tbrittoborges

library(tidyverse)

library(lubridate) # for the days() function
library(fuzzyjoin) # for the fuzzy_left_join() function

climate <- read_tsv('./timetable.csv')
#  date         temperature
#1 2018-11-21   100 
#2 2018-11-22    80 

tbrittoborges

SIRV	LexogenSIRVData	exon	2001	2484	.	-	0	gene_id "SIRV1"; transcript_id "SIRV101"; exon_assignment "SIRV101_0";
SIRV	LexogenSIRVData	exon	2001	2484	.	-	0	gene_id "SIRV1"; transcript_id "SIRV103"; exon_assignment "SIRV103_0";
SIRV	LexogenSIRVData	exon	2001	2484	.	-	0	gene_id "SIRV1"; transcript_id "SIRV104"; exon_assignment "SIRV104_0";
SIRV	LexogenSIRVData	exon	2001	2484	.	-	0	gene_id "SIRV1"; transcript_id "SIRV106"; exon_assignment "SIRV106_0";
SIRV	LexogenSIRVData	transcript	2001	11763	.	-	0	gene_id "SIRV1"; transcript_id "SIRV104";
SIRV	LexogenSIRVData	transcript	2001	11786	.	-	0	gene_id "SIRV1"; transcript_id "SIRV101";
SIRV	LexogenSIRVData	transcript	2001	11786	.	-	0	gene_id "SIRV1"; transcript_id "SIRV106";
SIRV	LexogenSIRVData	transcript	2001	11791	.	-	0	gene_id "SIRV1"; transcript_id "SIRV103";
SIRV	LexogenSIRVData	gene	2001	12643	.	-	0	gene_id "SIRV1";
SIRV	LexogenSIRVData	exon	2007	2484	.	-	0	gene_id "SIRV1"; transcript_id "SIRV102"; exon_assignment "SIRV102_0";

tbrittoborges

Places to visit

The castle

Philosophenweg:

A nice walk that you can start from the Old bridge or Bergstraße (Neuenheim). Also check the Neckarwiese, Alte brücke (old bridge) and Hauptstraße (main street)

Botanical Garden Heidelberg:

Although it's winter, the botanical garden has a small greenhouse. The garden is also within the main University Campus, and so offers a good opportunity to check it out.

Käthe Wohlfahrt:

tbrittoborges

# from https://stackoverflow.com/users/2490497/jangorecki
Rscript -e 'install.packages("eulerr", repos="https://cran.rstudio.com")'

tbrittoborges

#!/usr/bin/env python
# __author__ = 'tbrittoborges'

import subprocess
import tempfile

import sys
import utils

seqs = utils.fasta_parser('.fasta')

tbrittoborges

# from https://www.biostars.org/p/272373/#272461
cut -f1,2 genome.fa.fai > genome.size

tbrittoborges

import pandas as pd

x = pd.read_html('https://de.wikipedia.org/wiki/Medizinische_Abk%C3%BCrzungen')
x=pd.concat(x)
x.tail()
x.set_index(0)[1]

tbrittoborges

def read_fasta_from_str(fasta):
    """

    :param str fasta: multiple sequences in fasta string
    """
    from itertools import groupby

    def is_header(line):
        return line.startswith(">")

tbrittoborges

for f in raw_reads{39..50}.fq.gz
do
	echo  "$f   "
	gzip -cd $f | awk 'BEGIN { t=0.0;sq=0.0; n=0;} ;NR%4==2 {n++;L=length($0);t+=L;sq+=L*L;}END{m=t/n;printf("total %d avg=%f stddev=%f\n",n,m,sq/n-m*m);}'
	done

	

tbrittoborges

def better_table(table, caption, name):
    
    start = r"""
\begin{{table}}[!htb]
\sisetup{{round-mode=places, round-precision=2}}
\caption{{{}}}\label{{table:{}}}
\centering
""".format(caption, name)
    
    end = r"\end{table}"