| Previous changeset 93:8fcf31272f6e (2023-03-06) Next changeset 95:d63eff357515 (2023-03-27) |
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Commit message:
"planemo upload commit d4be85014b638f1d50b318d4b735be7f6e973140" |
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modified:
CHANGELOG.md sequence_overview.py shm_csr.xml show_time_as_float tests/test_shm_csr.py wrapper.sh |
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added:
1_Summary.txt __pycache__/gene_identification.cpython-39.pyc identified_genes.txt tests/.pytest_cache/.gitignore tests/.pytest_cache/CACHEDIR.TAG tests/.pytest_cache/README.md tests/.pytest_cache/v/cache/lastfailed tests/.pytest_cache/v/cache/nodeids tests/.pytest_cache/v/cache/stepwise tests/__pycache__/test_shm_csr.cpython-39-pytest-6.2.5.pyc |
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removed:
CONTROL_NWK377_PB_IGHC_MID1_40nt_2.txz a.out tests/__pycache__/test_shm_csr.cpython-37-pytest-6.2.5.pyc tests/__pycache__/test_shm_csr.cpython-39-pytest-7.2.1.pyc tests/data/.~lock.handleiding activeren pas.docx# tests/data/handleiding activeren pas.docx time_ns |
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| diff -r 8fcf31272f6e -r 84e9e5c8c101 1_Summary.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/1_Summary.txt Fri Mar 24 16:58:28 2023 +0000 |
| [ |
| b'@@ -0,0 +1,4099 @@\n+Sequence number\tSequence ID\tV-DOMAIN Functionality\tV-GENE and allele\tV-REGION score\tV-REGION identity %\tV-REGION identity nt\tV-REGION identity % (with ins/del events)\tV-REGION identity nt (with ins/del events)\tJ-GENE and allele\tJ-REGION score\tJ-REGION identity %\tJ-REGION identity nt\tD-GENE and allele\tD-REGION reading frame\tCDR1-IMGT length\tCDR2-IMGT length\tCDR3-IMGT length\tCDR-IMGT lengths\tFR-IMGT lengths\tAA JUNCTION\tJUNCTION frame\tOrientation\tV-DOMAIN Functionality comment\tV-REGION potential ins/del\tJ-GENE and allele comment\tV-REGION insertions\tV-REGION deletions\tSequence\t5prime trimmed-n nb\t3prime trimmed-n nb\tAnalysed sequence length\tSequence analysis category\t\n+1\tM01495:47:000000000-JFBTW:1:1102:9194:4681_1:N:0:\tproductive\tHomsap IGHV4-34*01 F, or Homsap IGHV4-34*02 F\t1100\t100.00\t220/220 nt\t\t\tHomsap IGHJ3*02 F\t205\t90.00\t45/50 nt\tHomsap IGHD6-19*01 F\t1\t8\t7\t18\t8.7.18\t[3.17.38.11]\tCARGTDSSGWYFVLRAFDIW\tin-frame\t+\t\t\t\t\t\tcgctgtctatggtgggtccttcagtggttactactggagctggatccgccagcccccagggaaggggctggagtggattggggaaatcaatcatagtggaagcaccaactacaacccgtccctcaagagtcgagtcaccatatcagtagacacgtccaagaaccagttctccctgaagctgagctctgtgaccgccgcggacacggctgtgtattactgtgcgagagggaccgatagcagtggctggtactttgtcttacgtgcttttgatatctggggccaagggacaatgttcaccgtcgcttcagggagtgcatccgccccaacccttttccccctcgtctcctgtgagaattcccctcgcgatat\t0\t0\t369\t2 (indelcorr)\t\n+2\tM01495:47:000000000-JFBTW:1:1102:4906:4844_1:N:0:\tproductive\tHomsap IGHV3-48*03 F\t1088\t98.65\t220/223 nt\t\t\tHomsap IGHJ4*02 F\t195\t89.58\t43/48 nt\tHomsap IGHD5-12*01 