ILLUMINA', 'ILLUMINA',\n", " 'ILLUMINA', 'ILLUMINA', 'ILLUMINA', 'ILLUMINA', 'ILLUMINA',\n", " 'ILLUMINA', 'ILLUMINA', 'ILLUMINA', 'ILLUMINA', 'ILLUMINA',\n", " 'ILLUMINA', 'ILLUMINA', 'ILLUMINA', 'ILLUMINA', 'ILLUMINA',\n", " 'ILLUMINA', 'ILLUMINA', 'ILLUMINA', 'ILLUMINA', 'ILLUMINA',\n", " 'ILLUMINA', 'ILLUMINA', 'ILLUMINA', 'ILLUMINA', 'ILLUMINA',\n", " 'ILLUMINA', 'ILLUMINA', 'ILLUMINA', 'ILLUMINA', 'ILLUMINA',\n", " 'ILLUMINA', 'ILLUMINA', 'ILLUMINA', 'ILLUMINA', 'ILLUMINA',\n", " 'ILLUMINA', 'ILLUMINA', 'ILLUMINA', 'ILLUMINA', 'ILLUMINA',\n", " 'ILLUMINA', 'ILLUMINA', 'ILLUMINA', 'ILLUMINA', 'ILLUMINA',\n", " 'ILLUMINA', 'ILLUMINA', 'ILLUMINA', 'ILLUMINA', 'ILLUMINA',\n", " 'ILLUMINA', 'ILLUMINA', 'ILLUMINA', 'ILLUMINA', 'ILLUMINA',\n", " 'ILLUMINA', 'ILLUMINA', 'ILLUMINA', 'ILLUMINA', 'ILLUMINA',\n", " 'ILLUMINA', 'ILLUMINA', 'ILLUMINA', 'ILLUMINA', 'ILLUMINA',\n", " 'ILLUMINA', 'ILLUMINA', 'ILLUMINA', 'ILLUMINA', 'ILLUMINA',\n", "...\n", " 'ILLUMINA', 'ILLUMINA', 'ILLUMINA', 'ILLUMINA', 'ILLUMINA',\n", " 'ILLUMINA', 'ILLUMINA', 'ILLUMINA', 'ILLUMINA', 'ILLUMINA',\n", " 'ILLUMINA', 'ILLUMINA', 'ILLUMINA', 'ILLUMINA', 'ILLUMINA',\n", " 'ILLUMINA', 'ILLUMINA', 'ILLUMINA', 'ILLUMINA', 'ILLUMINA',\n", " 'ILLUMINA', 'ILLUMINA', 'ILLUMINA', 'ILLUMINA', 'ILLUMINA',\n", " 'ILLUMINA', 'ILLUMINA', 'ILLUMINA', 'ILLUMINA', 'ILLUMINA',\n", " 'ILLUMINA', 'ILLUMINA', 'ILLUMINA', 'ILLUMINA', 'ILLUMINA',\n", " 'ILLUMINA', 'ILLUMINA', 'ILLUMINA', 'ILLUMINA', 'ILLUMINA',\n", " 'ILLUMINA', 'ILLUMINA', 'ILLUMINA', 'ILLUMINA', 'ILLUMINA',\n", " 'ILLUMINA', 'ILLUMINA', 'ILLUMINA', 'ILLUMINA', 'ILLUMINA',\n", " 'ILLUMINA', 'ILLUMINA', 'ILLUMINA', 'ILLUMINA', 'ILLUMINA',\n", " 'ILLUMINA', 'ILLUMINA', 'ILLUMINA', 'ILLUMINA', 'ILLUMINA',\n", " 'ILLUMINA', 'ILLUMINA', 'ILLUMINA', 'ILLUMINA', 'ILLUMINA',\n", " 'ILLUMINA', 'ILLUMINA', 'ILLUMINA', 'ILLUMINA', 'ILLUMINA',\n", " 'ILLUMINA', 'ILLUMINA', 'ILLUMINA', 'ILLUMINA', 'ILLUMINA',\n", " 'ILLUMINA', 'ILLUMINA', 'ILLUMINA', 'ILLUMINA', 'ILLUMINA',\n", " 'ILLUMINA', 'ILLUMINA', 'ILLUMINA', 'ILLUMINA', 'ILLUMINA',\n", " 'ILLUMINA', 'ILLUMINA', 'ILLUMINA', 'ILLUMINA', 'ILLUMINA',\n", " 'ILLUMINA', 'ILLUMINA', 'ILLUMINA', 'ILLUMINA', 'ILLUMINA'],\n", " dtype=object)
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