Make cleaning

2025-11-16 14:56:03 +01:00
parent 35d275c104
commit 30b7175702
367 changed files with 170866 additions and 11173 deletions
--- a/jupyterhub_volumes/web/obidoc/obitools/obipairing/forward.fastq
+++ b/jupyterhub_volumes/web/obidoc/obitools/obipairing/forward.fastq
@@ -0,0 +1,16 @@
+@M01334:147:000000000-LBRVD:1:1101:14968:1570 1:N:0:CTCACCAA+CTAGGCAA
+TGTTCCACGGGCAATCCTGAGCCAAATCTTTCATTTTGAAAAAATGAGAGATATAATGTATCTCTTATTTATTATAAGAAATAAAATATTTCTTATCTAATATTAAAGTTAGGTGCAGAGACTCAATGGGTGGAACTAGATCGGATGTGCA
+
+11>A>@3@A11>ACFFEG110BFB00BAFGHE2DFGG201110/B11111/D1D2222D2FDFDFGDGHHBGG2F222110D11@1D1FGHFHGFF@GE1F2FG22112B220F1@111/0>BF11B210B>//11B1<1BB<///<1122
+@M01334:147:000000000-LBRVD:1:1101:15946:1586 1:N:0:CTCACCAA+CTAGGCAA
+TCCTAACCCCATTGAGTCTCTGCACCTATCTTTAATATTAGATAAGAAATATTTTATTTCTTATAATAAATAAGAGATATTTTATATCTCTCATTTTTTCAAAATGAAAGATTTGGCTCAGGATTGCCCACGTAACGGAGATCGGAAGAGC
+
+1>>A111>>>AFGGB1FFGFGFF3BBF1GGHHH33D2GH2B1D211110D1DGHHBFGGGGG2FA2F221F21A1F0D1DGHH2FAFFGFHFFGHHHHGG22@1BD111@0FFHE11GC1001BGF1B1B/EF00??////BF////<000
+@M01334:147:000000000-LBRVD:1:1101:15399:1590 1:N:0:CTCACCAA+CTAGGCAA
+TGTTCCACCCATTGAGTCTCTGCACCTATCTTTAATATTAGATAAGAAATATTTTACTTCTTATAATAAATAAGAGTTATTTTATATCTCTCATTTTTTCAAAATGAAAGATTTGGCTCAGGATTGCCCGTGGAACTAGATCGGAAGAGCA
+
+11>A>@3B>>1CF111BBFAG3A3AAF1FFGHHF3FBGH221F211110D1DGHH2BBGBFF2F22D221D211111A2DDGG2F2FFFEGD1FFHHHGFD221B111110BFGD11F@1001BF0@@1/EA//1>F1B1FD/////00<1
+@M01334:147:000000000-LBRVD:1:1101:13773:1687 1:N:0:CTCACCAA+CTAGGCAA
+CTCGGATCACCATTGAGTCTCTGCACCTATCTTTAATATTAGATAAGAAAAAATATTATTTCTTATCTGAAATAAGAAATATTTTATATATTTCTTTTTCTCAAAATGAAAGATTTGGCTCAGGATTGCCCTGATCCGAGGGATAGCACCA
+
+3AAAAAADFFFFGGGGFGGGGGHHHHHHFHHHHHHHHGHHHHGHGGHFFHHHCGFHHHHHHHHHHHHHGHHGGFHFFHHHGHHHHBHHHGHHHHHHHHHHHHHFFHHFBDFBCGHHF4BGHFGFFHHBDGFHHEHHFAAEECEGF3FDGFC
--- a/jupyterhub_volumes/web/obidoc/obitools/obipairing/index.html
+++ b/jupyterhub_volumes/web/obidoc/obitools/obipairing/index.html
--- a/jupyterhub_volumes/web/obidoc/obitools/obipairing/index.xml
+++ b/jupyterhub_volumes/web/obidoc/obitools/obipairing/index.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="utf-8" standalone="yes"?>
+<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
+  <channel>
+    <title>obipairing on OBITools4 documentation</title>
+    <link>http://metabar:8888/obidoc/obitools/obipairing/</link>
+    <description>Recent content in obipairing on OBITools4 documentation</description>
