martinholub

# https://stevenmortimer.com/5-steps-to-change-github-default-branch-from-master-to-main/#step-3---point-head-to-main-branch

# Step 1 
# create main branch locally, taking the history from master
git branch -m master main

# Step 2 
# push the new local main branch to the remote repo (GitHub) 
git push -u origin main

martinholub

git push -d <remote_name> <branch_name>
git branch -d <branch_name>

martinholub

# https://stackoverflow.com/questions/449541/how-to-selectively-merge-or-pick-changes-from-another-branch-in-git

# merge branch SOURCE to DETINATION
git checkout DESTINATION
git merge --no-ff --no-commit SOURCE

# inspect and solve potential conflicts
git status
git diff --cached file1

martinholub

# Parse Arguments --------------------------------------------------------------
# reference: https://stackoverflow.com/a/14203146
POSITIONAL=()
while [[ $# -gt 0 ]]; do
  key="$1"

  case $key in
      -v|--vcf)
      vcf="$2"
      shift # past argument

martinholub

class TranscriptomicSNP(object):
    """ Generate a VCF file with transcriptomic coordinates

    Gets transcriptomic snp loci in format <transc> <SNPpos> <additional_info...>.

    # available:
    # <chrom> <transc> <start> <end>
    # <chrom> <SNVpos>

    """

martinholub

def rm_ext(fname, ext = None):
    """Removes extension from filename"""
    if not ext:
        ext = re.match(".*\.(.*)$", fname).group(1)
    else:
        ext = ext.strip(".")
    return re.sub("\." + ext + "$","", fname)

martinholub

for f in {input}
        do
            # mkdir --parents $f
            [[ $f == *.gz ]] && gunzip --keep $f
        done

martinholub

Bioinformatician's Toolbox

This document aggregates snippets that I found useful when working in bioinfromatics. It is work in progress and I will extend it as needed. It is mainly in form of toy examples or pseudcode. Please adjust it accodring to your needs.

MariaDB

mysql --user=root -p
/*get preview */
show databases;
USE <some_database>;
show tables;

martinholub

void add_buffer_gps(double lat, double lon){

  // offset by 90(180) to make positive and scale to 0..1
  latB = ((lat + 90) / 180.0) * pow(256,3);
  lonB = ((lon + 180) / 360.0) * pow(256,3);

  // byte shifting
  dataBuffer[0] = ( latB >> 16 ) & 0xFF;
  dataBuffer[1] = ( latB >> 8 ) & 0xFF;
  dataBuffer[2] = latB & 0xFF;

martinholub

from keras.callbacks import Callback as KerasCallback, CallbackList as KerasCallbackList
from keras.callbacks import TensorBoard
from keras.optimizers import Adam, RMSprop
import keras.backend as K

class SubTensorBoard(TensorBoard):
    """Subclassing of tensorboard to log and visualize custom metrics and others
  
    Note that for this to work, you will have to define a way how to handle `on_episode_end`
    calls.