F\t1\t8\t8\t14\t8.8.14\t[3.17.38.11]\tCARGVTVATISPFGYW\tin-frame\t+\t\t\t\t\t\ttgcagcctctggattcaccttcagtagttatgaaatgaactgggtccgccaggctccagggaaggggctggagtgggttttatacattagtagtagtggtagtaccatatactacgcagactctgtgaagggccgattcaccatctccagagacaacgccaagaactcactgtatctgcaaatgaacagtctgagagccgaggacacggctgtgtattactgtgcaagaggggttacggtggctacaattagcccctttggatactggggccagggaaccctggtcaccgtctcctcagggagtgcatccgccccaacccttttccccctcgtctcctgtgagaattcccctcgcgatat\t0\t0\t360\t2 (indelcorr)\t\n+3\tM01495:47:000000000-JFBTW:1:1102:9591:5411_1:N:0:\tproductive\tHomsap IGHV4-38-2*01 F\t1115\t100.00\t223/223 nt\t\t\tHomsap IGHJ4*02 F\t213\t93.75\t45/48 nt\tHomsap IGHD3-22*01 F\t2\t9\t7\t17\t9.7.17\t[3.17.38.11]\tCARDFRRYYDSSGSYVDYW\tin-frame\t+\t\t\t\t\t\tcgctgtctctggttactccatcagcagtggttactactggggctggatccggcagcccccagggaaggggctggagtggattgggagtatctatcatagtgggagcacctactacaacccgtccctcaagagtcgagtcaccatatcagtagacacgtccaagaaccagttctccctgaagctgagctctgtgaccgccgcagacacggccgtgtattactgtgcgagagatttccgtcgttactatgatagtagtggttcctatgttgactactggggccagggaaccctggtcaccgtctcctcagggagtgcatccgccccaacccttttccccctcgtctcctgtgagaattcccctcgcgatat\t0\t0\t369\t2 (indelcorr)\t\n+4\tM01495:47:000000000-JFBTW:1:1102:8366:6267_1:N:0:\tproductive\tHomsap IGHV3-74*01 F, or Homsap IGHV3-74*02 F\t980\t93.27\t208/223 nt\t\t\tHomsap IGHJ6*02 F\t301\t98.39\t61/62 nt\tHomsap IGHD2-15*01 F\t2\t8\t8\t22\t8.8.22\t[3.17.38.11]\tCARGYCSGGSCYSLYYYYYGMDVW\tin-frame\t+\t\t\t\t\t\ttgcagcctctggattcacctttagcagctatgccatgagctgggtccgccaggctccagggaaggggctggtgtgggtctcacgtattaatagtgacgggagtaccacaagctacgcggacttcgtgaagggccgattcaccatctccagagacaacgccaagaactcactgtatctgcaaatgaacagcctgagagccgaggacacggctgtgtattactgtgcgagaggatattgtagtggtggtagctgctactcgctttactactactactacggtatggacgtctggggccaagggaccacggtcaccgtctcctcagggagtgcatccgccccaacccttttccccctcgtctcctgtgagaattcccctcgcgatat\t0\t0\t384\t2 (indelcorr)\t\n+5\tM01495:47:000000000-JFBTW:1:1102:13215:6515_1:N:0\tproductive\tHomsap IGHV1-69*01 F, or Homsap IGHV1-69*12 F or Homsap IGHV1-69*13 F or Homsap IGHV1-69D*01 F\t1095\t100.00\t219/219 nt\t\t\tHomsap IGHJ4*02 F\t204\t91.67\t44/48 nt\tHomsap IGHD5-18*01 F\t3\t8\t8\t11\t8.8.11\t[2.17.38.11]\tCARDRSDGWFDYW\tin-frame\t+\t\t\t\t\t\tgcttctggaggcaccttcagcagctatgctatcagctgggtgcgacaggcccctggacaagggcttgagtggatgggagggatcatccctatctttggtacagcaaactacgcacagaagttccagggcagagtcacgattaccgcggacgaatccacgagcacagcctacatggagctgagcagcctgagatctgaggacacggccgtgtattactgtgcgagagatcgttcggatggttggtttgactactggggccagggaaccctggtcaccgtctcctcagggagtgcatccgccccaacccttttccccctcgtctcctgtgagaattcccctcgcgatat\t0\t0\t347\t2 (indelcorr)\t\n+6\tM01495:47:000000000-JFBTW:1:1102:17003:6688_1:N:0\tproductive\tHomsap I'..b'agggaaccctggtcaccgtctcctcagggagtgcatccgccccaacccttttccccctcggctcctgtgagaagtcccctcgcgatat\t0\t0\t341\t2 (indelcorr)\t\n+4093\tM02948:184:000000000-JK6TB:1:2119:13202:20116_1:N\tproductive\tHomsap IGHV1-2*02 F\t1005\t95.43\t209/219 nt\t\t\tHomsap IGHJ3*02 F\t196\t88.00\t44/50 nt\tHomsap IGHD3-16*01 F\t3\t8\t8\t10\t8.8.10\t[2.17.38.11]\tCATVRELGFDIW\tin-frame\t+\t\t\t\t\t\tgcttctggatacaccttcaccggctactatatgcactgggtgcgacaggcccctggacaagggcttgagtggatgggatggatcaaccctaacagtggtggcacaaactatgcacagaagtttcagggcagggtcaccatgaccgaggacacatctacagacacagcctacatggagctgagcagcctgagatctgaggacacggccgtgtattactgtgcaacggttagggagctggggtttgatatctggggccaagggacaatggtcaccgtctcttcagggagtgcatccgccccaacccttttccccctcgtctcctgtgagaattcccctcgcgatat\t0\t0\t344\t2 (indelcorr)\t\n+4094\tM02948:184:000000000-JK6TB:1:2119:26324:20804_1:N\tproductive\tHomsap IGHV1-2*02 F\t996\t94.98\t208/219 nt\t\t\tHomsap IGHJ4*02 F, or Homsap IGHJ4*03 F\t159\t81.25\t39/48 nt\tHomsap IGHD7-27*01 F\t1\t8\t8\t11\t8.8.11\t[2.17.38.11]\tCARPIPLTGTDYW\tin-frame\t+\t\t\t\t\t\tgcttctggaggcaccttcagcagctatgctatcagctgggtgcgacaggcccctggacaagggcttgagtggatgggatggatcaaccctaacagtggtggcacaaactatgcacagaagtttcagggcagggtcaccatgaccagggacacgtccatcagcacagcctacatggagctgagcagcctgagatctgacgacacggccgtgtattactgtgcgaggccgatacctctaactgggactgactactggggccaggggaccctagtcaccgtctcctcagggagtgcatccgccccaacccttttccccctcgtctccgtgagaattcccctcgcgatat\t0\t0\t346\t2 (indelcorr)\t\n+4095\tM02948:184:000000000-JK6TB:1:2119:20335:21283_1:N\tproductive\tHomsap IGHV1-69*01 F, or Homsap IGHV1-69*12 F or Homsap IGHV1-69*13 F or Homsap IGHV1-69D*01 F\t1095\t100.00\t219/219 nt\t\t\tHomsap IGHJ4*02 F\t195\t89.58\t43/48 nt\tHomsap IGHD2-21*02 F\t2\t8\t8\t14\t8.8.14\t[2.17.38.11]\tCARAYCGGDCFAFDYW\tin-frame\t+\t\t\t\t\t\tgcttctggaggcaccttcagcagctatgctatcagctgggtgcgacaggcccctggacaagggcttgagtggatgggagggatcatccctatctttggtacagcaaactacgcacagaagttccagggcagagtcacgattaccgcggacgaatccacgagcacagcctacatggagctgagcagcctgagatctgaggacacggccgtgtattactgtgcgagagcatattgtggtggtgactgctttgcgtttgactactggggccagggaaccctggtcaccgtctcctcagggagtgcatccgccccaacccttttccccctcgtctcctgtgagaattcccctcgcgatat\t0\t0\t356\t2 (indelcorr)\t\n+4096\tM02948:184:000000000-JK6TB:1:2119:15289:21461_1:N\tproductive\tHomsap IGHV1-69*01 F, or Homsap IGHV1-69*12 F or Homsap IGHV1-69*13 F or Homsap IGHV1-69D*01 F\t1086\t99.54\t218/219 nt\t\t\tHomsap IGHJ6*02 F\t301\t98.39\t61/62 nt\tHomsap IGHD5-12*01 F\t3\t8\t8\t21\t8.8.21\t[2.17.38.11]\tCARGGYSGYELIKYYYYYGMDVW\tin-frame\t+\t\t\t\t\t\tgcttctggaggcaccttcagcagctatgctatcagctgggtgcgacaggcccctggacaagggcttgagtggatgggagggatcatccctatctttggtacagtaaactacgcacagaagttccagggcagagtcacgattaccgcggacgaatccacgagcacagcctacatggagctgagcagcctgagatctgaggacacggccgtgtattactgtgcgaggggcggatatagtggctacgagttgatcaaatactactactactacggtatggacgtctggggccaagggaccacggtcaccgtctcctcagggagtgcatccgccccaacccttttccccctcgtctcctgtgagaattcccctcgcgatat\t0\t0\t377\t2 (indelcorr)\t\n+4097\tM02948:184:000000000-JK6TB:1:2119:8379:22530_1:N:\tproductive\tHomsap IGHV1-24*01 F\t1086\t99.54\t218/219 nt\t\t\tHomsap IGHJ4*02 F\t195\t89.58\t43/48 nt\tHomsap IGHD2-8*01 F\t3\t8\t8\t12\t8.8.12\t[2.17.38.11]\tCATGVGALLPIDYW\tin-frame\t+\t\t\t\t\t\tgtttccggatacaccctcactgaattatctatgcactgggtgcgacaggctcctggaaaagggcttgagtggatgggaggttttgatcctgaagatggtgaaacaatctacgcacagaagttccagggcagagtcaccatgaccgaggacacatctacagacacagcctacatggagctgagcagcctgagatctgaggacacggccgtgtattactgtgcaacaggggtgggagctttactcccgattgactactggggccagggaaccctggtcaccgtctcctcagggagtgcatccgccccaacccttttccccctcgtctcctgtgagaattcccctcgcgatat\t0\t0\t350\t2 (indelcorr)\t\n+4098\tM02948:184:000000000-JK6TB:1:2119:18285:24809_1:N\tproductive\tHomsap IGHV5-51*01 F, or Homsap IGHV5-51*03 F\t1110\t100.00\t222/222 nt\t\t\tHomsap IGHJ5*02 F\t219\t92.16\t47/51 nt\tHomsap IGHD3-10*01 