+    <generator>Hugo</generator>
+    <language>en-us</language>
+    <lastBuildDate></lastBuildDate>
+    <atom:link href="http://metabar:8888/obidoc/obitools/obipairing/index.xml" rel="self" type="application/rss+xml" />
+  </channel>
+</rss>
--- a/jupyterhub_volumes/web/obidoc/obitools/obipairing/paired.fastq
+++ b/jupyterhub_volumes/web/obidoc/obitools/obipairing/paired.fastq
@@ -0,0 +1,16 @@
+@M01334:147:000000000-LBRVD:1:1101:14968:1570 {"ali_length":137,"definition":"1:N:0:CTCACCAA+CTAGGCAA","mode":"join","score":1687,"score_norm":0.679,"seq_ab_match":93}
+tgttccacgggcaatcctgagccaaatctttcattttgaaaaaatgagagatataatgtatctcttatttattataagaaataaaatatttcttatctaatattaaagttaggtgcagagactcaatgggtggaactagatcggatgtgca..........agcaaaaaagaacaagtaacaagggaaaaccagagaaaaatcaataaaaaagaaaaaaagagagatataaagtatcaataaaataaaaaaagaaaaaaaataataaaaaactaataaaaaagaaaggtgcagagaaaaaaagggaggaaaa
+
+11>A>@3@A11>ACFFEG110BFB00BAFGHE2DFGG201110/B11111/D1D2222D2FDFDFGDGHHBGG2F222110D11@1D1FGHFHGFF@GE1F2FG22112B220F1@111/0>BF11B210B>//11B1<1BB<///<1122!!!!!!!!!!11--111111?111@11110?1112/@@11122@011FBB2121//B1111CEEHGFB11F2B2B2B2DFB12@212122B21/>/1D1GF>>EA1GGDD2D1///22B222GD/E11GGFAB1B0A313B3B0A111BB1111311>>11
+@M01334:147:000000000-LBRVD:1:1101:15946:1586 {"ali_dir":"right","ali_length":138,"definition":"1:N:0:CTCACCAA+CTAGGCAA","mode":"alignment","pairing_mismatches":{"(T:16)->(A:33)":14,"(T:33)->(A:17)":118,"(T:37)->(A:16)":125,"(T:38)->(A:16)":32,"(T:39)->(A:17)":44},"paring_fast_count":114,"paring_fast_overlap":138,"paring_fast_score":0.844,"score":5446,"score_norm":0.957,"seq_a_single":13,"seq_ab_match":132,"seq_b_single":13}
+gctcatccgaactacctaaccccattgagtctctgcacctatctttaatattagataagaaatattttatttcttataataaataagagatattttatatctctcattttttcaaaatgaaagatttggctcaggattgcccacgtaacggagatcggaagagc
+
+111/////2B112CMMOUO?MNObVHfcAVVHVWVVTQSWRXXIYYYXUSWiXaWeWWUWVSTTTWXgeUWWXXXWWgXWYYWVYWdUgSTTTXYYUVdTVWVXVgUWXXXVeYXfTCUXWW`QGUWfA@WSR?PRRWVARAc?UVMMOO?///BF////<000
+@M01334:147:000000000-LBRVD:1:1101:15399:1590 {"ali_length":4,"definition":"1:N:0:CTCACCAA+CTAGGCAA","mode":"join","score":126,"score_norm":1,"seq_ab_match":4}
+tgttccacccattgagtctctgcacctatctttaatattagataagaaatattttacttcttataataaataagagttattttatatctctcattttttcaaaatgaaagatttggctcaggattgcccgtggaactagatcggaagagca..........agcaaaaaagaaaaagtaaaacaaaatgagaaaaagcaactaaatttaatattagataagaaatataatactacataaaataaataagagatattttatatctctaaatttttcaaaaggaaagatttggctcaggatagcccgaggaaaa
