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Silas Kieser SilasK

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SilasK / AUC_analysis.py
Last active March 8, 2023 10:57
def auc_analysis(classifier,X,y,n_splits=6,random_state=0,show_plot=True):
import matplotlib.pyplot as plt
@SilasK
SilasK / import_long_reads.py
Created February 21, 2022 14:03
A function to add long reads to an atlas sample table https://github.com/metagenome-atlas/atlas/issues/273
#!/usr/bin/env python
import os, shutil
from atlas.color_logger import logger
from pathlib2 import Path
import pandas as pd
import argparse
from snakemake.shell import shell
@SilasK
SilasK / .screenrc
Last active February 14, 2023 12:52
Here are some of the hack I use to make my life working on the command line a bit easier
# STARTUP SCREENS
# ===============================================================
# Defines the time screen delays a new message when one message
# is currently displayed. The default is 1 second.
# msgminwait 2
# Time a message is displayed if screen is not disturbed by
# other activity. The dafault is 5 seconds:
# msgwait 2
@SilasK
SilasK / create_sample_table.py
Last active October 29, 2021 09:52
Create sample table from fastq files e.g. for use in snakemake
import os
import sys
import logging
logger = logging.getLogger(os.path.basename(__file__))
import pandas as pd
import numpy as np
from collections import defaultdict
@SilasK
SilasK / Atlas_gene_graph.ipynb
Created October 21, 2021 13:02
Linking Atlas genes to contigs and bins
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@SilasK
SilasK / Dram-get-all-modules.ipynb
Created January 22, 2021 15:06
Hack DRAM to calculate the coverage of all Kegg modules
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