diff --git a/scripts/Pre-processing.ipynb b/scripts/Pre-processing.ipynb
index 9ff43f2c57c96a7e5e1a2ea79bfe552982cb0390..6b1aacb508dcd95097f748f6845e8f0c67255d62 100644
--- a/scripts/Pre-processing.ipynb
+++ b/scripts/Pre-processing.ipynb
@@ -23,7 +23,10 @@
"execution_count": 1,
"id": "23c68491-3667-48a6-b38c-2a6092a1874a",
"metadata": {
- "scrolled": true
+ "scrolled": true,
+ "vscode": {
+ "languageId": "r"
+ }
},
"outputs": [
{
@@ -274,7 +277,11 @@
"cell_type": "code",
"execution_count": 2,
"id": "e28fdd55-ad64-456f-80a6-155be69b6fbd",
- "metadata": {},
+ "metadata": {
+ "vscode": {
+ "languageId": "r"
+ }
+ },
"outputs": [
{
"data": {
@@ -328,7 +335,11 @@
"cell_type": "code",
"execution_count": 3,
"id": "c1bf29b6-53ca-4861-ac8c-4937203e0bd0",
- "metadata": {},
+ "metadata": {
+ "vscode": {
+ "languageId": "r"
+ }
+ },
"outputs": [],
"source": [
"rf = EMOTE_read_features(start = 14, width = 19)"
@@ -346,7 +357,11 @@
"cell_type": "code",
"execution_count": 4,
"id": "c2c6d370-dd19-47d0-9bdc-7e168d1d8c34",
- "metadata": {},
+ "metadata": {
+ "vscode": {
+ "languageId": "r"
+ }
+ },
"outputs": [
{
"data": {
@@ -397,7 +412,11 @@
"cell_type": "code",
"execution_count": 5,
"id": "84ce999b-a51f-4dc7-b518-4468fe0fdb85",
- "metadata": {},
+ "metadata": {
+ "vscode": {
+ "languageId": "r"
+ }
+ },
"outputs": [
{
"data": {
@@ -455,7 +474,11 @@
"cell_type": "code",
"execution_count": 6,
"id": "9bb4d784-8ae4-49a8-b648-8972a19f1e12",
- "metadata": {},
+ "metadata": {
+ "vscode": {
+ "languageId": "r"
+ }
+ },
"outputs": [
{
"data": {
@@ -514,7 +537,11 @@
"cell_type": "code",
"execution_count": 7,
"id": "b13d7122-84f3-4ca4-a17f-0c6cb79ca173",
- "metadata": {},
+ "metadata": {
+ "vscode": {
+ "languageId": "r"
+ }
+ },
"outputs": [],
"source": [
"rf = EMOTE_add_read_feature(rf, name = \"Recognition.seq\", start = 1, width = 3, pattern = \"AGG\" , pattern_type = 2)\n",
@@ -525,7 +552,11 @@
"cell_type": "code",
"execution_count": 8,
"id": "a54f7041-4a64-498e-8a0b-112aa5806b68",
- "metadata": {},
+ "metadata": {
+ "vscode": {
+ "languageId": "r"
+ }
+ },
"outputs": [
{
"data": {
@@ -605,7 +636,11 @@
"cell_type": "code",
"execution_count": 9,
"id": "6000958d-e2c8-437a-896a-7ddf9bcd3bf9",
- "metadata": {},
+ "metadata": {
+ "vscode": {
+ "languageId": "r"
+ }
+ },
"outputs": [
{
"data": {
@@ -689,7 +724,11 @@
"cell_type": "code",
"execution_count": 10,
"id": "3b8ccb4d-98ad-487f-b577-37a09749f5ea",
- "metadata": {},
+ "metadata": {
+ "vscode": {
+ "languageId": "r"
+ }
+ },
"outputs": [
{
"data": {
@@ -766,36 +805,36 @@
"cell_type": "code",
"execution_count": 11,
"id": "a42ea938-09f8-49cb-946d-eaeb53de509a",
- "metadata": {},
