| Previous changeset 94:84e9e5c8c101 (2023-03-24) Next changeset 96:385dea3c6cb5 (2024-01-05) |
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Commit message:
planemo upload commit d96a736dcd6da34137f79861fbc6369716c332f1 |
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modified:
CHANGELOG.md shm_csr.xml show_time_as_float wrapper.sh |
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added:
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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removed:
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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| diff -r 84e9e5c8c101 -r d63eff357515 1_Summary.txt --- a/1_Summary.txt Fri Mar 24 16:58:28 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,4099 +0,0 @@\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 84e9e5c8c101 -r d63eff357515 CHANGELOG.md --- a/CHANGELOG.md Fri Mar 24 16:58:28 2023 +0000 +++ b/CHANGELOG.md Mon Mar 27 13:11:53 2023 +0000 |
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| @@ -1,3 +1,9 @@ +version 1.8.1 +----------------- ++ Fix a bug where input files with spaces could not be used. ++ Fix a bug were the data format was not properly set for filtered IMGT + archives. + version 1.8.0 ----------------- + Add options "Everything is IGA" and "Everything is IGG". |
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| diff -r 84e9e5c8c101 -r d63eff357515 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 84e9e5c8c101 -r d63eff357515 __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 84e9e5c8c101 -r d63eff357515 a.out |
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| Binary file a.out has changed |
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| diff -r 84e9e5c8c101 -r d63eff357515 identified_genes.txt --- a/identified_genes.txt Fri Mar 24 16:58:28 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,4099 +0,0 @@\n-Sequence ID\tbest_match\tnt_hit_percentage\tchunk_hit_percentage\tstart_locations\n-M01495:47:000000000-JFBTW:1:1102:9194:4681_1:N:0:\tIGM\t100\t100\t[304]\n-M01495:47:000000000-JFBTW:1:1102:4906:4844_1:N:0:\tIGM\t100\t100\t[295]\n-M01495:47:000000000-JFBTW:1:1102:9591:5411_1:N:0:\tIGM\t100\t100\t[304]\n-M01495:47:000000000-JFBTW:1:1102:8366:6267_1:N:0:\tIGM\t100\t100\t[319]\n-M01495:47:000000000-JFBTW:1:1102:13215:6515_1:N:0\tIGM\t100\t100\t[282]\n-M01495:47:000000000-JFBTW:1:1102:17003:6688_1:N:0\tIGM\t100\t100\t[288]\n-M01495:47:000000000-JFBTW:1:1102:23370:7403_1:N:0\tIGM\t100\t100\t[292]\n-M01495:47:000000000-JFBTW:1:1102:28961:8810_1:N:0\tIGM\t100\t100\t[300]\n-M01495:47:000000000-JFBTW:1:1102:14784:9156_1:N:0\tIGM\t100\t100\t[277]\n-M01495:47:000000000-JFBTW:1:1102:16981:9860_1:N:0\tIGM\t100\t100\t[292]\n-M01495:47:000000000-JFBTW:1:1102:27075:11310_1:N:\tIGM\t100\t100\t[306]\n-M01495:47:000000000-JFBTW:1:1102:8022:11357_1:N:0\tIGM\t100\t100\t[288]\n-M01495:47:000000000-JFBTW:1:1102:9646:12659_1:N:0\tIGM\t100\t100\t[282]\n-M01495:47:000000000-JFBTW:1:1102:17966:13001_1:N:\tIGM\t100\