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Markus J. Ankenbrand iimog

  • Center for Computational and Theoretical Biology
  • Würzburg
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iimog / minimal.fa
Created Nov 24, 2014
Example fasta that causes a NullPointerException in RDPClassifier crossvalidate
View minimal.fa
>164458368 Root;k__Viridiplantae;p__Streptophyta;c__asterids;o__Apiales;f__Apiaceae;g__Heracleum;s__Heracleum sphondylium
ACGCATTCACTTGCCCAAAACCACACACTCCTTGAGGAGCTGTGTTGGTTTGAGGGCGGAAATTGGCCTCCCATGCCTTCTCGCATGGTTGGCAAAAAAATGAGTCTCTGGCTATGGACGTCGTGACATTGGTGGTTGTAAAAGACCCTCTTGTCTTGTCGGGCGAATCCGGGTCATCTTAACGAGCTCCAGGACCCTTAGGCGGCACACATTGTGTGCGCTTCGA
>298507601 Root;k__Viridiplantae;p__Streptophyta;c__Liliopsida;o__Poales;f__Poaceae;g__Muhlenbergia;s__Muhlenbergia richardsonis
ACGCCAAAAGACACTCCCCACCCAACCTAGTGGGGACGTGGTATTTGGCTCCTCGTGTCGTTATGCACGGTGGGCAAAAGTTGGGGCTGCCGGCGGTGCCGATCACAGCACAAGGTGGATGACGCAAGTTGTTCTCGGTGCTACGATACAAGCCGTGTACGGCGATGCTATGGCCCTTTGGACCCATTTAATCGAAGCGCGCGTCGCTCGAACCGCGA
>298507603 Root;k__Viridiplantae;p__Streptophyta;c__Liliopsida;o__Poales;f__Poaceae;g__Muhlenbergia;s__Muhlenbergia seatonii
ACGYCAAAAGACACTCCCCRCCTATCTGAGTAGGGATGTGGTATTTGGCCCCTCGTGCCTTTGCGTGCGGTGGGCAAAAGTTGGGGCTGCCGGCGGAGCCGATCACAGCACAAGGTGGATGACGTAAGTTGTTCTCGGTGCTACGATAYGAGCCGCACACGGCAATGCTATGGCCCTTTGGACCCATCAATCGAAGCGCGTG
@iimog
iimog / minimal.tax
Created Nov 24, 2014
Example tax that causes a NullPointerException in RDPClassifier crossvalidate
View minimal.tax
0*Root*-1*0*rootrank
1*k__Viridiplantae*0*1*kingdom
2*p__Streptophyta*1*2*phylum
3*c__asterids*2*3*class
4*o__Apiales*3*4*order
5*f__Apiaceae*4*5*family
6*g__Heracleum*5*6*genus
7*s__Heracleum sphondylium*6*7*species
8*c__Liliopsida*2*3*class
9*o__Poales*8*4*order
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@iimog
iimog / TBro_Individual_CLA
Last active Apr 15, 2016
Individual Contributor License Agreement for TBro (derived from jQuery Foundation ICLA v3.0 https://contribute.jquery.org/CLA/)
View TBro_Individual_CLA
###Individual Contributor License Agreement
Thank you for Your interest in TBro. This document clarifies the terms under which You, the person signing this agreement, may make Contributions — which may include without limitation, software, bug fixes, configuration changes, documentation, or any other materials — to any of the projects owned or managed by TBroTeam.
Please read this agreement carefully. If You have questions about these terms, please contact us via [GitHub](https://github.com/TBroTeam).
You accept and agree to the following terms and conditions for Your present and future Contributions submitted to TBro. Except for the license granted herein to Us, You reserve all right, title, and interest in and to Your Contributions.
**Licenses**
View rich_dense.biom
{
"id":null,
"format": "Biological Observation Matrix 0.9.1-dev",
"format_url": "http://biom-format.org/documentation/format_versions/biom-1.0.html",
"type": "OTU table",
"generated_by": "QIIME revision 1.4.0-dev",
"date": "2011-12-19T19:00:00",
"rows":[
{"id":"GG_OTU_1", "metadata":{"taxonomy":["k__Bacteria", "p__Proteobacteria", "c__Gammaproteobacteria", "o__Enterobacteriales", "f__Enterobacteriaceae", "g__Escherichia", "s__"]}},
{"id":"GG_OTU_2", "metadata":{"taxonomy":["k__Bacteria", "p__Cyanobacteria", "c__Nostocophycideae", "o__Nostocales", "f__Nostocaceae", "g__Dolichospermum", "s__"]}},
@iimog
iimog / phinchHideOTU.biom
Last active Jan 5, 2017
Minimal biom file to demonstrate [a bug](https://github.com/PitchInteractiveInc/Phinch/issues/69) in Phinch.
View phinchHideOTU.biom
{
"id": "No Table ID",
"format": "Biological Observation Matrix 2.1.0",
"format_url": "http://biom-format.org",
"matrix_type": "sparse",
"generated_by": "BIOM-Format 2.1",
"date": "2016-05-03T08:13:41.848780",
"type": "OTU table",
"matrix_element_type": "float",
"shape": [3, 3],
View phinchSampleList.biom
{
"id": "No Table ID",
"format": "Biological Observation Matrix 2.1.0",
"format_url": "http://biom-format.org",
"matrix_type": "sparse",
"generated_by": "BIOM-Format 2.1",
"date": "2016-05-03T08:13:41.848780",
"type": "OTU table",
"matrix_element_type": "float",
"shape": [3, 3],
View phinchDonutScale.biom
{
"id": "No Table ID",
"format": "Biological Observation Matrix 2.1.0",
"format_url": "http://biom-format.org",
"matrix_type": "sparse",
"generated_by": "BIOM-Format 2.1",
"date": "2016-05-03T08:13:41.848780",
"type": "OTU table",
"matrix_element_type": "float",
"shape": [3, 3],
View phinchFilterBug.biom
{
"id": "No Table ID",
"format": "Biological Observation Matrix 2.1.0",
"format_url": "http://biom-format.org",
"matrix_type": "sparse",
"generated_by": "BIOM-Format 2.1",
"date": "2017-04-11T17:40:40.014828",
"type": "OTU table",
"matrix_element_type": "float",
"shape": [3, 3],
@iimog
iimog / extract_scales_bee_traits_from_html.py
Created Aug 23, 2017
A python script (using beautiful soup) to extract bee traits from the html pages at http://scales.ckff.si/scaletool/?menu=6&submenu=3 and save as FENNEC compatible tsv files
View extract_scales_bee_traits_from_html.py
# coding: utf-8
from bs4 import BeautifulSoup
import glob
trait_types = dict()
trait_values_numeric = dict()
trait_values_categorical = dict()
general_citation = "Budrys, E., Budriene., A. and Orlovskyte. S. 2014. Cavity-nesting wasps and bees database."