+ "metadata": {
+ "vscode": {
+ "languageId": "r"
+ }
+ },
"outputs": [
{
- "name": "stderr",
- "output_type": "stream",
- "text": [
- "Warning message in open.connection(con, \"rb\"):\n",
- "“cannot open file '../data/pre-processing_examples/Example_1_valid.fastq.gz': No such file or directoryâ€\n"
- ]
- },
- {
- "ename": "ERROR",
- "evalue": "Error in open.connection(con, \"rb\"): cannot open the connection\n",
- "output_type": "error",
- "traceback": [
- "Error in open.connection(con, \"rb\"): cannot open the connection\nTraceback:\n",
- "1. FastqStreamer(\"../data/pre-processing_examples/Example_1_valid.fastq.gz\")",
- "2. FastqStreamer(\"../data/pre-processing_examples/Example_1_valid.fastq.gz\")",
- "3. callGeneric(con, n = 1e+06, readerBlockSize = readerBlockSize, \n . verbose = verbose)",
- "4. eval(call, parent.frame())",
- "5. eval(call, parent.frame())",
- "6. FastqStreamer(con, n = 1e+06, readerBlockSize = readerBlockSize, \n . verbose = verbose)",
- "7. FastqStreamer(con, n = 1e+06, readerBlockSize = readerBlockSize, \n . verbose = verbose)",
- "8. open(con, \"rb\")",
- "9. open.connection(con, \"rb\")"
- ]
+ "data": {
+ "text/plain": [
+ "DNAStringSet object of length 4820:\n",
+ " width seq\n",
+ " [1] 19 GAAGTAGAATCAGTAATTT\n",
+ " [2] 19 CATGCGAGAGCGGTATTAT\n",
+ " [3] 19 TTCTTCCTACTAAGAACAC\n",
+ " [4] 19 TCCTCCGCTTATTGATATG\n",
+ " [5] 19 AAACGTTCAGCATTAAGTA\n",
+ " ... ... ...\n",
+ "[4816] 19 ATGTAAGTTATTTAAATAA\n",
+ "[4817] 19 CAAAACGTTAAGCGAATAA\n",
+ "[4818] 19 GCACAAAAAATGACCAAGA\n",
+ "[4819] 19 TCAGTCAAGCTGATTTAAA\n",
+ "[4820] 19 TAAAAGCTACGCACGTTTT"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
}
],
"source": [
- "fq_streamer = FastqStreamer(\"../data/pre-processing_examples/Example_1_valid.fastq.gz\")\n",
+ "fq_streamer = FastqStreamer(\"../data/pre-processing_examples/Example_1_demux/Example_1_valid.fastq.gz\")\n",
"sr <- yield(fq_streamer)\n",
"sr@sread"
]
@@ -810,10 +849,36 @@
},
{
"cell_type": "code",
- "execution_count": null,
+ "execution_count": 12,
"id": "a8ae5dcd-3eef-4c81-8d09-2520d9c0b8ad",
- "metadata": {},
- "outputs": [],
+ "metadata": {
+ "vscode": {
+ "languageId": "r"
+ }
+ },
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "BStringSet object of length 4820:\n",
+ " width seq\n",
+ " [1] 73 CCAGCGA:SRR2017586.3.1 HWI-ST865:389:HAUHUADXX:1:1101:1718:2167 length=50\n",
+ " [2] 73 CAAGGAA:SRR2017586.4.1 HWI-ST865:389:HAUHUADXX:1:1101:1598:2170 length=50\n",
+ " [3] 73 AGCGAGA:SRR2017586.7.1 HWI-ST865:389:HAUHUADXX:1:1101:1926:2194 length=50\n",
+ " [4] 73 AGGCGAA:SRR2017586.8.1 HWI-ST865:389:HAUHUADXX:1:1101:2348:2120 length=50\n",