t100\t[292]\n-M01495:47:000000000-JFBTW:1:1102:11807:13387_1:N:\tIGM\t100\t100\t[294]\n-M01495:47:000000000-JFBTW:1:1102:6490:14138_1:N:0\tIGM\t100\t100\t[306]\n-M01495:47:000000000-JFBTW:1:1102:23544:14892_1:N:\tIGM\t100\t100\t[292]\n-M01495:47:000000000-JFBTW:1:1102:29236:15050_1:N:\tIGM\t100\t25\t[]\n-M01495:47:000000000-JFBTW:1:1102:21000:15162_1:N:\tIGM\t100\t100\t[283]\n-M01495:47:000000000-JFBTW:1:1102:14819:15847_1:N:\tIGM\t100\t100\t[277]\n-M01495:47:000000000-JFBTW:1:1102:8944:16097_1:N:0\tIGM\t100\t100\t[306]\n-M01495:47:000000000-JFBTW:1:1102:7824:17280_1:N:0\tIGM\t100\t100\t[295]\n-M01495:47:000000000-JFBTW:1:1102:25893:17527_1:N:\tIGM\t100\t100\t[288]\n-M01495:47:000000000-JFBTW:1:1102:17807:18307_1:N:\tIGM\t100\t100\t[289]\n-M01495:47:000000000-JFBTW:1:1102:8540:18953_1:N:0\tIGM\t100\t100\t[301]\n-M01495:47:000000000-JFBTW:1:1102:27342:19689_1:N:\tIGM\t100\t100\t[307]\n-M01495:47:000000000-JFBTW:1:1102:25946:20495_1:N:\tIGM\t100\t100\t[291]\n-M01495:47:000000000-JFBTW:1:1102:25170:20585_1:N:\tIGM\t100\t100\t[303]\n-M01495:47:000000000-JFBTW:1:1102:20292:21460_1:N:\tIGM\t100\t100\t[298]\n-M01495:47:000000000-JFBTW:1:2114:8633:1335_1:N:0:\tIGM\t100\t100\t[327]\n-M01495:47:000000000-JFBTW:1:2114:14139:1455_1:N:0\tIGM\t100\t100\t[283]\n-M01495:47:000000000-JFBTW:1:2114:9278:1992_1:N:0:\tIGM\t100\t100\t[291]\n-M01495:47:000000000-JFBTW:1:2114:11850:2153_1:N:0\tIGM\t100\t100\t[304]\n-M01495:47:000000000-JFBTW:1:2114:24209:2253_1:N:0\tIGM\t100\t100\t[301]\n-M01495:47:000000000-JFBTW:1:2114:21800:2538_1:N:0\tIGM\t100\t100\t[292]\n-M01495:47:000000000-JFBTW:1:2114:17433:3200_1:N:0\tIGM\t100\t100\t[276]\n-M01495:47:000000000-JFBTW:1:2114:22959:3407_1:N:0\tIGA1\t0\t0\t[]\n-M01495:47:000000000-JFBTW:1:2114:24190:4186_1:N:0\tIGM\t100\t100\t[289]\n-M01495:47:000000000-JFBTW:1:2114:13069:4325_1:N:0\tIGM\t100\t100\t[308]\n-M01495:47:000000000-JFBTW:1:2114:5957:4390_1:N:0:\tIGM\t100\t100\t[298]\n-M01495:47:000000000-JFBTW:1:2114:16302:4519_1:N:0\tIGM\t100\t100\t[303]\n-M01495:47:000000000-JFBTW:1:2114:14868:4698_1:N:0\tIGM\t100\t100\t[285]\n-M01495:47:000000000-JFBTW:1:2114:19368:5550_1:N:0\tIGM\t100\t100\t[271]\n-M01495:47:000000000-JFBTW:1:2114:10965:5784_1:N:0\tIGM\t100\t100\t[295]\n-M01495:47:000000000-JFBTW:1:2114:18219:6440_1:N:0\tIGM\t100\t100\t[295]\n-M01495:47:000000000-JFBTW:1:2114:21307:6590_1:N:0\tIGM\t100\t100\t[319]\n-M01495:47:000000000-JFBTW:1:2114:19102:6595_1:N:0\tIGM\t100\t100\t[281]\n-M01495:47:000000000-JFBTW:1:2114:10913:6755_1:N:0\tIGM\t100\t100\t[321]\n-M01495:47:000000000-JFBTW:1:2114:13978:6909_1:N:0\tIGM\t100\t100\t[280]\n-M01495:47:000000000-JFBTW:1:2114:20874:6936_1:N:0\tIGM\t100\t100\t[285]\n-M01495:47:000000000-JFBTW:1:2114:5302:7234_1:N:0:\tIGM\t100\t100\t[273]\n-M01495:47:000000000-JFBTW:1:2114:14919:7492_1:N:0\tIGM\t100\t100\t[279]\n-M01495:47:000000000-JFBTW:1:2114:23354:7866_1:N:0\tIGM\t100\t100\t[295]\n-M01495:47:000000000-JFBTW:1:2114:10928:8128_1:N:0\tIGM\t100\t100\t[303]\n-M01495:47:000000000-JFBTW:1:2114:4116:8288_1:N:0:\tIGM\t100\t50