+
+11>A>@3B>>1CF111BBFAG3A3AAF1FFGHHF3FBGH221F211110D1DGHH2BBGBFF2F22D221D211111A2DDGG2F2FFFEGD1FFHHHGFD221B111110BFGD11F@1001BF0@@1/EA//1>F1B1FD/////00<1!!!!!!!!!!11//111110B122B12000B222B222B01111111@122B22122ED2B12F@D2GF2FAD2D2222D222212D2GF2HGD1GFADAD1D1222D1D111221B0011101GFDD12FFD1B000A1011B11B1111111311>>11
+@M01334:147:000000000-LBRVD:1:1101:13773:1687 {"ali_dir":"left","ali_length":54,"definition":"1:N:0:CTCACCAA+CTAGGCAA","mode":"alignment","pairing_mismatches":{"(C:39)->(A:16)":102,"(C:39)->(A:17)":121,"(T:39)->(A:14)":101},"paring_fast_count":42,"paring_fast_overlap":54,"paring_fast_score":0.824,"score":2888,"score_norm":0.944,"seq_a_single":97,"seq_ab_match":51,"seq_b_single":97}
+ctcggatcaccattgagtctctgcacctatctttaatattagataagaaaaaatattatttcttatctgaaataagaaatattttatatatttctttttctcaaaatgaaagatttggctcaggattgccctgatccgagggatagcaccattgagtctctgcacctatccttttcttttgtattctagttcgagaacccccttgttttctcaaaacacggatttggctcaggatagccctgctatca
+
+3AAAAAADFFFFGGGGFGGGGGHHHHHHFHHHHHHHHGHHHHGHGGHFFHHHCGFHHHHHHHHHHHHHGHHGGFHFFHHHGHHHHBHHHGHHHHHHHXVVJIommmegikl]bVWgVDRXIlbkkVfPSWVWccVVT^ebggjkkCVeWcd1@CF>0/11@11B011F0/0000/00111@@D1111GA01AFGCEEE///0//BAFD0000HGGFAB011B00CBAB11FA1B11>1111@31>111
--- a/jupyterhub_volumes/web/obidoc/obitools/obipairing/paired_alignment.fastq
+++ b/jupyterhub_volumes/web/obidoc/obitools/obipairing/paired_alignment.fastq
@@ -0,0 +1,8 @@
+@M01334:147:000000000-LBRVD:1:1101:15946:1586 {"ali_dir":"right","ali_length":138,"definition":"1:N:0:CTCACCAA+CTAGGCAA","mode":"alignment","pairing_mismatches":{"(T:16)->(A:33)":14,"(T:33)->(A:17)":118,"(T:37)->(A:16)":125,"(T:38)->(A:16)":32,"(T:39)->(A:17)":44},"paring_fast_count":114,"paring_fast_overlap":138,"paring_fast_score":0.844,"score":5446,"score_norm":0.957,"seq_a_single":13,"seq_ab_match":132,"seq_b_single":13}
+gctcatccgaactacctaaccccattgagtctctgcacctatctttaatattagataagaaatattttatttcttataataaataagagatattttatatctctcattttttcaaaatgaaagatttggctcaggattgcccacgtaacggagatcggaagagc
+
+111/////2B112CMMOUO?MNObVHfcAVVHVWVVTQSWRXXIYYYXUSWiXaWeWWUWVSTTTWXgeUWWXXXWWgXWYYWVYWdUgSTTTXYYUVdTVWVXVgUWXXXVeYXfTCUXWW`QGUWfA@WSR?PRRWVARAc?UVMMOO?///BF////<000
+@M01334:147:000000000-LBRVD:1:1101:13773:1687 {"ali_dir":"left","ali_length":54,"definition":"1:N:0:CTCACCAA+CTAGGCAA","mode":"alignment","pairing_mismatches":{"(C:39)->(A:16)":102,"(C:39)->(A:17)":121,"(T:39)->(A:14)":101},"paring_fast_count":42,"paring_fast_overlap":54,"paring_fast_score":0.824,"score":2888,"score_norm":0.944,"seq_a_single":97,"seq_ab_match":51,"seq_b_single":97}
