Renan Valieris rvalieris
rvalieris
/ qpdata_to_geojson.groovy
Created
September 2, 2025 13:42
Converts Qupath qpdata annotations to geojson
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| import static groovy.io.FileType.FILES | |
| def WSI_DIR = '/path/to/WSI/' | |
| def WSI_EXT = '.svs' | |
| def WSI_ANNOTS_DIR = '/path/to/qpdata/annots/' | |
| def WSI_ANNOTS_EXT = '.qpdata' | |
| def OUT_DIR = '/path/to/outputs/' | |
| def wsi_map = [:] |
rvalieris
/ svs_to_tiff.py
Last active
October 26, 2022 17:07
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| import pyvips | |
| a = pyvips.Image.new_from_file('input.svs') | |
| image_desc = a.get('tiff.ImageDescription') | |
| a.set_type(pyvips.GValue.gstr_type, 'image-description', image_desc) | |
| a.tiffsave('output.tif', pyramid=True, tile=True, compression='jpeg', tile_height=256, tile_width=256, Q=80) |
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| import psutil | |
| import random | |
| ports = set(map(lambda k: k.laddr.port,psutil.net_connections())) | |
| print(random.choice(list(set(range(2000,10000)) - ports))) |
rvalieris
/ 0001-uncomment-sysroot-change.patch
Created
September 22, 2018 00:13
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| From ce9d3edd1b0f3397cf6558a650d1a0ee2edbb823 Mon Sep 17 00:00:00 2001 | |
| From: rvalieris <[email protected]> | |
| Date: Fri, 21 Sep 2018 21:16:05 -0300 | |
| Subject: [PATCH] uncomment sysroot change | |
| --- | |
| recipe/build.sh | 30 ++++++++++++++++-------------- | |
| 1 file changed, 16 insertions(+), 14 deletions(-) | |
| diff --git a/recipe/build.sh b/recipe/build.sh |
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| library(signeR) | |
| library(VariantAnnotation) | |
| library(BSgenome.Hsapiens.UCSC.hg19) | |
| library(BiocParallel) | |
| register(MulticoreParam(workers=5)) # use 5 cores | |
| vcf = readVcf("a.vcf") | |
| split_vcf = split(vcf,ceiling(seq_along(vcf)/1000)) # split vcf into chunks of 1000 rows |
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| #!/usr/bin/env python3 | |
| import requests | |
| import hashlib | |
| import getpass | |
| password = getpass.getpass() | |
| hash = hashlib.sha1(password.encode("utf8")).hexdigest().upper() | |
| head, rest = hash[:5], hash[5:] | |
| r = requests.get("https://api.pwnedpasswords.com/range/%s" % head) |
rvalieris
/ gen_mat2.R
Created
May 2, 2018 16:59
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| change_triplet <- c( | |
| "C>A:ACA","C>A:ACC","C>A:ACG","C>A:ACT","C>A:CCA","C>A:CCC","C>A:CCG", | |
| "C>A:CCT","C>A:GCA","C>A:GCC","C>A:GCG","C>A:GCT","C>A:TCA","C>A:TCC", | |
| "C>A:TCG","C>A:TCT","C>G:ACA","C>G:ACC","C>G:ACG","C>G:ACT","C>G:CCA", | |
| "C>G:CCC","C>G:CCG","C>G:CCT","C>G:GCA","C>G:GCC","C>G:GCG","C>G:GCT", | |
| "C>G:TCA","C>G:TCC","C>G:TCG","C>G:TCT","C>T:ACA","C>T:ACC","C>T:ACG", | |
| "C>T:ACT","C>T:CCA","C>T:CCC","C>T:CCG","C>T:CCT","C>T:GCA","C>T:GCC", | |
| "C>T:GCG","C>T:GCT","C>T:TCA","C>T:TCC","C>T:TCG","C>T:TCT","T>A:ATA", | |
| "T>A:ATC","T>A:ATG","T>A:ATT","T>A:CTA","T>A:CTC","T>A:CTG","T>A:CTT", |
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| change_triplet <- c( | |
| "C>A:ACA","C>A:ACC","C>A:ACG","C>A:ACT","C>A:CCA","C>A:CCC","C>A:CCG", | |
| "C>A:CCT","C>A:GCA","C>A:GCC","C>A:GCG","C>A:GCT","C>A:TCA","C>A:TCC", | |
| "C>A:TCG","C>A:TCT","C>G:ACA","C>G:ACC","C>G:ACG","C>G:ACT","C>G:CCA", | |
| "C>G:CCC","C>G:CCG","C>G:CCT","C>G:GCA","C>G:GCC","C>G:GCG","C>G:GCT", | |
| "C>G:TCA","C>G:TCC","C>G:TCG","C>G:TCT","C>T:ACA","C>T:ACC","C>T:ACG", | |
| "C>T:ACT","C>T:CCA","C>T:CCC","C>T:CCG","C>T:CCT","C>T:GCA","C>T:GCC", | |
| "C>T:GCG","C>T:GCT","C>T:TCA","C>T:TCC","C>T:TCG","C>T:TCT","T>A:ATA", | |
| "T>A:ATC","T>A:ATG","T>A:ATT","T>A:CTA","T>A:CTC","T>A:CTG","T>A:CTT", |
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| #!/bin/bash | |
| set -e | |
| perl Configure.pl --backend=moar --gen-moar --prefix="$PREFIX" | |
| make | |
| make rakudo-test | |
| make install |
rvalieris
/ download.file.path
Created
January 16, 2018 19:05
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| --- a/configure 2017-08-22 07:59:12.000000000 -0300 | |
| +++ b/configure 2018-01-16 16:41:25.378540069 -0200 | |
| @@ -3298,7 +3298,7 @@ | |
| ## Download NLopt source code | |
| ## curl -O http://ab-initio.mit.edu/nlopt/nlopt-${NLOPT_VERSION}.tar.gz | |
| - $("${R_HOME}/bin/Rscript" --vanilla -e "download.file(url='${NLOPT_URL}', destfile='${NLOPT_TGZ}')") | |
| + $("${R_HOME}/bin/Rscript" --vanilla -e "download.file(url='${NLOPT_URL}', destfile='${NLOPT_TGZ}', method='curl', extra='-L')") | |
| ## Extract NLopt source code and remove .tar.gz |
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