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August 13, 2024 10:23
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| { | |
| "cells": [ | |
| { | |
| "cell_type": "code", | |
| "execution_count": 1, | |
| "id": "d30d1c6f", | |
| "metadata": {}, | |
| "outputs": [], | |
| "source": [ | |
| "import bioframe\n", | |
| "import pypairix\n", | |
| "import dask.dataframe as dd\n", | |
| "import dask.array as da\n", | |
| "import polars as pl\n", | |
| "import pandas as pd" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 2, | |
| "id": "f15833ff", | |
| "metadata": {}, | |
| "outputs": [], | |
| "source": [ | |
| "# add later properties, like: columns, parallel, use_statistics, low_memory, memory_map+use_pyarrow=True.\n", | |
| "\n", | |
| "df = pl.scan_parquet('pairsToPolarsgzip.parquet', hive_schema={\"read_id\": pl.String, \"chrom1\": pl.String, \"pos1\":pl.UInt32, \"chrom2\": pl.String, \"pos2\":pl.UInt32, \"strand1\":pl.String, \"strand2\":pl.String, \"pairs_type\":pl.String})" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 4, | |
| "id": "a9811098", | |
| "metadata": {}, | |
| "outputs": [ | |
| { | |
| "data": { | |
| "text/html": [ | |
| "<div><style>\n", | |
| ".dataframe > thead > tr,\n", | |
| ".dataframe > tbody > tr {\n", | |
| " text-align: right;\n", | |
| " white-space: pre-wrap;\n", | |
| "}\n", | |
| "</style>\n", | |
| "<small>shape: (65_220_657, 8)</small><table border=\"1\" class=\"dataframe\"><thead><tr><th>read_id</th><th>chrom1</th><th>pos1</th><th>chrom2</th><th>pos2</th><th>strand1</th><th>strand2</th><th>pairs_type</th></tr><tr><td>str</td><td>str</td><td>u32</td><td>str</td><td>u32</td><td>str</td><td>str</td><td>str</td></tr></thead><tbody><tr><td>"."</td><td>"chr1"</td><td>3000037</td><td>"chr1"</td><td>3139797</td><td>"-"</td><td>"-"</td><td>"LL"</td></tr><tr><td>"."</td><td>"chr1"</td><td>3000088</td><td>"chr1"</td><td>42957984</td><td>"-"</td><td>"+"</td><td>"LL"</td></tr><tr><td>"."</td><td>"chr1"</td><td>3000112</td><td>"chr1"</td><td>5448692</td><td>"-"</td><td>"+"</td><td>"LL"</td></tr><tr><td>"."</td><td>"chr1"</td><td>3000227</td><td>"chr1"</td><td>27069655</td><td>"+"</td><td>"-"</td><td>"LL"</td></tr><tr><td>"."</td><td>"chr1"</td><td>3000228</td><td>"chr1"</td><td>87485253</td><td>"+"</td><td>"+"</td><td>"LL"</td></tr><tr><td>…</td><td>…</td><td>…</td><td>…</td><td>…</td><td>…</td><td>…</td><td>…</td></tr><tr><td>"."</td><td>"chrY"</td><td>2902279</td><td>"chrY"</td><td>2902428</td><td>"+"</td><td>"-"</td><td>"LL"</td></tr><tr><td>"."</td><td>"chrY"</td><td>2902282</td><td>"chrY"</td><td>2902487</td><td>"+"</td><td>"-"</td><td>"LL"</td></tr><tr><td>"."</td><td>"chrY"</td><td>2902286</td><td>"chrY"</td><td>2902430</td><td>"+"</td><td>"-"</td><td>"LL"</td></tr><tr><td>"."</td><td>"chrY"</td><td>2902375</td><td>"chrY"</td><td>2902555</td><td>"+"</td><td>"-"</td><td>"LL"</td></tr><tr><td>"."</td><td>"chrY"</td><td>2902405</td><td>"chrY"</td><td>2902560</td><td>"+"</td><td>"-"</td><td>"LL"</td></tr></tbody></table></div>" | |
