Commands are:
cpan
install Module::Build
when makepl_arg etc. are set to a non-standard, local folder.
Error message is:
Philipp Bayer philippbayer
philippbayer
/ problems.md
Last active
February 11, 2016 04:31
Solution for weird Module::Build install bug under perl
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| >cat /etc/*-release | |
| Fedora release 23 (Twenty Three) | |
| [more about Fedora I deleted] | |
| >cat /proc/version | |
| Linux version 4.3.3-301.fc23.x86_64 ([email protected]) (gcc version 5.3.1 20151207 (Red Hat 5.3.1-2) (GCC) ) #1 SMP Fri Jan 15 14:03:17 UTC 2016 | |
| >javac -version | |
| javac 1.8.0_71 | |
| >java -version | |
| openjdk version "1.8.0_71" | |
| OpenJDK Runtime Environment (build 1.8.0_71-b15) |
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| <!DOCTYPE html> | |
| <meta charset="utf-8"> | |
| <style> | |
| .node { | |
| stroke: #fff; | |
| stroke-width: 1.5px; | |
| } | |
| .link { |
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| <!DOCTYPE html> | |
| <meta charset="utf-8"> | |
| <style> | |
| .node { | |
| stroke: #fff; | |
| stroke-width: 1.5px; | |
| } | |
| .link { |
philippbayer
/ plot_gene_covs.R
Last active
November 11, 2015 09:01
This R script creates a nice faceted plot of read coverage of reads based on bedtools genomecov -d output, to which one column with gene names was added
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| # Fileformat is | |
| # Gene Chr Pos Cov | |
| # gene_A A01 40 0 | |
| # gene_A A01 41 2 | |
| # ... | |
| # gene_D A01 508 41 | |
| # gene_D A01 509 42 | |
| # ... | |
| geneCov <- read.table("./test_genes.txt", sep="\t", header=F) |
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| urls={"1":"ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/release/20130502/ALL.chr1.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz", | |
| "10":"ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/release/20130502/ALL.chr10.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz", | |
| "11":"ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/release/20130502/ALL.chr11.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz", | |
| "12":"ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/release/20130502/ALL.chr12.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz", | |
| "13":"ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/release/20130502/ALL.chr13.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz", | |
| "14":"ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/release/20130502/ALL.chr14.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz", | |
| "15":"ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/release/20130502/ALL.chr15.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz", | |
| "16": |
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| In R: | |
| png("heatmap_before_sorting.png") | |
| image(distance_matrix) | |
| dev.off() | |
| library("gclus") | |
| ordered <- order.single(distance_matrix, clusters=NULL) | |
| sorted_matrix <- distance_matrix[ordered, ordered] | |
| In Python: |
philippbayer
/ similarity.py
Created
January 3, 2014 05:35
My solution for "String Similarity" for HackerRank
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| def get_similarity(a, suffix): | |
| from itertools import izip | |
| score = 0 | |
| for a, b in izip(a, suffix): | |
| if a != b: | |
| break | |
| score += 1 | |
| return score | |
| def stringSimilarity(a): |
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| SELECT query, calls, total_time, rows, 100.0 * shared_blks_hit | |
| nullif(shared_blks_hit + shared_blks_read, 0) AS hit_percent | |
| FROM pg_stat_statements ORDER BY total_time DESC LIMIT 5; | |
| -- | |
| query | calls | total_time | rows | hit_percent | |
| ----------------------------------------------------------------------------------------------------------- |
philippbayer
/ natural_sort.go
Last active
June 30, 2019 18:00
A perverted kind of natural sort in golang
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| package main | |
| import ( | |
| "fmt" | |
| "log" | |
| "sort" | |
| "strconv" | |
| "strings" | |
| "unicode" | |
| ) |