tbrittoborges

#
import operator
sequence = "ACGACTGATCGATCGATCGATGCATCGATCGACGAT"
random_positions = random.sample(xrange(len(sequence)), 30)
get_positions = operator.itemgetter(*random_positions)
get_positions(sequence)
('T', 'C', 'G', 'C', 'A', 'C', 'C', 'T', 'A', 'T', 'G', 'T', 'A', 'T', 'C', 'C', 'T', 'T', 'A', 'G', 'T', 'A', 'A', 'A', 'C', 'G', 'G', 'C', 'G', 'A')

from itertools import groupby

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}"

tbrittoborges

df['new'] = df['new'].str.split('/') # example how to listfy a column of strings
temp = pd.DataFrame(df['new'].dropna().tolist())

temp = temp.stack()
temp.index = temp.index.droplevel(1) # index need to be coherent with the original dataframe
temp.name = 'new_colum' # name of the new column in the original dataframe

df = df.join(temp)

tbrittoborges

\documentclass{article}
\usepackage{tikz}
\usepackage{array}
\usepackage{siunitx}

\usetikzlibrary{shapes.geometric, shapes.misc, arrows, fit, calc}

\newcommand\addvmargin[1]{
  \node[fit=(current bounding box),inner ysep=#1,inner xsep=0]{};
}

tbrittoborges

# run this in you bash command line
# list all r3 packages installed with conda:
conda list | grep r3 | awk '{print $1}')

# remove all pakages r3
for i in $(conda list | grep r3 | awk '{print $1}'); do conda remove -y $i; done

# finally, remove R
conda remove r-essentials

tbrittoborges

def reverse_complement(sequence):    
     tab = str.maketrans("ACGT", "TGCA")
     return sequence.translate(tab)[::-1]

def apply_rc(row):
     if row['strand'] == '-':
         row['seq'] = reverse_complement(row['seq'])
    
     return row
        

tbrittoborges

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[[

tbrittoborges

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'])

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 read_fasta_from_str(fasta):
    """

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

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