+ " [5] 73 ACAGGAG:SRR2017586.9.1 HWI-ST865:389:HAUHUADXX:1:1101:2374:2223 length=50\n",
+ " ... ... ...\n",
+ "[4816] 77 AACAGCA:SRR2017586.9991.1 HWI-ST865:389:HAUHUADXX:1:1101:4623:12299 length=50\n",
+ "[4817] 77 GAAGAAA:SRR2017586.9992.1 HWI-ST865:389:HAUHUADXX:1:1101:4633:12362 length=50\n",
+ "[4818] 77 GCAAAAA:SRR2017586.9996.1 HWI-ST865:389:HAUHUADXX:1:1101:4779:12322 length=50\n",
+ "[4819] 77 CGAGGCA:SRR2017586.9999.1 HWI-ST865:389:HAUHUADXX:1:1101:5003:12298 length=50\n",
+ "[4820] 78 GGGCGCG:SRR2017586.10000.1 HWI-ST865:389:HAUHUADXX:1:1101:5227:12298 length=50"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ }
+ ],
"source": [
"sr@id"
]
@@ -845,10 +910,36 @@
},
{
"cell_type": "code",
- "execution_count": null,
+ "execution_count": 13,
"id": "ccf94585-eff7-4fc6-b781-f4e461309d75",
- "metadata": {},
- "outputs": [],
+ "metadata": {
+ "vscode": {
+ "languageId": "r"
+ }
+ },
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "DNAStringSet object of length 10000:\n",
+ " width seq\n",
+ " [1] 24 CAAGTTCAGCAGGAATGCCGAGAC\n",
+ " [2] 24 CAAGCAGCAGGAATGCCGAGACCG\n",
+ " [3] 24 CAAGGAAGTAGAATCAGTAATTTG\n",
+ " [4] 24 CAAGCATGCGAGAGCGGTATTATC\n",
+ " [5] 24 CAAGTTAAGGGCGCACGGTGGATG\n",
+ " ... ... ...\n",
+ " [9996] 24 TCGGTTAAGTTATTAAGGGCGCAC\n",
+ " [9997] 24 TCGGTAGGATGTTGGCTTAGAAGC\n",
+ " [9998] 24 TCGGTTAAGTTATTAAGGGCGCAC\n",
+ " [9999] 24 TCGGCAGCAGGAATGCCGAGACCG\n",
+ "[10000] 24 TCGGTTCAGCAGGAATGCCGAGAC"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ }
+ ],
"source": [
"fq_streamer = FastqStreamer(\"../data/pre-processing_examples/Example_2.fastq.gz\")\n",
"sr <- yield(fq_streamer)\n",
@@ -867,10 +958,59 @@
},
{
"cell_type": "code",
- "execution_count": null,
+ "execution_count": 14,
"id": "d644a577-2a85-4470-b7a2-1a16b200bd37",
- "metadata": {},
- "outputs": [],
+ "metadata": {
+ "vscode": {
+ "languageId": "r"
+ }
+ },
+ "outputs": [
+ {
+ "data": {
+ "text/html": [
+ "<table class=\"dataframe\">\n",
+ "<caption>A EMOTE_features: 2 × 7</caption>\n",
+ "<thead>\n",
+ "\t<tr><th scope=col>name</th><th scope=col>start</th><th scope=col>width</th><th scope=col>pattern_type</th><th scope=col>pattern</th><th scope=col>max_mismatch</th><th scope=col>readid_prepend</th></tr>\n",
+ "\t<tr><th scope=col><chr></th><th scope=col><dbl></th><th scope=col><dbl></th><th scope=col><dbl></th><th scope=col><list></th><th scope=col><dbl></th><th scope=col><lgl></th></tr>\n",
+ "</thead>\n",
+ "<tbody>\n",
+ "\t<tr><td>readseq</td><td>5</td><td>20</td><td>1</td><td> ACTG</td><td>0</td><td>FALSE</td></tr>\n",
+ "\t<tr><td>barcode</td><td>1</td><td> 4</td><td>2</td><td>TCGG, CAAG</td><td>0</td><td>FALSE</td></tr>\n",
