Andreas Wilm andreas-wilm

## cudtools_colormap.py
import numpy as np
import matplotlib.pyplot as plt

# use the colorblind friendly colors
# https://code.google.com/p/python-cudtools/source/browse/cudtools.py
import cudtools

numlines = 20


## timestamp.c
/* -*- c-file-style: "k&r"; indent-tabs-mode: nil; -*- */
#include <stdio.h>
#include <stdlib.h>

#include <time.h>

/* returns a timestamp in the form of YYYY-mm-dd HH-MM.
 * buf needs to be able to hold 19+1 characters (incl. \0).
 * returns 0 on success -1 otherwise.
 */

## pysam_alignedpairs.py

# assuming:
# - refsq is set and always the same
# - bamfh is an open pysam samfile
for r in bamfh:
    if r.is_unmapped:
      continue

    for (qapos, rpos) in r.get_aligned_pairs():
        # qapos is the aligned index, i.e. this ignores clipping. add that

## fisher_pv_comb.py
from math import log
from scipy import stats

def fisher_comb(pv1, pv2):
    """
    Fisher's method for combining p-values:
    https://en.wikipedia.org/wiki/Fisher's_method

    See for example breseq-0.18b:polymorphism_statistics.r


## argparse_logging_skeleton.py
#!/usr/bin/env python

# Example for using repeateable -v and -q for setting logging level
# with argparse. works with python 2 and 3. based on
# https://www.reddit.com/r/Python/comments/3nctlm/what_python_tools_should_i_be_using_on_every/
#
# masklinn: """A trick I like is using repeatable -v and -q to select
# the logging level. The logging levels are actually integers with a
# 10 increment (DEBUG is 10, CRITICAL is 50).  It's very easy with
# argparse's count action or click's count=True"""

## timestamp.py
from datetime import datetime
def timestamp():
    return datetime.now().isoformat()

## myip.sh
# found at #nfhack17
dig +short myip.opendns.com @resolver1.opendns.com

## install-singularity.sh
set -euo pipefail

VERSION=2.4.2

pushd /tmp/
wget https://github.com/singularityware/singularity/releases/download/$VERSION/singularity-$VERSION.tar.gz
tar xzf singularity-${VERSION}.tar.gz
cd singularity-${VERSION}
./configure --prefix=/usr/local
make

## keybase.md

      
              1 file
            
          
              0 forks
            
          
              0 comments
            
          
              0 stars
            
          
                andreas-wilm
                / keybase.md
            
            
              Created
              June 29, 2018 09:20
            
          
    Keybase proof

I hereby claim:

I am andreas-wilm on github.
I am andreaswilm (https://keybase.io/andreaswilm) on keybase.
I have a public key ASCHyaZnBYiR0MNExSduKh5LsVgFwldPfSI1mnHKOYKDZAo

To claim this, I am signing this object:

  
## nextflow_sample_map_str.nf
#!/usr/bin/env nextflow

/* this is a minimal working example for a bug we recently ran into.
 * in a nutshell: we can function (gen_sample_map_str) in every call to
 * process GenomicsDB.  * the function has static input and should
 * produce identical output each time, but it doesn't. the question is
 * why.
 *
 * yes, we can do tihs different, i.e. construct the string once and yes
 * some things don't make sense in this current minimalistic form.
	import numpy as np
	import matplotlib.pyplot as plt

	# use the colorblind friendly colors
	# https://code.google.com/p/python-cudtools/source/browse/cudtools.py
	import cudtools

	numlines = 20
	/* -- c-file-style: "k&r"; indent-tabs-mode: nil; -- */
	#include <stdio.h>
	#include <stdlib.h>

	#include <time.h>

	/* returns a timestamp in the form of YYYY-mm-dd HH-MM.
	* buf needs to be able to hold 19+1 characters (incl. \0).
	* returns 0 on success -1 otherwise.
	*/

	# assuming:
	# - refsq is set and always the same
	# - bamfh is an open pysam samfile
	for r in bamfh:
	if r.is_unmapped:
	continue

	for (qapos, rpos) in r.get_aligned_pairs():
	# qapos is the aligned index, i.e. this ignores clipping. add that
	from math import log
	from scipy import stats

	def fisher_comb(pv1, pv2):
	"""
	Fisher's method for combining p-values:
	https://en.wikipedia.org/wiki/Fisher's_method

	See for example breseq-0.18b:polymorphism_statistics.r
	#!/usr/bin/env python

	# Example for using repeateable -v and -q for setting logging level
	# with argparse. works with python 2 and 3. based on
	# https://www.reddit.com/r/Python/comments/3nctlm/what_python_tools_should_i_be_using_on_every/
	#
	# masklinn: """A trick I like is using repeatable -v and -q to select
	# the logging level. The logging levels are actually integers with a
	# 10 increment (DEBUG is 10, CRITICAL is 50). It's very easy with
	# argparse's count action or click's count=True"""
	from datetime import datetime
	def timestamp():
	return datetime.now().isoformat()
	# found at #nfhack17
	dig +short myip.opendns.com @resolver1.opendns.com
	set -euo pipefail

	VERSION=2.4.2

	pushd /tmp/
	wget https://github.com/singularityware/singularity/releases/download/$VERSION/singularity-$VERSION.tar.gz
	tar xzf singularity-${VERSION}.tar.gz
	cd singularity-${VERSION}
	./configure --prefix=/usr/local
	make
	#!/usr/bin/env nextflow

	/* this is a minimal working example for a bug we recently ran into.
	* in a nutshell: we can function (gen_sample_map_str) in every call to
	* process GenomicsDB. * the function has static input and should
	* produce identical output each time, but it doesn't. the question is
	* why.
	*
	* yes, we can do tihs different, i.e. construct the string once and yes
	* some things don't make sense in this current minimalistic form.