Tabea Kischka Tabea-K

## pip_list.sh
pip list -v

## correct_WhatsApp_picture_exifdate.sh
#!/bin/bash
# This small script can set the exif metadata of a jpeg file
# to the date and time given in the file name assigned by WhatsApp
# when downloading the image.
# The filename needs to be in a format like this (the automatically assigned
# format as of 2019-02-12):
# "WhatsApp Image 2018-09-20 at 17.18.42.jpeg"

# In order to modify all jpeg files in a folder,
# run the command like this:

## pycharm_cheatsheet.md

      
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                Tabea-K
                / pycharm_cheatsheet.md
            
            
              Created
              February 11, 2019 10:36
            
              
                Cheatsheet with some useful pycharm shortcuts for Mac
              
          
    Replace all

crtl + shift + R

  
## download_refseq.sh
CURRDATE=`date +%Y-%m-%d`
ASSEMBLY=hg38
mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -D  "${ASSEMBLY}" -e "select * \
      from refGene" > "${CURRDATE}_${ASSEMBLY}_refGene.txt"

## mutect_filters.md

      
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                Tabea-K
                / mutect_filters.md
            
            
              Created
              February 6, 2019 12:37
            
              
                Definition of MuTect2 filters, taken from vcf header.
              
          
    Definition of MuTect filters


Filter
Description


alt_allele_in_normal
Evidence seen in the normal sample


clustered_events
Clustered events observed in the tumor


germline_risk
Evidence indicates this site is germline, not somatic


homologous_mapping_event
More than three events were observed in the tumor


multi_event_alt_allele_in_normal
Multiple events observed in tumor and normal


panel_of_normals
Seen in at least 2 samples in the panel of normals


## retrieve_gene_description_by_refseq_id.py
#!/usr/bin/python

from Bio import Entrez

Entrez.email = 'A.N.Other@example.com'

def get_gene_info(refseq_id):
    """
    Queries the ncbi refseq database for the gene summary
    """

## fasta_manipulation.md

      
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                Tabea-K
                / fasta_manipulation.md
            
            
              Last active
              January 11, 2019 15:36
            
          
    Die Datei seq.fasta muss immer auf dem Desktop liegen!
header entfernen

um die header Zeilen zu entfernen:
grep -v ">" ~/Desktop/seq.fasta > ~/Desktop/seq_ohne_header.fasta

  
## create_empty_python_project_template.sh
#!/bin/bash
# This creates a more or less empty template for a python package
# containing unit tests
# Author: Tabea Kischka, 2018-07-02
# Version 2.0, last update: 2018-08-28

###########################################################################################################
# get options
###########################################################################################################

## colorblind.gpl
GIMP Palette
Name: colorblind_grayscale
Columns: 3
# Based on http://jfly.iam.u-tokyo.ac.jp/color/image/pallete.jpg
  0   0   0  seq_OrRd_4_01
 42  42  42  seq_OrRd_4_01
165 165 165  seq_OrRd_4_02
230 159   0  seq_OrRd_4_02
167 167 167  seq_OrRd_4_03
 86 180 233  seq_OrRd_4_03

## README.md

      
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                Tabea-K
                / README.md
            
            
              Last active
              February 18, 2019 09:51
            
              
                An example for how to generate a pretty fasta alignment with LaTeX, using the textshade package
              
          
    Run using the command
pdflatex test.tex
An overleaf document can be found here: https://www.overleaf.com/read/tynwkrwwpfmk
When you click on the link you can also the resulting PDF
	#!/bin/bash
	# This small script can set the exif metadata of a jpeg file
	# to the date and time given in the file name assigned by WhatsApp
	# when downloading the image.
	# The filename needs to be in a format like this (the automatically assigned
	# format as of 2019-02-12):
	# "WhatsApp Image 2018-09-20 at 17.18.42.jpeg"

	# In order to modify all jpeg files in a folder,
	# run the command like this:
	CURRDATE=`date +%Y-%m-%d`
	ASSEMBLY=hg38
	mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -D "${ASSEMBLY}" -e "select * \
	from refGene" > "${CURRDATE}_${ASSEMBLY}_refGene.txt"
Filter	Description
alt_allele_in_normal	Evidence seen in the normal sample
clustered_events	Clustered events observed in the tumor
germline_risk	Evidence indicates this site is germline, not somatic
homologous_mapping_event	More than three events were observed in the tumor
multi_event_alt_allele_in_normal	Multiple events observed in tumor and normal
panel_of_normals	Seen in at least 2 samples in the panel of normals
	#!/usr/bin/python

	from Bio import Entrez

	Entrez.email = 'A.N.Other@example.com'

	def get_gene_info(refseq_id):
	"""
	Queries the ncbi refseq database for the gene summary
	"""
	#!/bin/bash
	# This creates a more or less empty template for a python package
	# containing unit tests
	# Author: Tabea Kischka, 2018-07-02
	# Version 2.0, last update: 2018-08-28

	###########################################################################################################
	# get options
	###########################################################################################################
	GIMP Palette
	Name: colorblind_grayscale
	Columns: 3
	# Based on http://jfly.iam.u-tokyo.ac.jp/color/image/pallete.jpg
	0 0 0 seq_OrRd_4_01
	42 42 42 seq_OrRd_4_01
	165 165 165 seq_OrRd_4_02
	230 159 0 seq_OrRd_4_02
	167 167 167 seq_OrRd_4_03
	86 180 233 seq_OrRd_4_03