F\t2\t8\t8\t21\t8.8.21\t[3.17.38.11]\tCARVHYYYGSGSYYLPSFWFDPW\tin-frame\t+\t\t\t\t\t\taagggttctggatacagctttaccagctactggatcggctgggtgcgccagatgcccgggaaaggcctggagtggatggggatcatctatcctggtgactctgataccagatacagcccgtccttccaaggccaggtcaccatctcagccgacaagtccatcagcaccgcctacctgcagtggagcagcctgaaggcctcggacaccgccatgtattactgtgcgagagtacattattactatggttcggggagttattatctcccctctttctggttcgacccctggggccagggaaccctggtcaccgtctcctcagggagtgcatccgccccaacccttttccccctcgtctcctgtgagaattcccctcgcgatat\t0\t0\t380\t2 (indelcorr)\t\n' |
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| diff -r 8fcf31272f6e -r 84e9e5c8c101 CHANGELOG.md --- a/CHANGELOG.md Mon Mar 06 11:36:32 2023 +0000 +++ b/CHANGELOG.md Fri Mar 24 16:58:28 2023 +0000 |
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| @@ -1,3 +1,8 @@ +version 1.8.0 +----------------- ++ Add options "Everything is IGA" and "Everything is IGG". ++ Make sure IGM naive and naive memory are part of the galaxy output. + version 1.7.0 ----------------- + Use the name of the input file to generate the name of the output IMGT |
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| diff -r 8fcf31272f6e -r 84e9e5c8c101 CONTROL_NWK377_PB_IGHC_MID1_40nt_2.txz |
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| Binary file CONTROL_NWK377_PB_IGHC_MID1_40nt_2.txz has changed |
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| diff -r 8fcf31272f6e -r 84e9e5c8c101 __pycache__/gene_identification.cpython-39.pyc |
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| Binary file __pycache__/gene_identification.cpython-39.pyc has changed |
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| diff -r 8fcf31272f6e -r 84e9e5c8c101 a.out |
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| Binary file a.out has changed |
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| diff -r 8fcf31272f6e -r 84e9e5c8c101 identified_genes.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/identified_genes.txt Fri Mar 24 16:58:28 2023 +0000 |
| [ |
| b'@@ -0,0 +1,4099 @@\n+Sequence 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|
| b |
| diff -r 8fcf31272f6e -r 84e9e5c8c101 sequence_overview.py --- a/sequence_overview.py Mon Mar 06 11:36:32 2023 +0000 +++ b/sequence_overview.py Fri Mar 24 16:58:28 2023 +0000 |
| b |
| @@ -25,6 +25,8 @@ "IGA1": 0, "IGA2": 0, "IGE": 0, + "IGA": 0, # IGA and IGG without subclasses only exist when the + "IGG": 0, # everything is IGA or IGG option is chosen. "IGG1": 0, "IGG2": 0, "IGG3": 0, |
| b |
| diff -r 8fcf31272f6e -r 84e9e5c8c101 shm_csr.xml --- a/shm_csr.xml Mon Mar 06 11:36:32 2023 +0000 +++ b/shm_csr.xml Fri Mar 24 16:58:28 2023 +0000 |
| [ |
| @@ -1,4 +1,4 @@ -<tool id="shm_csr" name="SHM & CSR pipeline" version="1.7.0" profile="16.04"> +<tool id="shm_csr" name="SHM & CSR pipeline" version="1.8.0" profile="16.04"> <description></description> <requirements> <requirement type="package" version="3.7.1">python</requirement> @@ -28,9 +28,10 @@ $__tool_directory__/wrapper.sh "$input" custom $out_file $out_file.files_path "${in_file.name}" "-" $functionality $unique - $naive_output_cond.naive_output $naive_output_ca - $naive_output_cg $naive_output_cm $naive_output_ce - $naive_output_all $filter_unique.filter_unique_select + $naive_output_cond.naive_output $naive_output_ca $naive_output_cg + $naive_output_cm $naive_output_ce $naive_output_all $naive_output_igm_naive + $naive_output_igm_naive_memory + $filter_unique.filter_unique_select $filter_unique.filter_unique_clone_count $class_filter_cond.class_filter $empty_region_filter @@ -41,7 +42,8 @@ $out_file $out_file.files_path "${in_file.name}" "-" $functionality $unique $naive_output_cond.naive_output $naive_output_ca $naive_output_cg - $naive_output_cm $naive_output_ce $naive_output_all + $naive_output_cm $naive_output_ce $naive_output_all $naive_output_igm_naive + $naive_output_igm_naive_memory $filter_unique.filter_unique_select 2 $class_filter_cond.class_filter @@ -100,6 +102,8 @@ <option value="19_0">>19% class</option> <option value="101_101_all">Do not assign (sub)class</option> <option value="101_101_IGM">Everything is IGM</option> + <option value="101_101_IGA">Everything is IGA</option> + <option value="101_101_IGG">Everything is IGG</option> </param> </conditional> <conditional name="naive_output_cond"> @@ -120,18 +124,39 @@ <data format="imgt_archive" name="naive_output_ca" label = "Filtered IMGT IGA: ${in_file.name}" > <filter>naive_output_cond['naive_output'] == "yes"</filter> <filter>class_filter_cond['class_filter'] != "101_101"</filter> + <filter>class_filter_cond['class_filter'] != "101_101_IGG"</filter> + <filter>class_filter_cond['class_filter'] != "101_101_IGM"</filter> </data> <data format="imgt_archive" name="naive_output_cg" label = "Filtered IMGT IGG: ${in_file.name}" > <filter>naive_output_cond['naive_output'] == "yes"</filter> <filter>class_filter_cond['class_filter'] != "101_101"</filter> + <filter>class_filter_cond['class_filter'] != "101_101_IGA"</filter> + <filter>class_filter_cond['class_filter'] != "101_101_IGM"</filter> </data> <data format="imgt_archive" name="naive_output_cm" label = "Filtered IMGT IGM: ${in_file.name}" > <filter>naive_output_cond['naive_output'] == "yes"</filter> <filter>class_filter_cond['class_filter'] != "101_101"</filter> + <filter>class_filter_cond['class_filter'] != "101_101_IGA"</filter> + <filter>class_filter_cond['class_filter'] != "101_101_IGG"</filter> </data> <data format="imgt_archive" name="naive_output_ce" label = "Filtered IMGT IGE: ${in_file.name}" > <filter>naive_output_cond['naive_output'] == "yes"</filter> <filter>class_filter_cond['class_filter'] != "101_101"</filter> + <filter>class_filter_cond['class_filter'] != "101_101_IGA"</filter> + <filter>class_filter_cond['class_filter'] != "101_101_IGG"</filter> + <filter>class_filter_cond['class_filter'] != "101_101_IGM"</filter> + </data> + <data format="imgt archive" name="naive_output_igm_naive" label = "Filtered naive IGM sequences (mutations below 2%): ${in_file.name}"> + <filter>naive_output_cond['naive_output'] == "yes"</filter> + <filter>class_filter_cond['class_filter'] != "101_101"</filter> + <filter>class_filter_cond['class_filter'] != "101_101_IGA"</filter> + <filter>class_filter_cond['class_filter'] != "101_101_IGG"</filter> + </data> + <data