Jeremy Volkening jvolkening
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| diff -rupN '--exclude=.git' cutadapt/cutadapt/report.py cutadapt_patched/cutadapt/report.py | |
| --- cutadapt/cutadapt/report.py 2015-03-26 13:00:26.163894349 -0500 | |
| +++ cutadapt_patched/cutadapt/report.py 2015-03-26 12:58:56.944023106 -0500 | |
| @@ -252,3 +252,55 @@ def print_statistics(adapters_pair, pair | |
| print(' Please see the detailed output above.') | |
| sys.stdout = old_stdout | |
| + | |
| +def print_succinct(adapters_pair, paired, stats, | |
| + modifiers, modifiers2, writers, file=None): |
jvolkening
/ gist:a605754053356a53e35dadac7466a3b7
Created
May 28, 2016 20:32
snippet from phyml.xml
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| <inputs> | |
| <conditional name="support_condition"> | |
| <param name="branchSupport" type="select"> | |
| <option value="0">No bootstrap</option> | |
| <option value="1">Bootstrap</option> | |
| <option value="-1">likelihood aLRT statistics</option> | |
| <option value="-2">likelihood Chi2-based</option> | |
| <option value="-4" selected='true'>SH-like</option> | |
| <option value="-5">Approximate Bayes branch supports</option> | |
| </param> |
jvolkening
/ example_collection_workflow.png
Last active
November 26, 2016 04:57
jvolkening
/ mzml_reindex.pl
Created
February 23, 2017 06:10
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| #!/usr/bin/env perl | |
| # re-calculates index offsets and SHA1 sum for indexed mzML file that has been | |
| # modified for some reason | |
| use strict; | |
| use warnings; | |
| use XML::Parser; | |
| use Digest::SHA; |
jvolkening
/ gist:9d09edfedb997dc8be3d1dc87fb0d709
Created
March 8, 2017 14:53
percolator_concat_stderr
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| Percolator version 3.01, Build Date Nov 16 2016 14:58:22 | |
| Copyright (c) 2006-9 University of Washington. All rights reserved. | |
| Written by Lukas Käll (lukall@u.washington.edu) in the | |
| Department of Genome Sciences at the University of Washington. | |
| Issued command: | |
| percolator -t 0.02 -m test.concat.psm.tsv -r test.concat.pep.tsv test.concat.pin | |
| Started Wed Mar 8 08:48:30 2017 | |
| Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 | |
| Reading tab-delimited input from datafile test.concat.pin | |
| Features: |
jvolkening
/ gist:94d2bad18b906ed09c6dc8859ca88b27
Created
March 8, 2017 14:55
percolator_sep_stderr
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| Percolator version 3.01, Build Date Nov 16 2016 14:58:22 | |
| Copyright (c) 2006-9 University of Washington. All rights reserved. | |
| Written by Lukas Käll (lukall@u.washington.edu) in the | |
| Department of Genome Sciences at the University of Washington. | |
| Issued command: | |
| percolator -Y -t 0.02 -m test.sep.psm.tsv -r test.sep.pep.tsv test.sep.pin | |
| Started Wed Mar 8 08:47:56 2017 | |
| Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 | |
| Reading tab-delimited input from datafile test.sep.pin | |
| Features: |
jvolkening
/ test_1000.fq
Created
June 26, 2018 03:23