| ], | |
| "text/plain": [ | |
| "shape: (65_220_657, 8)\n", | |
| "┌─────────┬────────┬─────────┬────────┬──────────┬─────────┬─────────┬────────────┐\n", | |
| "│ read_id ┆ chrom1 ┆ pos1 ┆ chrom2 ┆ pos2 ┆ strand1 ┆ strand2 ┆ pairs_type │\n", | |
| "│ --- ┆ --- ┆ --- ┆ --- ┆ --- ┆ --- ┆ --- ┆ --- │\n", | |
| "│ str ┆ str ┆ u32 ┆ str ┆ u32 ┆ str ┆ str ┆ str │\n", | |
| "╞═════════╪════════╪═════════╪════════╪══════════╪═════════╪═════════╪════════════╡\n", | |
| "│ . ┆ chr1 ┆ 3000037 ┆ chr1 ┆ 3139797 ┆ - ┆ - ┆ LL │\n", | |
| "│ . ┆ chr1 ┆ 3000088 ┆ chr1 ┆ 42957984 ┆ - ┆ + ┆ LL │\n", | |
| "│ . ┆ chr1 ┆ 3000112 ┆ chr1 ┆ 5448692 ┆ - ┆ + ┆ LL │\n", | |
| "│ . ┆ chr1 ┆ 3000227 ┆ chr1 ┆ 27069655 ┆ + ┆ - ┆ LL │\n", | |
| "│ . ┆ chr1 ┆ 3000228 ┆ chr1 ┆ 87485253 ┆ + ┆ + ┆ LL │\n", | |
| "│ … ┆ … ┆ … ┆ … ┆ … ┆ … ┆ … ┆ … │\n", | |
| "│ . ┆ chrY ┆ 2902279 ┆ chrY ┆ 2902428 ┆ + ┆ - ┆ LL │\n", | |
| "│ . ┆ chrY ┆ 2902282 ┆ chrY ┆ 2902487 ┆ + ┆ - ┆ LL │\n", | |
| "│ . ┆ chrY ┆ 2902286 ┆ chrY ┆ 2902430 ┆ + ┆ - ┆ LL │\n", | |
| "│ . ┆ chrY ┆ 2902375 ┆ chrY ┆ 2902555 ┆ + ┆ - ┆ LL │\n", | |
| "│ . ┆ chrY ┆ 2902405 ┆ chrY ┆ 2902560 ┆ + ┆ - ┆ LL │\n", | |
| "└─────────┴────────┴─────────┴────────┴──────────┴─────────┴─────────┴────────────┘" | |
| ] | |
| }, | |
| "execution_count": 4, | |
| "metadata": {}, | |
| "output_type": "execute_result" | |
| } | |
| ], | |
| "source": [ | |
| "\"\"\"sort pairs files \n", | |
| " (the lexicographic order for chromosomes, \n", | |
| " the numeric order for the positions, \n", | |
| " the lexicographic order for pair types).\n", | |
| "\"\"\"\n", | |
| "filtered_df = df.filter(pl.col(\"pos1\").is_not_null())\n", | |
| "filtered_df.sort([\"chrom1\",\"chrom2\", \"pos1\", \"pos2\", \"strand1\", \"strand2\"]).collect()" | |
| ] | |
| } | |
| ], | |
| "metadata": { | |
| "kernelspec": { | |
| "display_name": "main", | |
| "language": "python", | |
| "name": "python3" | |
| }, | |
| "language_info": { | |
| "codemirror_mode": { | |
| "name": "ipython", | |
| "version": 3 | |
| }, | |
| "file_extension": ".py", | |
| "mimetype": "text/x-python", | |
| "name": "python", | |
| "nbconvert_exporter": "python", | |
| "pygments_lexer": "ipython3", | |
| "version": "3.9.19" | |
| } | |
| }, | |
| "nbformat": 4, | |
| "nbformat_minor": 5 | |
| } |
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