\t[]\n-M01495:47:000000000-JFBTW:1:2114:8381:9107_1:N:0:\tIGM\t100\t50\t[]\n-M01495:47:000000000-JFBTW:1:2114:10555:9479_1:N:0\tIGM\t'..b'\n-M02948:184:000000000-JK6TB:1:1117:17568:12931_1:N\tIGM\t100\t100\t[307]\n-M02948:184:000000000-JK6TB:1:1117:13865:12988_1:N\tIGM\t100\t100\t[289]\n-M02948:184:000000000-JK6TB:1:1117:9587:13647_1:N:\tIGM\t100\t100\t[312]\n-M02948:184:000000000-JK6TB:1:1117:10682:13806_1:N\tIGM\t100\t100\t[300]\n-M02948:184:000000000-JK6TB:1:1117:19261:13898_1:N\tIGM\t100\t100\t[316]\n-M02948:184:000000000-JK6TB:1:1117:10606:13930_1:N\tIGM\t100\t100\t[286]\n-M02948:184:000000000-JK6TB:1:1117:12150:14058_1:N\tIGM\t100\t100\t[318]\n-M02948:184:000000000-JK6TB:1:1117:4760:14520_1:N:\tIGM\t100\t100\t[285]\n-M02948:184:000000000-JK6TB:1:1117:15450:14732_1:N\tIGM\t100\t100\t[310]\n-M02948:184:000000000-JK6TB:1:1117:17421:15079_1:N\tIGM\t100\t100\t[285]\n-M02948:184:000000000-JK6TB:1:1117:21456:15379_1:N\tIGM\t100\t100\t[286]\n-M02948:184:000000000-JK6TB:1:1117:23384:16050_1:N\tIGM\t100\t100\t[264]\n-M02948:184:000000000-JK6TB:1:1117:22041:16080_1:N\tIGM\t100\t100\t[301]\n-M02948:184:000000000-JK6TB:1:1117:26980:17333_1:N\tIGM\t100\t100\t[280]\n-M02948:184:000000000-JK6TB:1:1117:14804:18251_1:N\tIGM\t100\t100\t[288]\n-M02948:184:000000000-JK6TB:1:1117:16950:18819_1:N\tIGM\t100\t100\t[289]\n-M02948:184:000000000-JK6TB:1:1117:16290:19394_1:N\tIGM\t100\t100\t[291]\n-M02948:184:000000000-JK6TB:1:1117:20297:19526_1:N\tIGM\t100\t100\t[297]\n-M02948:184:000000000-JK6TB:1:1117:5982:19890_1:N:\tIGM\t100\t100\t[298]\n-M02948:184:000000000-JK6TB:1:1117:5843:20401_1:N:\tIGM\t100\t100\t[298]\n-M02948:184:000000000-JK6TB:1:1117:27074:20847_1:N\tIGM\t100\t100\t[285]\n-M02948:184:000000000-JK6TB:1:1117:14131:21761_1:N\tIGM\t100\t100\t[310]\n-M02948:184:000000000-JK6TB:1:1117:24033:21804_1:N\tIGM\t100\t100\t[295]\n-M02948:184:000000000-JK6TB:1:1117:22906:22438_1:N\tIGM\t100\t100\t[312]\n-M02948:184:000000000-JK6TB:1:1117:9507:23245_1:N:\tIGM\t100\t100\t[292]\n-M02948:184:000000000-JK6TB:1:1117:14223:24761_1:N\tIGM\t100\t100\t[280]\n-M02948:184:000000000-JK6TB:1:2119:23556:2103_1:N:\tIGM\t100\t100\t[289]\n-M02948:184:000000000-JK6TB:1:2119:18568:2463_1:N:\tIGM\t100\t100\t[294]\n-M02948:184:000000000-JK6TB:1:2119:25354:3692_1:N:\tIGM\t100\t100\t[298]\n-M02948:184:000000000-JK6TB:1:2119:25840:3796_1:N:\tIGM\t100\t100\t[294]\n-M02948:184:000000000-JK6TB:1:2119:18102:4158_1:N:\tIGM\t100\t100\t[292]\n-M02948:184:000000000-JK6TB:1:2119:19008:4548_1:N:\tIGM\t100\t100\t[301]\n-M02948:184:000000000-JK6TB:1:2119:26295:5166_1:N:\tIGM\t100\t100\t[304]\n-M02948:184:000000000-JK6TB:1:2119:8781:7984_1:N:0\tIGM\t100\t100\t[330]\n-M02948:184:000000000-JK6TB:1:2119:27777:9754_1:N:\tIGM\t100\t100\t[309]\n-M02948:184:000000000-JK6TB:1:2119:14209:10051_1:N\tIGM\t100\t100\t[285]\n-M02948:184:000000000-JK6TB:1:2119:27849:10307_1:N\tIGM\t100\t100\t[309]\n-M02948:184:000000000-JK6TB:1:2119:29402:10613_1:N\tIGM\t100\t100\t[298]\n-M02948:184:000000000-JK6TB:1:2119:18492:10696_1:N\tIGM\t100\t100\t[282]