+ "</tbody>\n",
+ "</table>\n"
+ ],
+ "text/latex": [
+ "A EMOTE\\_features: 2 × 7\n",
+ "\\begin{tabular}{lllllll}\n",
+ " name & start & width & pattern\\_type & pattern & max\\_mismatch & readid\\_prepend\\\\\n",
+ " <chr> & <dbl> & <dbl> & <dbl> & <list> & <dbl> & <lgl>\\\\\n",
+ "\\hline\n",
+ "\t readseq & 5 & 20 & 1 & ACTG & 0 & FALSE\\\\\n",
+ "\t barcode & 1 & 4 & 2 & TCGG, CAAG & 0 & FALSE\\\\\n",
+ "\\end{tabular}\n"
+ ],
+ "text/markdown": [
+ "\n",
+ "A EMOTE_features: 2 × 7\n",
+ "\n",
+ "| name <chr> | start <dbl> | width <dbl> | pattern_type <dbl> | pattern <list> | max_mismatch <dbl> | readid_prepend <lgl> |\n",
+ "|---|---|---|---|---|---|---|\n",
+ "| readseq | 5 | 20 | 1 | ACTG | 0 | FALSE |\n",
+ "| barcode | 1 | 4 | 2 | TCGG, CAAG | 0 | FALSE |\n",
+ "\n"
+ ],
+ "text/plain": [
+ " name start width pattern_type pattern max_mismatch readid_prepend\n",
+ "1 readseq 5 20 1 ACTG 0 FALSE \n",
+ "2 barcode 1 4 2 TCGG, CAAG 0 FALSE "
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ }
+ ],
"source": [
"rf = EMOTE_read_features(start = 5, width = 20)\n",
"rf = EMOTE_add_read_feature(rf, name = \"barcode\", start = 1, width = 4, pattern = c(\"TCGG\",\"CAAG\") , pattern_type = 2, readid_prepend = F)\n",
@@ -899,10 +1039,71 @@
},
{
"cell_type": "code",
- "execution_count": null,
+ "execution_count": 15,
"id": "0d9359ed-ae1c-4e2d-b005-eaf269b446b8",
- "metadata": {},
- "outputs": [],
+ "metadata": {
+ "vscode": {
+ "languageId": "r"
+ }
+ },
+ "outputs": [
+ {
+ "name": "stderr",
+ "output_type": "stream",
+ "text": [
+ "Demux report already exists set force=T to overwrite: ../data/pre-processing_examples/Example_2_demux/Example_2_parse_report.csv\n",
+ "\n"
+ ]
+ },
+ {
+ "data": {
+ "text/html": [
+ "<table class=\"dataframe\">\n",
+ "<caption>A spec_tbl_df: 3 × 6</caption>\n",
+ "<thead>\n",
+ "\t<tr><th scope=col>barcode_group</th><th scope=col>is_valid_readseq</th><th scope=col>is_valid_barcode</th><th scope=col>is_valid</th><th scope=col>pc_valid</th><th scope=col>demux_filename</th></tr>\n",
+ "\t<tr><th scope=col><chr></th><th scope=col><dbl></th><th scope=col><dbl></th><th scope=col><dbl></th><th scope=col><dbl></th><th scope=col><chr></th></tr>\n",
+ "</thead>\n",
+ "<tbody>\n",
+ "\t<tr><td>CAAG </td><td>4960</td><td>4977</td><td>4960</td><td>0.9965843</td><td>../data/pre-processing_examples/Example_2_demux/Example_2_CAAG_valid.fastq.gz</td></tr>\n",
+ "\t<tr><td>INVALID</td><td> 27</td><td> 0</td><td> 0</td><td>0.0000000</td><td>../data/pre-processing_examples/Example_2_demux/Example_2_invalid.fastq.gz </td></tr>\n",
