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Wojtek Bażant wbazant

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wbazant / sample_attributes_from_ena.sh
Created June 19, 2018 10:50
Get sample attributes for an ENA sample
sampleAttributes() {
curl -s "https://www.ebi.ac.uk/ena/data/view/$1&display=xml " \
| perl -MXML::LibXML -e '
for my $attr (XML::LibXML->load_xml(string => do {local $/ ; <> }) -> findnodes("./ROOT/SAMPLE/SAMPLE_ATTRIBUTES/*")) {
print $attr->findvalue("./TAG") . "\t" . $attr->findvalue("./VALUE"). "\n"
} '
}
sampleAttributes SRS1334254
@wbazant
wbazant / Cross references pipeline
Created August 1, 2018 13:34
<!DOCTYPE html>
<html>
<head>
<meta charset="utf-8">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>Lab meeting 24.07.2018</title>
<link rel="stylesheet" href="https://stackedit.io/style.css" />
</head>
@wbazant
wbazant / cross-references.md
Created August 1, 2018 13:36
cross-references
<title>cross-references</title>
@wbazant
wbazant / Schisto_studies.md
Last active October 16, 2018 09:52
ParaSite 11
<title>ParaSite 11</title>
@wbazant
wbazant / genes_not_in_trees_wbps13.tsv
Last active June 27, 2019 15:19
WormBase ParaSite 14: genes that are not part of any gene trees
Protopolystoma xenopodis (PRJEB1201) 26263 37906 0.69
Romanomermis culicivorax (PRJEB1358) 24769 48376 0.51
Gyrodactylus salaris (PRJNA244375) 7929 15436 0.51
Heterorhabditis bacteriophora (PRJNA13977) 8366 20964 0.40
Soboliphyme baturini (PRJEB516) 4960 13193 0.38
Saccharomyces cerevisiae 2516 6692 0.38
Parascaris equorum (PRJEB514) 5558 14472 0.38
Ixodes scapularis 7405 20486 0.36
Steinernema glaseri (PRJNA204943) 11383 34137 0.33
Meloidogyne floridensis (PRJEB6016) 16701 49938 0.33
@wbazant
wbazant / R-package-with-singularity.md
Last active April 3, 2024 14:00
Singularity container for an R module on a research cluster

Singularity container for an R module on a research cluster for VEuPathDB

Introduction

To use this technology, we need Singularity installed in the target environment by root, which is possibly the largest obstacle for us.

Writing a development container

Here is a container for analysing 16s rRNA data in MicrobiomeDB, requiring an R package DADA2. DADA2 releases to BioConductor, but we want the ability to load an arbitrary commit for development.

We can build on somebody's container with r-devtools, and add our libraries:

@wbazant
wbazant / MALED-diarrhea.sample-details.tsv
Last active January 14, 2020 19:01
We can make this file beautiful and searchable if this error is corrected: It looks like row 9 should actually have 4 columns, instead of 3 in line 8.
born stunted born stunted whether the individual was born stunted (LAZ less than -2) parent
severely stunted at sampling severely stunted at sampling whether the individual was found severely stunted at sampling (LAZ less than -3) Anthropometry
stunted 3 months after sampling stunted 3 months after sampling whether the individual was found stunted 3 months aftet sampling (LAZ less than -2) Anthropometry
stunted at sampling stunted at sampling whether the individual was found severely stunted 3 months after sampling (LAZ less than -3) Anthropometry
laz 1 month after sampling LAZ 1 month after sampling Length-to-height Z-score 1 month after sampling Anthropometry
laz 3 months after sampling LAZ 3 months after sampling Length-to-height Z-score 3 months after sampling Anthropometry
laz at enrollment LAZ at enrollment Length-to-height Z-score at enrollment Anthropometry
laz at sampling LAZ at sampling Length-to-height Z-score at sampling Anthropometry
mean daily feeds at breast mean daily feeds at breast Mean dail