\n-M02948:184:000000000-JK6TB:1:2119:25677:12561_1:N\tIGM\t100\t100\t[294]\n-M02948:184:000000000-JK6TB:1:2119:20993:15005_1:N\tIGM\t100\t100\t[297]\n-M02948:184:000000000-JK6TB:1:2119:17307:15015_1:N\tIGM\t100\t100\t[285]\n-M02948:184:000000000-JK6TB:1:2119:1886:15267_1:N:\tIGM\t100\t100\t[303]\n-M02948:184:000000000-JK6TB:1:2119:13588:15982_1:N\tIGM\t100\t100\t[263]\n-M02948:184:000000000-JK6TB:1:2119:5420:16684_1:N:\tIGM\t100\t100\t[271]\n-M02948:184:000000000-JK6TB:1:2119:15460:16883_1:N\tIGM\t100\t100\t[306]\n-M02948:184:000000000-JK6TB:1:2119:25603:17304_1:N\tIGM\t100\t100\t[295]\n-M02948:184:000000000-JK6TB:1:2119:7541:17447_1:N:\tIGM\t100\t100\t[315]\n-M02948:184:000000000-JK6TB:1:2119:7468:18468_1:N:\tIGM\t100\t100\t[283]\n-M02948:184:000000000-JK6TB:1:2119:13724:18826_1:N\tIGM\t100\t50\t[]\n-M02948:184:000000000-JK6TB:1:2119:6580:18915_1:N:\tIGM\t100\t100\t[309]\n-M02948:184:000000000-JK6TB:1:2119:11269:19571_1:N\tIGM\t100\t100\t[276]\n-M02948:184:000000000-JK6TB:1:2119:13202:20116_1:N\tIGM\t100\t100\t[279]\n-M02948:184:000000000-JK6TB:1:2119:26324:20804_1:N\tIGM\t100\t100\t[282]\n-M02948:184:000000000-JK6TB:1:2119:20335:21283_1:N\tIGM\t100\t100\t[291]\n-M02948:184:000000000-JK6TB:1:2119:15289:21461_1:N\tIGM\t100\t100\t[312]\n-M02948:184:000000000-JK6TB:1:2119:8379:22530_1:N:\tIGM\t100\t100\t[285]\n-M02948:184:000000000-JK6TB:1:2119:18285:24809_1:N\tIGM\t100\t100\t[315]\n' |
| b |
| diff -r 84e9e5c8c101 -r d63eff357515 shm_csr.xml --- a/shm_csr.xml Fri Mar 24 16:58:28 2023 +0000 +++ b/shm_csr.xml Mon Mar 27 13:11:53 2023 +0000 |
| [ |
| @@ -1,4 +1,4 @@ -<tool id="shm_csr" name="SHM & CSR pipeline" version="1.8.0" profile="16.04"> +<tool id="shm_csr" name="SHM & CSR pipeline" version="1.8.1" profile="16.04"> <description></description> <requirements> <requirement type="package" version="3.7.1">python</requirement> @@ -22,12 +22,13 @@ </requirements> <command interpreter="bash"> <![CDATA[ - #set $input=$in_file.name + #import os + #set $input=os.path.basename($in_file.name) ln -s "$in_file" "$input" && #if str ( $filter_unique.filter_unique_select ) == "remove": $__tool_directory__/wrapper.sh "$input" custom $out_file $out_file.files_path - "${in_file.name}" "-" $functionality $unique + "$input" "-" $functionality $unique $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 @@ -146,13 +147,13 @@ <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}"> + <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}"> + <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> |
| b |
| diff -r 84e9e5c8c101 -r d63eff357515 show_time_as_float |
| b |
| Binary file show_time_as_float has changed |
| b |
| diff -r 84e9e5c8c101 -r d63eff357515 tests/.pytest_cache/.gitignore --- a/tests/.pytest_cache/.gitignore Fri Mar 24 16:58:28 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,2 +0,0 @@ -# Created by pytest automatically. -* |
| b |