+ "\t<tr><td>TCGG </td><td>4984</td><td>4996</td><td>4984</td><td>0.9975981</td><td>../data/pre-processing_examples/Example_2_demux/Example_2_TCGG_valid.fastq.gz</td></tr>\n",
+ "</tbody>\n",
+ "</table>\n"
+ ],
+ "text/latex": [
+ "A spec\\_tbl\\_df: 3 × 6\n",
+ "\\begin{tabular}{llllll}\n",
+ " barcode\\_group & is\\_valid\\_readseq & is\\_valid\\_barcode & is\\_valid & pc\\_valid & demux\\_filename\\\\\n",
+ " <chr> & <dbl> & <dbl> & <dbl> & <dbl> & <chr>\\\\\n",
+ "\\hline\n",
+ "\t CAAG & 4960 & 4977 & 4960 & 0.9965843 & ../data/pre-processing\\_examples/Example\\_2\\_demux/Example\\_2\\_CAAG\\_valid.fastq.gz\\\\\n",
+ "\t INVALID & 27 & 0 & 0 & 0.0000000 & ../data/pre-processing\\_examples/Example\\_2\\_demux/Example\\_2\\_invalid.fastq.gz \\\\\n",
+ "\t TCGG & 4984 & 4996 & 4984 & 0.9975981 & ../data/pre-processing\\_examples/Example\\_2\\_demux/Example\\_2\\_TCGG\\_valid.fastq.gz\\\\\n",
+ "\\end{tabular}\n"
+ ],
+ "text/markdown": [
+ "\n",
+ "A spec_tbl_df: 3 × 6\n",
+ "\n",
+ "| barcode_group <chr> | is_valid_readseq <dbl> | is_valid_barcode <dbl> | is_valid <dbl> | pc_valid <dbl> | demux_filename <chr> |\n",
+ "|---|---|---|---|---|---|\n",
+ "| CAAG | 4960 | 4977 | 4960 | 0.9965843 | ../data/pre-processing_examples/Example_2_demux/Example_2_CAAG_valid.fastq.gz |\n",
+ "| INVALID | 27 | 0 | 0 | 0.0000000 | ../data/pre-processing_examples/Example_2_demux/Example_2_invalid.fastq.gz |\n",
+ "| TCGG | 4984 | 4996 | 4984 | 0.9975981 | ../data/pre-processing_examples/Example_2_demux/Example_2_TCGG_valid.fastq.gz |\n",
+ "\n"
+ ],
+ "text/plain": [
+ " barcode_group is_valid_readseq is_valid_barcode is_valid pc_valid demux_filename \n",
+ "1 CAAG 4960 4977 4960 0.9965843 ../data/pre-processing_examples/Example_2_demux/Example_2_CAAG_valid.fastq.gz\n",
+ "2 INVALID 27 0 0 0.0000000 ../data/pre-processing_examples/Example_2_demux/Example_2_invalid.fastq.gz \n",
+ "3 TCGG 4984 4996 4984 0.9975981 ../data/pre-processing_examples/Example_2_demux/Example_2_TCGG_valid.fastq.gz"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ }
+ ],
"source": [
"EMOTE_demultiplex(\n",
" fastq_file = \"../data/pre-processing_examples/Example_2.fastq.gz\",\n",
@@ -931,10 +1132,36 @@
},
{
"cell_type": "code",
- "execution_count": null,
+ "execution_count": 16,
"id": "cb6ab678-8bb7-4ef4-9168-1a6988bcc1f8",
- "metadata": {},
- "outputs": [],
+ "metadata": {
+ "vscode": {
+ "languageId": "r"
+ }
+ },
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "DNAStringSet object of length 4984:\n",
+ " width seq\n",
+ " [1] 20 AGAAAAGCCAGATTTAATTA\n",
+ " [2] 20 TTTAAAGAATTAGATCAAAA\n",
+ " [3] 20 TGAATGACAATATGTCAACG\n",
+ " [4] 20 TTAAGTTATTAAGGGCGCAC\n",
+ " [5] 20 TAAGTTATTAAGGGCGCACG\n",
