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Pierre Lindenbaum lindenb

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@lindenb
lindenb / chatGPT. monopoly.md
Created April 23, 2023 16:37
Génère moi un jeu de plateau inspiré de #Monopoly se situant dans un labo de Recherche en génétique. L'argent est remplacé par des publications.

Pas de problème, voici les règles pour un jeu de plateau inspiré de Monopoly, mais situé dans un laboratoire de recherche en génétique, où les joueurs achètent des laboratoires plutôt que des propriétés :

Matériel :

  • Plateau de jeu
  • Cartes "Chercheurs invités"
  • Cartes "Subventions"
  • Pions (molécule d'ADN, microscope, fiole, pipette, gant de laboratoire)
  • Billets de publications scientifiques (au lieu d'argent)
  • Laboratoires (au lieu de propriétés)
@lindenb
lindenb / README.md
Last active February 15, 2023 21:21
Biostar Images vs text carbon planet climate

Don't upload images when you can just copy and paste the text.

The following PNG image has a weight of 357,000 bytes

https://www.biostars.org/media/images/8be0316c-0f5a-4e5b-a769-1e4d0afb

while the text containing the very same information is about only 1,109 bytes, hence a much lower carbon footprint.

##sequence-region JAFJXZ010000052.1 1 250
@lindenb
lindenb / biostars9550377.nf
Last active January 6, 2023 18:05
biostars9550377 "speeding up bcftools view"
/* author Pierre Lindenbaum */
params.vcfs="NO_FILE"
params.samples="NO_FILE"
workflow {
each_vcf = Channel.fromPath(params.vcfs).splitText().map{it.trim()}
c2vcf = CHROMS_IN_VCF(each_vcf)

with include{MyTest}

Cannot find a component with name 'MyTest' in module: .../20230103.nf.class/./class.nf

 -- Check script 'test.nf' at line: 2 or see '.nextflow.log' file for more details

without include{MyTest}

@lindenb
lindenb / Makefile
Created September 22, 2022 19:33
biostar9539326.c proper way to alter bgzf-compressed fastq files using htslib, multithreaded
CC?=gcc
ifeq ($(HTSLIB),)
$(error undefined $$HTSLIB)
endif
CFLAGS= -Wall -O3 -I$(HTSLIB)
LDFLAGS= -L$(HTSLIB) -lz -lhts
@lindenb
lindenb / Biostar9532375.java
Created July 26, 2022 21:38
Biostar9532375 Remove redundant nucleotide sequences in a FASTA file containing ambiguous N
import java.io.*;
import java.util.*;
public class Biostar9532375 {
private static class Sequence {
String name;
StringBuilder seq=new StringBuilder();
boolean same(char c1,char c2) {
if(c1==c2) return true;
if(c1=='N' || c2=='N') return true;
return false;
@lindenb
lindenb / biostar9528296.c
Last active June 23, 2022 07:35
https://www.biostars.org/p/9528296/ How to search the human genome for sequences that differ from a given sequence by a set number of mismatches? C
#include <stdio.h>
#include <string.h>
#include <stdlib.h>
#include <ctype.h>
#define MAX_SEQ_LENGTH 100
static char compl(char c) {
switch(c) {
case 'A': return 'T';
@lindenb
lindenb / Usage.md
Created June 11, 2022 12:49
https://www.biostars.org/p/9526679/ How to merge 20K single-sample VCFs *without* using plink or plink2? #bcftools #nextflow

Usage

find path/to/dir -type f -name "S*.vcf.gz" > jeter.list
nextflow run --vcfs ${PWD}/jeter.list biostar9526718.nf

add -C config.cfg toconfigure your cluster config....

@lindenb
lindenb / biostar9524046.nf
Created May 21, 2022 14:26
biostar9524046.nf https://www.biostars.org/p/9524046/ Forum:Compare the samples in a VCF concordance picard
nextflow.enable.dsl=2
params.vcf=""
workflow {
picard = downloadPicard()
samples_ch = vcf2samples(params.vcf).splitCsv(header: false,sep:'\t',strip:true)
pair_ch = samples_ch.combine(samples_ch).filter{T->!T[1].equals(T[3])}
concordances_ch = concordance(picard,pair_ch)