+ctcggatcaccattgagtctctgcacctatctttaatattagataagaaaaaatattatttcttatctgaaataagaaatattttatatatttctttttctcaaaatgaaagatttggctcaggattgccctgatccgagggatagcaccattgagtctctgcacctatccttttcttttgtattctagttcgagaacccccttgttttctcaaaacacggatttggctcaggatagccctgctatca
+
+3AAAAAADFFFFGGGGFGGGGGHHHHHHFHHHHHHHHGHHHHGHGGHFFHHHCGFHHHHHHHHHHHHHGHHGGFHFFHHHGHHHHBHHHGHHHHHHHXVVJIommmegikl]bVWgVDRXIlbkkVfPSWVWccVVT^ebggjkkCVeWcd1@CF>0/11@11B011F0/0000/00111@@D1111GA01AFGCEEE///0//BAFD0000HGGFAB011B00CBAB11FA1B11>1111@31>111
--- a/jupyterhub_volumes/web/obidoc/obitools/obipairing/paired_exact.fastq
+++ b/jupyterhub_volumes/web/obidoc/obitools/obipairing/paired_exact.fastq
@@ -0,0 +1,16 @@
+@M01334:147:000000000-LBRVD:1:1101:14968:1570 {"ali_length":137,"definition":"1:N:0:CTCACCAA+CTAGGCAA","mode":"join","score":1687,"score_norm":0.679,"seq_ab_match":93}
+tgttccacgggcaatcctgagccaaatctttcattttgaaaaaatgagagatataatgtatctcttatttattataagaaataaaatatttcttatctaatattaaagttaggtgcagagactcaatgggtggaactagatcggatgtgca..........agcaaaaaagaacaagtaacaagggaaaaccagagaaaaatcaataaaaaagaaaaaaagagagatataaagtatcaataaaataaaaaaagaaaaaaaataataaaaaactaataaaaaagaaaggtgcagagaaaaaaagggaggaaaa
+
+11>A>@3@A11>ACFFEG110BFB00BAFGHE2DFGG201110/B11111/D1D2222D2FDFDFGDGHHBGG2F222110D11@1D1FGHFHGFF@GE1F2FG22112B220F1@111/0>BF11B210B>//11B1<1BB<///<1122!!!!!!!!!!11--111111?111@11110?1112/@@11122@011FBB2121//B1111CEEHGFB11F2B2B2B2DFB12@212122B21/>/1D1GF>>EA1GGDD2D1///22B222GD/E11GGFAB1B0A313B3B0A111BB1111311>>11
+@M01334:147:000000000-LBRVD:1:1101:15946:1586 {"ali_dir":"right","ali_length":138,"definition":"1:N:0:CTCACCAA+CTAGGCAA","mode":"alignment","pairing_mismatches":{"(T:16)->(A:33)":14,"(T:33)->(A:17)":118,"(T:37)->(A:16)":125,"(T:38)->(A:16)":32,"(T:39)->(A:17)":44},"score":5446,"score_norm":0.957,"seq_a_single":13,"seq_ab_match":132,"seq_b_single":13}
+gctcatccgaactacctaaccccattgagtctctgcacctatctttaatattagataagaaatattttatttcttataataaataagagatattttatatctctcattttttcaaaatgaaagatttggctcaggattgcccacgtaacggagatcggaagagc
+
+111/////2B112CMMOUO?MNObVHfcAVVHVWVVTQSWRXXIYYYXUSWiXaWeWWUWVSTTTWXgeUWWXXXWWgXWYYWVYWdUgSTTTXYYUVdTVWVXVgUWXXXVeYXfTCUXWW`QGUWfA@WSR?PRRWVARAc?UVMMOO?///BF////<000
+@M01334:147:000000000-LBRVD:1:1101:15399:1590 {"ali_length":137,"definition":"1:N:0:CTCACCAA+CTAGGCAA","mode":"join","score":3033,"score_norm":0.796,"seq_ab_match":109}