+ " ... ... ...\n",
+ "[4980] 20 TTAAGTTATTAAGGGCGCAC\n",
+ "[4981] 20 TAGGATGTTGGCTTAGAAGC\n",
+ "[4982] 20 TTAAGTTATTAAGGGCGCAC\n",
+ "[4983] 20 CAGCAGGAATGCCGAGACCG\n",
+ "[4984] 20 TTCAGCAGGAATGCCGAGAC"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ }
+ ],
"source": [
"fq_streamer = FastqStreamer(\"../data/pre-processing_examples/Example_2_demux/Example_2_TCGG_valid.fastq.gz\")\n",
"sr <- yield(fq_streamer)\n",
@@ -959,10 +1186,36 @@
},
{
"cell_type": "code",
- "execution_count": null,
+ "execution_count": 17,
"id": "6c933c7e-0124-48d9-a4e9-11a9778da695",
- "metadata": {},
- "outputs": [],
+ "metadata": {
+ "vscode": {
+ "languageId": "r"
+ }
+ },
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "DNAStringSet object of length 10000:\n",
+ " width seq\n",
+ " [1] 50 TCAGCCAGTGCACGCAAAAAAAAAAAAAAAAAAAAAAAAAAAATCGGAAG\n",
+ " [2] 50 TGGGGGTAGCGAGCTTGTGGGAAGCGGTCTTTGGCGATGTGGGGGTTAAA\n",
+ " [3] 50 TTCGAATCCTACATCTGGAGCCAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n",
+ " [4] 50 ATTATCCAGTCCATGTCTTTGATTATTGCCATGATGTATATTGGGGCTAA\n",
+ " [5] 50 AATTCTTGGTGTAGGGGTAAAATCCGTAGAGATCAAGAGGAAAAAAAAAA\n",
+ " ... ... ...\n",
+ " [9996] 50 CACCGCCCGTCACACCATGGGAGTTGTGTTTGCCTTAAGTCAGGATGCTA\n",
+ " [9997] 50 CATTAAAGGCGAAGGAGTCTTATACAAAAAAAAAAAAAAAAAAAAAAAAA\n",
+ " [9998] 50 ATTGGAGTGAAGGCAAATCCACCTCTGTATTTGAAAAAAAAAAAAAAAAA\n",
+ " [9999] 50 AGCACCGCTATAGGAACTCAACCTATGGTTCACCTTTGCATCAGCATTGA\n",
+ "[10000] 50 CACACCATGGGAGTTGTGTTTGCCCCAAAAAAAAAAAAAAAAAAAAAAAA"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ }
+ ],
"source": [
"fq_streamer = FastqStreamer(\"../data/pre-processing_examples/Example_3.fastq.gz\")\n",
"sr <- yield(fq_streamer)\n",
@@ -980,9 +1233,13 @@
},
{
"cell_type": "code",
- "execution_count": null,
+ "execution_count": 18,
"id": "bd2100af-f92d-4cb6-8199-6c4b945bb434",
- "metadata": {},
+ "metadata": {
+ "vscode": {
+ "languageId": "r"
+ }
+ },
"outputs": [],
"source": [
"rf = EMOTE_read_features(start = 1, width = 50)"
@@ -1007,10 +1264,59 @@
},
{
"cell_type": "code",
- "execution_count": null,
+ "execution_count": 19,
"id": "233819ea-b139-4950-a735-8800952aa769",
- "metadata": {},
- "outputs": [],
+ "metadata": {
+ "vscode": {
+ "languageId": "r"
+ }
+ },
+ "outputs": [
+ {
+ "data": {
+ "text/html": [
+ "<table class=\"dataframe\">\n",
+ "<caption>A EMOTE_features: 2 × 7</caption>\n",
+ "<thead>\n",
+ "\t<tr><th scope=col>name</th><th scope=col>start</th><th scope=col>width</th><th scope=col>pattern_type</th><th scope=col>pattern</th><th scope=col>max_mismatch</th><th scope=col>readid_prepend</th></tr>\n",