| diff -r 84e9e5c8c101 -r d63eff357515 tests/.pytest_cache/CACHEDIR.TAG --- a/tests/.pytest_cache/CACHEDIR.TAG Fri Mar 24 16:58:28 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,4 +0,0 @@ -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 84e9e5c8c101 -r d63eff357515 tests/.pytest_cache/README.md --- a/tests/.pytest_cache/README.md Fri Mar 24 16:58:28 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,8 +0,0 @@ -# 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 84e9e5c8c101 -r d63eff357515 tests/.pytest_cache/v/cache/lastfailed --- a/tests/.pytest_cache/v/cache/lastfailed Fri Mar 24 16:58:28 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,25 +0,0 @@ -{ - "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 |
| b |
| diff -r 84e9e5c8c101 -r d63eff357515 tests/.pytest_cache/v/cache/nodeids --- a/tests/.pytest_cache/v/cache/nodeids Fri Mar 24 16:58:28 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,25 +0,0 @@ -[ - "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 84e9e5c8c101 -r d63eff357515 tests/.pytest_cache/v/cache/stepwise --- a/tests/.pytest_cache/v/cache/stepwise Fri Mar 24 16:58:28 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,1 +0,0 @@ -[] \ No newline at end of file |
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| diff -r 84e9e5c8c101 -r d63eff357515 tests/data/.~lock.handleiding activeren pas.docx# --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tests/data/.~lock.handleiding activeren pas.docx# Mon Mar 27 13:11:53 2023 +0000 |
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| @@ -0,0 +1,1 @@ +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 84e9e5c8c101 -r d63eff357515 wrapper.sh --- a/wrapper.sh Fri Mar 24 16:58:28 2023 +0000 +++ b/wrapper.sh Mon Mar 27 13:11:53 2023 +0000 |
| [ |
| @@ -23,10 +23,10 @@ class_filter=${19} empty_region_filter=${20} fast=${21} - -BASENAME=$(basename $input) -# Cut off .txz or .tgz suffix +BASENAME=$(basename "$input") +# Cut off .txz or .tgz suffix and also replace spaces with underscores. NEW_IMGT_PREFIX="new_IMGT_${BASENAME%.*}" +NEW_IMGT_PREFIX=${NEW_IMGT_PREFIX// /_} #exec 5> debug_output.txt #BASH_XTRACEFD="5" @@ -44,16 +44,16 @@ echo "unpacking IMGT file" -type="`file -L $input`" +type="$(file -L "$input")" if [[ "$type" == *"Zip archive"* ]] ; then echo "Zip archive" echo "unzip $input -d $PWD/files/" - unzip $input -d $PWD/files/ + unzip "$input" -d $PWD/files/ elif [[ "$type" == *"XZ compressed data"* ]] ; then echo "ZX archive" - echo "tar -xJf $input -C $PWD/files/" + echo "tar -xJf "$input" -C $PWD/files/" mkdir -p "$PWD/files/$title" - tar -xJf $input -C "$PWD/files/$title" + tar -xJf "$input" -C "$PWD/files/$title" else echo "Unrecognized format $type" echo "Unrecognized format $type" > $log @@ -112,7 +112,7 @@ echo "---------------- creating new IMGT zips ----------------" echo "---------------- creating new IMGT zips ----------------<br />" >> $log -python $dir/split_imgt_file.py --outdir $outdir $input $outdir/merged.txt \ +python $dir/split_imgt_file.py --outdir $outdir "$input" $outdir/merged.txt \ --prefix "${NEW_IMGT_PREFIX}" \ - IGA IGA1 IGA2 IGG IGG1 IGG2 IGG3 IGG4 IGM IGE |