format="imgt archive" name="naive_output_igm_naive_memory" label = "Filtered naive memory IGM sequences (mutations over 2%): ${in_file.name}"> + <filter>naive_output_cond['naive_output'] == "yes"</filter> + <filter>class_filter_cond['class_filter'] != "101_101"</filter> + <filter>class_filter_cond['class_filter'] != "101_101_IGA"</filter> + <filter>class_filter_cond['class_filter'] != "101_101_IGG"</filter> </data> <data format="imgt_archive" name="naive_output_all" label = "Filtered IMGT all: ${in_file.name}" > <filter>naive_output_cond['naive_output'] == "yes"</filter> |
| b |
| diff -r 8fcf31272f6e -r 84e9e5c8c101 show_time_as_float |
| b |
| Binary file show_time_as_float has changed |
| b |
| diff -r 8fcf31272f6e -r 84e9e5c8c101 tests/.pytest_cache/.gitignore --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tests/.pytest_cache/.gitignore Fri Mar 24 16:58:28 2023 +0000 |
| b |
| @@ -0,0 +1,2 @@ +# Created by pytest automatically. +* |
| b |
| diff -r 8fcf31272f6e -r 84e9e5c8c101 tests/.pytest_cache/CACHEDIR.TAG --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tests/.pytest_cache/CACHEDIR.TAG Fri Mar 24 16:58:28 2023 +0000 |
| b |
| @@ -0,0 +1,4 @@ +Signature: 8a477f597d28d172789f06886806bc55 +# This file is a cache directory tag created by pytest. +# For information about cache directory tags, see: +# http://www.bford.info/cachedir/spec.html |
| b |
| diff -r 8fcf31272f6e -r 84e9e5c8c101 tests/.pytest_cache/README.md --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tests/.pytest_cache/README.md Fri Mar 24 16:58:28 2023 +0000 |
| [ |
| @@ -0,0 +1,8 @@ +# pytest cache directory # + +This directory contains data from the pytest's cache plugin, +which provides the `--lf` and `--ff` options, as well as the `cache` fixture. + +**Do not** commit this to version control. + +See [the docs](https://docs.pytest.org/en/stable/cache.html) for more information. |
| b |
| diff -r 8fcf31272f6e -r 84e9e5c8c101 tests/.pytest_cache/v/cache/lastfailed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tests/.pytest_cache/v/cache/lastfailed Fri Mar 24 16:58:28 2023 +0000 |
| [ |
| @@ -0,0 +1,25 @@ +{ + "test_shm_csr.py::test_results_match_validation[IGA_pie.txt]": true, + "test_shm_csr.py::test_results_match_validation[IGG_pie.txt]": true, + "test_shm_csr.py::test_results_match_validation[aa_histogram_sum.txt]": true, + "test_shm_csr.py::test_results_match_validation[aa_histogram_sum_IGA.txt]": true, + "test_shm_csr.py::test_results_match_validation[aa_histogram_sum_IGG.txt]": true, + "test_shm_csr.py::test_results_match_validation[absolute_mutations.txt]": true, + "test_shm_csr.py::test_results_match_validation[frequency_ranges_classes.txt]": true, + "test_shm_csr.py::test_results_match_validation[frequency_ranges_subclasses.txt]": true, + "test_shm_csr.py::test_results_match_validation[mutation_by_id.txt]": true, + "test_shm_csr.py::test_results_match_validation[relative_mutations.txt]": true, + "test_shm_csr.py::test_results_match_validation[scatter.txt]": true, + "test_shm_csr.