+ "\t<tr><th scope=col><chr></th><th scope=col><dbl></th><th scope=col><dbl></th><th scope=col><dbl></th><th scope=col><list></th><th scope=col><dbl></th><th scope=col><lgl></th></tr>\n",
+ "</thead>\n",
+ "<tbody>\n",
+ "\t<tr><td>readseq</td><td>1</td><td>50</td><td>1</td><td> ACTG</td><td>0</td><td>FALSE</td></tr>\n",
+ "\t<tr><td>PolyA </td><td>1</td><td>50</td><td>3</td><td>AAAAAA.+</td><td>0</td><td>FALSE</td></tr>\n",
+ "</tbody>\n",
+ "</table>\n"
+ ],
+ "text/latex": [
+ "A EMOTE\\_features: 2 × 7\n",
+ "\\begin{tabular}{lllllll}\n",
+ " name & start & width & pattern\\_type & pattern & max\\_mismatch & readid\\_prepend\\\\\n",
+ " <chr> & <dbl> & <dbl> & <dbl> & <list> & <dbl> & <lgl>\\\\\n",
+ "\\hline\n",
+ "\t readseq & 1 & 50 & 1 & ACTG & 0 & FALSE\\\\\n",
+ "\t PolyA & 1 & 50 & 3 & AAAAAA.+ & 0 & FALSE\\\\\n",
+ "\\end{tabular}\n"
+ ],
+ "text/markdown": [
+ "\n",
+ "A EMOTE_features: 2 × 7\n",
+ "\n",
+ "| name <chr> | start <dbl> | width <dbl> | pattern_type <dbl> | pattern <list> | max_mismatch <dbl> | readid_prepend <lgl> |\n",
+ "|---|---|---|---|---|---|---|\n",
+ "| readseq | 1 | 50 | 1 | ACTG | 0 | FALSE |\n",
+ "| PolyA | 1 | 50 | 3 | AAAAAA.+ | 0 | FALSE |\n",
+ "\n"
+ ],
+ "text/plain": [
+ " name start width pattern_type pattern max_mismatch readid_prepend\n",
+ "1 readseq 1 50 1 ACTG 0 FALSE \n",
+ "2 PolyA 1 50 3 AAAAAA.+ 0 FALSE "
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ }
+ ],
"source": [
"rf = EMOTE_add_read_feature(rf, name = \"PolyA\",start = 1,width = 50, pattern = \"AAAAAA.+\" , pattern_type = 3, readid_prepend = F)\n",
"rf"
@@ -1036,10 +1342,59 @@
},
{
"cell_type": "code",
- "execution_count": null,
+ "execution_count": 20,
"id": "3377e5b5-be74-481c-bfa5-96e5b63d608e",
- "metadata": {},
- "outputs": [],
+ "metadata": {
+ "vscode": {
+ "languageId": "r"
+ }
+ },
+ "outputs": [
+ {
+ "data": {
+ "text/html": [
+ "<table class=\"dataframe\">\n",
+ "<caption>A data.frame: 2 × 5</caption>\n",
+ "<thead>\n",
+ "\t<tr><th scope=col>group</th><th scope=col>is_valid_readseq</th><th scope=col>total_read</th><th scope=col>pc_valid</th><th scope=col>demux_filename</th></tr>\n",
+ "\t<tr><th scope=col><chr></th><th scope=col><int></th><th scope=col><int></th><th scope=col><dbl></th><th scope=col><chr></th></tr>\n",
+ "</thead>\n",
+ "<tbody>\n",
+ "\t<tr><td>INVALID</td><td> 0</td><td>1788</td><td>0.0000</td><td>../data/pre-processing_examples/Example_3_demux/Example_3_invalid.fastq.gz</td></tr>\n",
+ "\t<tr><td>VALID </td><td>8212</td><td>8212</td><td>0.8212</td><td>../data/pre-processing_examples/Example_3_demux/Example_3_valid.fastq.gz </td></tr>\n",
+ "</tbody>\n",
+ "</table>\n"
+ ],
+ "text/latex": [
+ "A data.frame: 2 × 5\n",