+tgttccacccattgagtctctgcacctatctttaatattagataagaaatattttacttcttataataaataagagttattttatatctctcattttttcaaaatgaaagatttggctcaggattgcccgtggaactagatcggaagagca..........agcaaaaaagaaaaagtaaaacaaaatgagaaaaagcaactaaatttaatattagataagaaatataatactacataaaataaataagagatattttatatctctaaatttttcaaaaggaaagatttggctcaggatagcccgaggaaaa
+
+11>A>@3B>>1CF111BBFAG3A3AAF1FFGHHF3FBGH221F211110D1DGHH2BBGBFF2F22D221D211111A2DDGG2F2FFFEGD1FFHHHGFD221B111110BFGD11F@1001BF0@@1/EA//1>F1B1FD/////00<1!!!!!!!!!!11//111110B122B12000B222B222B01111111@122B22122ED2B12F@D2GF2FAD2D2222D222212D2GF2HGD1GFADAD1D1222D1D111221B0011101GFDD12FFD1B000A1011B11B1111111311>>11
+@M01334:147:000000000-LBRVD:1:1101:13773:1687 {"ali_dir":"left","ali_length":54,"definition":"1:N:0:CTCACCAA+CTAGGCAA","mode":"alignment","pairing_mismatches":{"(C:39)->(A:16)":102,"(C:39)->(A:17)":121,"(T:39)->(A:14)":101},"score":2888,"score_norm":0.944,"seq_a_single":97,"seq_ab_match":51,"seq_b_single":97}
+ctcggatcaccattgagtctctgcacctatctttaatattagataagaaaaaatattatttcttatctgaaataagaaatattttatatatttctttttctcaaaatgaaagatttggctcaggattgccctgatccgagggatagcaccattgagtctctgcacctatccttttcttttgtattctagttcgagaacccccttgttttctcaaaacacggatttggctcaggatagccctgctatca
+
+3AAAAAADFFFFGGGGFGGGGGHHHHHHFHHHHHHHHGHHHHGHGGHFFHHHCGFHHHHHHHHHHHHHGHHGGFHFFHHHGHHHHBHHHGHHHHHHHXVVJIommmegikl]bVWgVDRXIlbkkVfPSWVWccVVT^ebggjkkCVeWcd1@CF>0/11@11B011F0/0000/00111@@D1111GA01AFGCEEE///0//BAFD0000HGGFAB011B00CBAB11FA1B11>1111@31>111
--- a/jupyterhub_volumes/web/obidoc/obitools/obipairing/paired_join.fastq
+++ b/jupyterhub_volumes/web/obidoc/obitools/obipairing/paired_join.fastq
@@ -0,0 +1,8 @@
+@M01334:147:000000000-LBRVD:1:1101:14968:1570 {"ali_length":137,"definition":"1:N:0:CTCACCAA+CTAGGCAA","mode":"join","score":1687,"score_norm":0.679,"seq_ab_match":93}
+tgttccacgggcaatcctgagccaaatctttcattttgaaaaaatgagagatataatgtatctcttatttattataagaaataaaatatttcttatctaatattaaagttaggtgcagagactcaatgggtggaactagatcggatgtgca..........agcaaaaaagaacaagtaacaagggaaaaccagagaaaaatcaataaaaaagaaaaaaagagagatataaagtatcaataaaataaaaaaagaaaaaaaataataaaaaactaataaaaaagaaaggtgcagagaaaaaaagggaggaaaa
+
+11>A>@3@A11>ACFFEG110BFB00BAFGHE2DFGG201110/B11111/D1D2222D2FDFDFGDGHHBGG2F222110D11@1D1FGHFHGFF@GE1F2FG22112B220F1@111/0>BF11B210B>//11B1<1BB<///<1122!!!!!!!!!!11--111111?111@11110?1112/@@11122@011FBB2121//B1111CEEHGFB11F2B2B2B2DFB12@212122B21/>/1D1GF>>EA1GGDD2D1///22B222GD/E11GGFAB1B0A313B3B0A111BB1111311>>11