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| @SALLY:297:D1JLYACXX:7:1101:9691:17720 1:N:0: | |
| AATTTTAGTCATGACAATAAATATAATACAGGAATAGTAGCTGATATGTTTTTAGTATTTACCATTTAAAATTTCCTTGCAATGTATTGTTATTCATGTCT | |
| + | |
| CCCFFFFFHHHHHJJJJJJJJJJJJJIJJJJJJJJIIHIIIJJGJJJJJJIJJHIGIIIJJIIJJJJJJJJJJJJHIJJJJJJJIHHHHHHHFFFFFFFED | |
| @SALLY:297:D1JLYACXX:7:1101:9506:17722 1:N:0: | |
| AATAATAATTACCTGTATTAGTACATTATTTAATTGTACCAAATCTCTTATATATAGTTAGTTCAGATATTTGGGGGGCTTTCCAGGTAGCTCAGTCGTAA | |
| + | |
| CCCFFFFFHHHHHJJHIJJJJHIJJJJJJJJGHIJIHIJJJJJJJJJJJJJIJJIJJJJJJIJJIJJIJIJJJJJHIDDDDDDDEDDCDDDDDDDDDDDDD | |
| @SALLY:297:D1JLYACXX:7:1101:9656:17723 1:N:0: | |
| CTACAGTTTATTTTTATTCATTTAATTTTTTTTTTTAACTTACATTTTGGAGAAGGAAATGGCAACCCACTCCAGGACTCTCTCCTGGAAAATACCATGGA |
jvolkening
/ test_100.fq
Created
November 25, 2018 17:47
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| @M03709:10:000000000-AHW42:1:2106:18413:15530 1:N:0:AAGAGGCA+ACTGCATA | |
| GCGCACCACCGGCCCGTCTCGCCCGCCTCGCCGGGGAGGTGGAGCATGAGCGCGCGTGCTAGGACCCGAAAGATGGTGAACTATGCCTGGGCAGGGCGAAGCCAGAGGAAACTCTGGTGGAGGTCCGTAGCGGTCCTGACGTGCAAATCGGTCGTCCGACCCGGGTATAGGGGCGAAAGACTAATCGAACCATCTAGTAGCTGGTTCCCTCCGAAGTTTCCCCAGGATAGCTGGCGCTCGGGGCGGCGGTG | |
| + | |
| AABCCCCFCCCCGGGGGGGGGGGGGGGGGGGGCGGGGFFEHGHHHEGHHHHGGGGGGGGGHHHHHHGG@FGGHGHHGHHHHHHHHHHGHHGHGGGGGGGGGGHHGGFGEHHHHHHHGGHDHHGGHHGHGGGGGADGGFGGGCAFGGEFGGFFFFFFFFFFFFFFA.@FFFFFDFFFCFFFFFFFFFFFFFFFFFFFFBFBFFFFFFFFFFFFFDFF9FFFFFFF?EFFFEFFBFFFFFFFFAAAFFCFB-- | |
| @M03709:10:000000000-AHW42:1:2106:11146:15531 1:N:0:AAGAGGCA+ACTGCATA | |
| CCTCAGGATAGCTGGCGCTCGGGGCGGCGGTGCAGTTTTACCCGGTAAAGCGAATGATTAGAGGTCTTGGGGCCGAAACGATCTCAACCTATTCTCAAACTTTCAATGGGTAAGACGCCCGGCTCGCTGGCGTGGAGCCGGGCCGTGGAATGCGAGCGCTCAGTGGGCCACTTTTGGTAAGCAGAACTGGCGCTGCGGGATGAACCGAACGCCGGGTTAAGGCGCCCGATGCCGACGCTCATCAGAGCCCA | |
| + | |
| AAAABFFF4DFBGFBAE2AEE??EGGGGGGGEEEHEGBGHHF?E>>EFFFGGGCEHFFHH3GGFB0GFDFCC<BCGCGCGFHEHHHG0GHHFHHDBDDFFFHHGGHHGFF<0GDFHD@DCC-@@ |
jvolkening
/ test_1000_new.fq
Created
November 25, 2018 17:53
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| @M03709:10:000000000-AHW42:1:2106:18711:1744 1:N:0:AAGAGGCA+ACTGCATA | |
| TATTCGTACTGAAAATCAAGATCAAGCGAGCTTTTGCCCTTCTGCTCCACGGGAGGTTTCTGGCCTCCCTGAGCTCGCCTTAGGACACCTGCGTTACGCTTTGACAGGTGTACCGCCCCAGTCAAACTCCCCACCTGACGCTGTCCCCGGAGCGGGGACAGCGTCAGGTGGGGAGTTTGACTGGGGCGGTACACCTGTCAAAGCG | |
| + | |
| >1>>>1B1>A3311DGG1111BB111B000EGHHHFGFGHHGHBAFFAAF////A?EFGFG21AAFGGGHC0BFGGAEEEE1111B0BFG0FCEGFFFEF/?12B11/BBFFFF/<<<<//@@121FGFGCBCCCG000/<<.<1<<G@?--@-----9..9-;A9?B;B.9---9;B//BF/A--A-----/99//99////BB | |
| @M03709:10:000000000-AHW42:1:2106:16158:1799 1:N:0:AAGAGGCA+ACTGCATA | |
| ACTTTAAATCCTTTAACGAGGATCCATTGGAGGGCAAGTCTGGTGCCAGCAGCCGCGGTAATTCCAGCTCCAATAGCGTATATTAAAGTTGCTGCAGTTAAAAAGCTCGTAGTTGGAT | |
| + | |
| 1>AAA331DD@FGGCGGE1110ACFBHHFFHHGGGGGFHHHHCG01A11/A0AGEG??E//FGDF2DGFFHGFGHHHGE?E1FE221BFFDFFHHHHHFFFD11/>FHEGCGGHB11< | |
| @M03709:10:000000000-AHW42:1:2106:12433:1810 1:N:0:AAGAGGCA+ACTGCATA | |
| GTTCAGACATTTGGTGTATGTGCTTGGCTGAGGAGCCACTGGAGCGAGGCTACCATCTGTGGGATTATGACTGAACGCCTCTAAGTCAGAATCCCCCCTAAAC |
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