Mike Dacre MikeDacre
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| Server packet stats: | |
| packets udp tcp tcpconn | |
| 506158 0 505786 106 | |
| Server rpc stats: | |
| calls badcalls badauth badclnt xdrcall | |
| 506154 0 0 0 0 | |
| Server reply cache: | |
| hits misses nocache |
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| START eqtlbma 2014-10-23 15:43:38 | |
| version 1.2 compiled Oct 23 2014 15:01:56 | |
| cmd-line: eqtlbma --geno list_genotypes.txt --scoord snp_coords.bed.gz --pheno list_explevels.txt --fcoord gene_coords.bed.gz --anchor TSS --cis 1000 --out out_eqtlbma --step 3 --covar list_covariates.txt --gridL grid_phi2_oma2_general.txt --gridS grid_phi2_oma2_with-configs.txt --bfs all --mvlr | |
| cwd: /home/mike/my_packages/eqtlbma-git/eqtlbma_tutorial_data | |
| load file list_explevels.txt ... | |
| items loaded: 3 | |
| load file list_genotypes.txt ... | |
| items loaded: 3 | |
| load samples ... | |
| nb of samples (phenotypes): 200 |
MikeDacre
/ syslog.log
Last active
August 29, 2015 14:07
Kernel error log from 2014-10-13, fraser-server, USB3 related bugs
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| Oct 13 09:25:50 fraser-server kernel: [774197.362929] usb 2-3: USB disconnect, device number 2 | |
| Oct 13 09:25:50 fraser-server kernel: [774197.362931] usb 2-3.1: USB disconnect, device number 3 | |
| Oct 13 09:25:50 fraser-server kernel: [774197.362933] usb 2-3.1.1: USB disconnect, device number 7 | |
| Oct 13 09:25:50 fraser-server kernel: [774197.364620] sd 12:0:0:0: [sdj] Synchronizing SCSI cache | |
| Oct 13 09:25:50 fraser-server kernel: [774197.373022] usb 1-3.1-port2: cannot reset (err = -71) | |
| Oct 13 09:25:50 fraser-server kernel: [774197.373519] usb 1-3.1-port2: cannot reset (err = -71) | |
| Oct 13 09:25:50 fraser-server kernel: [774197.374019] usb 1-3.1-port2: cannot reset (err = -71) | |
| Oct 13 09:25:50 fraser-server kernel: [774197.374518] usb 1-3.1-port2: cannot reset (err = -71) | |
| Oct 13 09:25:50 fraser-server kernel: [774197.375019] usb 1-3.1-port2: cannot reset (err = -71) | |
| Oct 13 09:25:50 fraser-server kernel: [774197.375020] usb 1-3.1-port2: Cannot enable. Maybe the USB cable is bad? |
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| #!/usr/bin/env python3 | |
| # -*- coding: utf-8 -*- | |
| # vim:fenc=utf-8 tabstop=4 expandtab shiftwidth=4 softtabstop=4 | |
| """ | |
| #==================================================================================== | |
| # | |
| # FILE: logme (python 3) | |
| # AUTHOR: Michael D Dacre, [email protected] | |
| # ORGANIZATION: Stanford University | |
| # LICENSE: Open Source - Public - Do as you wish (no license) - Mike Dacre |
MikeDacre
/ get_chromosome_length.py
Last active
August 29, 2015 14:04
Take a list of FastA files (or just one file) and count the length of the chromosome
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| #!/usr/bin/env python3 | |
| # -*- coding: utf-8 -*- | |
| # vim:fenc=utf-8 tabstop=4 expandtab shiftwidth=4 softtabstop=4 | |
| # | |
| # Copyright © Mike Dacre <[email protected]> | |
| # | |
| # Distributed under terms of the MIT license | |
| """ | |
| #==================================================================================== | |
| # |
MikeDacre
/ cnvnator_mouse.patch
Last active
August 29, 2015 14:04
Patch for http://sv.gersteinlab.org/cnvnator/ including the black6 genome
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| Only in ./: cnvnator | |
| diff -u ../../../CNVnator_v0.3/src/cnvnator.cpp ./cnvnator.cpp | |
| --- ../../../CNVnator_v0.3/src/cnvnator.cpp 2014-02-01 20:29:35.000000000 -0800 | |
| +++ ./cnvnator.cpp 2014-07-21 13:06:23.022155584 -0700 | |
| @@ -39,7 +39,7 @@ | |
| usage += argv[0]; | |
| usage += " -pe file1.bam ... -qual val(20) -over val(0.8) [-f file]\n"; | |
| usage += "\n"; | |
| - usage += "Valid genomes (-genome option) are: NCBI36, hg18, GRCh37, hg19\n"; | |
| + usage += "Valid genomes (-genome option) are: NCBI36, hg18, GRCh37, hg19, black6\n"; |
MikeDacre
/ bed2vcf.py
Last active
January 8, 2016 21:29
Convert simplified bed file(s) plus a reference genome into a vcf file. Formats in source.
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| #!/usr/bin/env python3 | |
| # -*- coding: utf-8 -*- | |
| # Distributed under terms of the MIT license | |
| """ | |
| ================================================================================ | |
| FILE: bed2vcf (python 3) | |
| AUTHOR: Michael D Dacre, [email protected] | |
| ORGANIZATION: Stanford University | |
| LICENSE: MIT License, Property of Stanford, Use as you wish |
MikeDacre
/ vcf_simplify.py
Last active
January 4, 2016 04:28
Simplify a 1000genomes vcf file to a smaller file with all genotypes encoded as 0/1/2, where 0: homozygote 1; 1: heterozygote; 2:homozygote 2
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| #!/usr/bin/env python3 | |
| # -*- coding: utf-8 -*- | |
| # vim:fenc=utf-8 tabstop=4 expandtab shiftwidth=4 softtabstop=4 | |
| # | |
| # Copyright © Mike Dacre <[email protected]> | |
| # | |
| # Distributed under terms of the MIT license | |
| """ | |
| =============================================================================== |
MikeDacre
/ std-arg.py
Last active
December 21, 2015 17:59
Cumbersome python3 functions to give user the choice between either using STDIN, STDOUT, STDERR, or using -i, -o, and -l. The idea is that we want to use the protection of a `with"` statement if using the '-i' and '-o' flags for input and output files, while still allowing the use of STDIN and STDERR. It makes use of sys and argparse. It is cumb…
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| #!/usr/bin/env python3 | |
| # -*- coding: utf-8 -*- | |
| # vim:fenc=utf-8 tabstop=4 expandtab shiftwidth=4 softtabstop=4 | |
| """ | |
| #==================================================================================== | |
| # | |
| # FILE: std-arg.py | |
| # AUTHOR: Michael D Dacre, [email protected] | |
| # LICENSE: Open Source | |
| # CREATED: 2013-08-26 10:56 |
MikeDacre
/ selective-backup.py
Last active
December 14, 2015 07:48
A simple backup program to create a selective backup by duplicating a directory tree with hard links. This allows users to choose only the files they wish backed up. It requires a third party backup solution (e.g. rsync or CrashPlan), to do the actual backup. The script allows users to choose the backup location, and also uses `find` to search t…
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| #!/bin/env python3 | |
| dsript="""\ | |
| #=============================================================================== | |
| # | |
| # FILE: selective-backup.py | |
| # | |
| # USAGE: ./selective-backup.py [-o] [-l] [-r] file1 [file2]...[folder1... | |
| # | |
| # DESCRIPTION: Duplicate a directory to a given location using only hard links | |
| # REQUIREMENTS: python3 |