+ "\\begin{tabular}{lllll}\n",
+ " group & is\\_valid\\_readseq & total\\_read & pc\\_valid & demux\\_filename\\\\\n",
+ " <chr> & <int> & <int> & <dbl> & <chr>\\\\\n",
+ "\\hline\n",
+ "\t INVALID & 0 & 1788 & 0.0000 & ../data/pre-processing\\_examples/Example\\_3\\_demux/Example\\_3\\_invalid.fastq.gz\\\\\n",
+ "\t VALID & 8212 & 8212 & 0.8212 & ../data/pre-processing\\_examples/Example\\_3\\_demux/Example\\_3\\_valid.fastq.gz \\\\\n",
+ "\\end{tabular}\n"
+ ],
+ "text/markdown": [
+ "\n",
+ "A data.frame: 2 × 5\n",
+ "\n",
+ "| group <chr> | is_valid_readseq <int> | total_read <int> | pc_valid <dbl> | demux_filename <chr> |\n",
+ "|---|---|---|---|---|\n",
+ "| INVALID | 0 | 1788 | 0.0000 | ../data/pre-processing_examples/Example_3_demux/Example_3_invalid.fastq.gz |\n",
+ "| VALID | 8212 | 8212 | 0.8212 | ../data/pre-processing_examples/Example_3_demux/Example_3_valid.fastq.gz |\n",
+ "\n"
+ ],
+ "text/plain": [
+ " group is_valid_readseq total_read pc_valid demux_filename \n",
+ "1 INVALID 0 1788 0.0000 ../data/pre-processing_examples/Example_3_demux/Example_3_invalid.fastq.gz\n",
+ "2 VALID 8212 8212 0.8212 ../data/pre-processing_examples/Example_3_demux/Example_3_valid.fastq.gz "
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ }
+ ],
"source": [
"report = EMOTE_parse_read(\n",
" fastq_file = \"../data/pre-processing_examples/Example_3.fastq.gz\",\n",
@@ -1059,12 +1414,38 @@
},
{
"cell_type": "code",
- "execution_count": null,
+ "execution_count": 21,
"id": "3ce07100-5c95-47fe-a7e3-d71729e854b3",
- "metadata": {},
- "outputs": [],
+ "metadata": {
+ "vscode": {
+ "languageId": "r"
+ }
+ },
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "DNAStringSet object of length 8212:\n",
+ " width seq\n",
+ " [1] 50 TGGGGGTAGCGAGCTTGTGGGAAGCGGTCTTTGGCGATGTGGGGGTTAAA\n",
+ " [2] 22 TTCGAATCCTACATCTGGAGCC\n",
+ " [3] 50 ATTATCCAGTCCATGTCTTTGATTATTGCCATGATGTATATTGGGGCTAA\n",
+ " [4] 40 AATTCTTGGTGTAGGGGTAAAATCCGTAGAGATCAAGAGG\n",
+ " [5] 50 AATGGGGTGCACAAAGAGAAGCAATACTGCGAAGTGGAGCCAATCTTCAA\n",
+ " ... ... ...\n",
+ "[8208] 50 CACCGCCCGTCACACCATGGGAGTTGTGTTTGCCTTAAGTCAGGATGCTA\n",
+ "[8209] 25 CATTAAAGGCGAAGGAGTCTTATAC\n",
+ "[8210] 33 ATTGGAGTGAAGGCAAATCCACCTCTGTATTTG\n",
+ "[8211] 50 AGCACCGCTATAGGAACTCAACCTATGGTTCACCTTTGCATCAGCATTGA\n",
+ "[8212] 26 CACACCATGGGAGTTGTGTTTGCCCC"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ }
+ ],
"source": [
- "fq_streamer = FastqStreamer(\"../data/pre-processing_examples/Example_3_valid.fastq.gz\")\n",
+ "fq_streamer = FastqStreamer(\"../data/pre-processing_examples/Example_3_demux/Example_3_valid.fastq.gz\")\n",
"sr <- yield(fq_streamer)\n",
"sr@sread"
]