py::test_results_match_validation[shm_overview.txt]": true, + "test_shm_csr.py::test_results_match_validation[tandems_by_id.txt]": true, + "test_shm_csr.py::test_results_match_validation[transitions_IGA1_sum.txt]": true, + "test_shm_csr.py::test_results_match_validation[transitions_IGA2_sum.txt]": true, + "test_shm_csr.py::test_results_match_validation[transitions_IGA_sum.txt]": true, + "test_shm_csr.py::test_results_match_validation[transitions_IGE_sum.txt]": true, + "test_shm_csr.py::test_results_match_validation[transitions_IGG1_sum.txt]": true, + "test_shm_csr.py::test_results_match_validation[transitions_IGG2_sum.txt]": true, + "test_shm_csr.py::test_results_match_validation[transitions_IGG3_sum.txt]": true, + "test_shm_csr.py::test_results_match_validation[transitions_IGG4_sum.txt]": true, + "test_shm_csr.py::test_results_match_validation[transitions_IGG_sum.txt]": true, + "test_shm_csr.py::test_results_match_validation[transitions_all_sum.txt]": true +} \ No newline at end of file |
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| diff -r 8fcf31272f6e -r 84e9e5c8c101 tests/.pytest_cache/v/cache/nodeids --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tests/.pytest_cache/v/cache/nodeids Fri Mar 24 16:58:28 2023 +0000 |
| [ |
| @@ -0,0 +1,25 @@ +[ + "test_shm_csr.py::test_results_match_validation[IGA_pie.txt]", + "test_shm_csr.py::test_results_match_validation[IGG_pie.txt]", + "test_shm_csr.py::test_results_match_validation[aa_histogram_sum.txt]", + "test_shm_csr.py::test_results_match_validation[aa_histogram_sum_IGA.txt]", + "test_shm_csr.py::test_results_match_validation[aa_histogram_sum_IGG.txt]", + "test_shm_csr.py::test_results_match_validation[absolute_mutations.txt]", + "test_shm_csr.py::test_results_match_validation[frequency_ranges_classes.txt]", + "test_shm_csr.py::test_results_match_validation[frequency_ranges_subclasses.txt]", + "test_shm_csr.py::test_results_match_validation[mutation_by_id.txt]", + "test_shm_csr.py::test_results_match_validation[relative_mutations.txt]", + "test_shm_csr.py::test_results_match_validation[scatter.txt]", + "test_shm_csr.py::test_results_match_validation[shm_overview.txt]", + "test_shm_csr.py::test_results_match_validation[tandems_by_id.txt]", + "test_shm_csr.py::test_results_match_validation[transitions_IGA1_sum.txt]", + "test_shm_csr.py::test_results_match_validation[transitions_IGA2_sum.txt]", + "test_shm_csr.py::test_results_match_validation[transitions_IGA_sum.txt]", + "test_shm_csr.py::test_results_match_validation[transitions_IGE_sum.txt]", + "test_shm_csr.py::test_results_match_validation[transitions_IGG1_sum.txt]", + "test_shm_csr.py::test_results_match_validation[transitions_IGG2_sum.txt]", + "test_shm_csr.py::test_results_match_validation[transitions_IGG3_sum.txt]", + "test_shm_csr.py::test_results_match_validation[transitions_IGG4_sum.txt]", + "test_shm_csr.py::test_results_match_validation[transitions_IGG_sum.txt]", + "test_shm_csr.py::test_results_match_validation[transitions_all_sum.txt]" +] \ No newline at end of file |
