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";

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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")'

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

import subprocess
import tempfile

import sys
import utils

seqs = utils.fasta_parser('.fasta')

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

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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]

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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(">")

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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

	

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def analyse(genome, set_a, match_a='any', region_a='any',
            set_b=None, match_b='any', region_b='any',
            combine='or', genes=None, window_a=-1, window_b=-1,
            datadir=None):
  
# It takes the name of the genome assembly to use, and at least a list of set A regulator names.
# A simple analysis run with a custom regulator would be:

from dorina.run import analyse
results = analyse('hg19', ['/path/to/custom/regulator.bed', 'PARCLIP_PUM2_hg19'])

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def junction_type2(row):
    """Junction type classification"""
    # if there is no exons supported by realible junctions
    # return a interable with empty strings
    if row['exons_w_junct_sup'] is None:
        return ['', '']
    
    type_ = []
    # each row is a junction
    j_start, j_end, exons, strand = row.loc[[