+@M01334:147:000000000-LBRVD:1:1101:15399:1590 {"ali_length":4,"definition":"1:N:0:CTCACCAA+CTAGGCAA","mode":"join","score":126,"score_norm":1,"seq_ab_match":4}
+tgttccacccattgagtctctgcacctatctttaatattagataagaaatattttacttcttataataaataagagttattttatatctctcattttttcaaaatgaaagatttggctcaggattgcccgtggaactagatcggaagagca..........agcaaaaaagaaaaagtaaaacaaaatgagaaaaagcaactaaatttaatattagataagaaatataatactacataaaataaataagagatattttatatctctaaatttttcaaaaggaaagatttggctcaggatagcccgaggaaaa
+
+11>A>@3B>>1CF111BBFAG3A3AAF1FFGHHF3FBGH221F211110D1DGHH2BBGBFF2F22D221D211111A2DDGG2F2FFFEGD1FFHHHGFD221B111110BFGD11F@1001BF0@@1/EA//1>F1B1FD/////00<1!!!!!!!!!!11//111110B122B12000B222B222B01111111@122B22122ED2B12F@D2GF2FAD2D2222D222212D2GF2HGD1GFADAD1D1222D1D111221B0011101GFDD12FFD1B000A1011B11B1111111311>>11
--- a/jupyterhub_volumes/web/obidoc/obitools/obipairing/reverse.fastq
+++ b/jupyterhub_volumes/web/obidoc/obitools/obipairing/reverse.fastq
@@ -0,0 +1,16 @@
+@M01334:147:000000000-LBRVD:1:1101:14968:1570 2:N:0:CTCACCAA+CTAGGCAA
+TTTTCCTCCCTTTTTTTCTCTGCACCTTTCTTTTTTATTAGTTTTTTATTATTTTTTTTCTTTTTTTATTTTATTGATACTTTATATCTCTCTTTTTTTCTTTTTTATTGATTTTTCTCTGGTTTTCCCTTGTTACTTGTTCTTTTTTGCT
+
+11>>1131111BB111A0B3B313A0B1BAFGG11E/DG222B22///1D2DDGG1AE>>FG1D1/>/12B221212@21BFD2B2B2B2F11BFGHEEC1111B//1212BBF110@22111@@/2111?01111@111?111111--11
+@M01334:147:000000000-LBRVD:1:1101:15946:1586 2:N:0:CTCACCAA+CTAGGCAA
+CCGTTACGTGGGCAATCCTGAGCCAATTCTTTCTTTTTGAAAAAATGAGAGATATAAAATATCTCTTATTTATTATAAGAAATAAAATATTTCTTATCTAATATTAATGATAGGTGCAGTGACTCTATGGGGTTAGGTAGTTCGGATGAGC
+
+111>>111B111111BA0B1101B001BAGGH22DGGH?01110/B11111/D1D2221D1DBEDGH1GHH2GG2F222110D@111D1DFGEGFBG@GB1B2FG22222B220B11111111B@11B210/?E/00B211B2/////111
+@M01334:147:000000000-LBRVD:1:1101:15399:1590 2:N:0:CTCACCAA+CTAGGCAA
+TTTTCCTCGGGCTATCCTGAGCCAAATCTTTCCTTTTGAAAAATTTAGAGATATAAAATATCTCTTATTTATTTTATGTAGTATTATATTTCTTATCTAATATTAAATTTAGTTGCTTTTTCTCATTTTGTTTTACTTTTTCTTTTTTGCT
+
+11>>1131111111B11B1101A000B1DFF21DDFG1011100B122111D1D2221D1DADAFG1DGH2FG2D212222D2222D2DAF2FG2D@F21B2DE22122B221@11111110B222B222B00021B221B011111//11
+@M01334:147:000000000-LBRVD:1:1101:13773:1687 2:N:0:CTCACCAA+CTAGGCAA
+TGATAGCAGGGCTATCCTGAGCCAAATCCGTGTTTTGAGAAAACAAGGGGGTTCTCGAACTAGAATACAAAAGAAAAGGATAGGTGCAGAGACTCAATGGTGCTATCCCTCGGATCAGGGCAATCCTTAGCCAAATCTTTCATTTTTTGAA
+
+111>13@1111>11B1AF11BABC00B110BAFGGH0000DFAB//0///EEECGFA10AG1111D@@11100/0000/0F110B11@11/0>FC@1B>1B11FEFEC>E>///?<0110/?/FF<G22111@00@<GHHB>FHHH1///1