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| diff -r 8fcf31272f6e -r 84e9e5c8c101 tests/.pytest_cache/v/cache/stepwise --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tests/.pytest_cache/v/cache/stepwise Fri Mar 24 16:58:28 2023 +0000 |
| [ |
| @@ -0,0 +1,1 @@ +[] \ No newline at end of file |
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| diff -r 8fcf31272f6e -r 84e9e5c8c101 tests/__pycache__/test_shm_csr.cpython-37-pytest-6.2.5.pyc |
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| diff -r 8fcf31272f6e -r 84e9e5c8c101 tests/__pycache__/test_shm_csr.cpython-39-pytest-6.2.5.pyc |
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| diff -r 8fcf31272f6e -r 84e9e5c8c101 tests/__pycache__/test_shm_csr.cpython-39-pytest-7.2.1.pyc |
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| diff -r 8fcf31272f6e -r 84e9e5c8c101 tests/data/.~lock.handleiding activeren pas.docx# --- a/tests/data/.~lock.handleiding activeren pas.docx# Mon Mar 06 11:36:32 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,1 +0,0 @@ -Vorderman\, R.H.P. (MOLEPI) ,rhpvorderman,sasc-pc-6,21.02.2023 15:01,file:///home/rhpvorderman/.config/libreoffice/4; \ No newline at end of file |
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| diff -r 8fcf31272f6e -r 84e9e5c8c101 tests/data/handleiding activeren pas.docx |
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| diff -r 8fcf31272f6e -r 84e9e5c8c101 tests/test_shm_csr.py --- a/tests/test_shm_csr.py Mon Mar 06 11:36:32 2023 +0000 +++ b/tests/test_shm_csr.py Fri Mar 24 16:58:28 2023 +0000 |
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| @@ -74,6 +74,8 @@ naive_output_cm = "None" naive_output_ce = "None" naive_output_all = "None" + naive_output_igm_naive = "None" + naive_output_igm_naive_memory = "None" filter_unique = "remove" filter_unique_count = '2' class_filter = '70_70' @@ -100,6 +102,8 @@ naive_output_cm, naive_output_ce, naive_output_all, + naive_output_igm_naive, + naive_output_igm_naive_memory, filter_unique, filter_unique_count, class_filter, |
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| diff -r 8fcf31272f6e -r 84e9e5c8c101 time_ns |
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| diff -r 8fcf31272f6e -r 84e9e5c8c101 wrapper.sh --- a/wrapper.sh Mon Mar 06 11:36:32 2023 +0000 +++ b/wrapper.sh Fri Mar 24 16:58:28 2023 +0000 |
| b |
| @@ -16,11 +16,13 @@ naive_output_cm=${12} naive_output_ce=${13} naive_output_all=${14} -filter_unique=${15} -filter_unique_count=${16} -class_filter=${17} -empty_region_filter=${18} -fast=${19} +naive_output_igm_naive=${15} +naive_output_igm_naive_memory=${16} +filter_unique=${17} +filter_unique_count=${18} +class_filter=${19} +empty_region_filter=${20} +fast=${21} BASENAME=$(basename $input) # Cut off .txz or .tgz suffix @@ -822,6 +824,8 @@ cp $outdir/${NEW_IMGT_PREFIX}_IGG.txz ${naive_output_cg} cp $outdir/${NEW_IMGT_PREFIX}_IGM.txz ${naive_output_cm} cp $outdir/${NEW_IMGT_PREFIX}_IGE.txz ${naive_output_ce} + cp $outdir/${NEW_IMGT_PREFIX}_IGM_NAIVE.txz ${naive_output_igm_naive} + cp $outdir/${NEW_IMGT_PREFIX}_IGM_NAIVE_MEMORY.txz ${naive_output_igm_naive_memory} fi fi |