kevin3’s gists

kevin3 / GPU-tensorflow-keras-check.py

Created June 5, 2022 10:58

testing if installed GPU enabled keras and tensorflow

	###test if Using GPU for ML
	#These commands in the Python terminal should bring up both a CPU and a GPU device, if TensorFlow correctly identifies your GPU.
	import tensorflow as tf
	tf.__version__
	import keras
	keras.__version__
	from tensorflow.python.client import device_lib
	print(device_lib.list_local_devices())

kevin3 / printfirst10char-awk.sh

Created February 26, 2022 16:51

awk '{print substr($0,1,10)}' bam.list

kevin3 / Convert_time.py

Created October 5, 2021 18:25

	def read_date(date):
	if isinstance(date, int):
	return pd.to_datetime(date,unit='D', origin='1899-12-30')
	#return xlrd.xldate.xldate_as_datetime(date, 0)
	else:
	return(pd.to_datetime(date))


	print("Converting 42985 to")
	print(read_date(42985 ))

kevin3 / run-kraken-krona.sh

Created July 15, 2021 14:34

	~/bin/kraken2/kraken2 --db ~/k2_standard_16gb_20210517 --use-names --gzip-compressed $1 --output $1.kraken --report $1.kraken.report
	cut -f2,3 $1.kraken > $1.kraken.kronainput
	ktImportTaxonomy -tax /home/kev/Krona-master/KronaTools/taxonomy $1.kraken.kronainput -o $1.kraken.kronainput.html

kevin3 / extract-unmapped-reads-bam.sh

Created July 15, 2021 14:29

	#!/bin/bash
	samtools view -b -f 4 $1 > $1.unmapped.bam
	samtools index $1.unmapped.bam
	java -Xmx8g -jar /opt/picard/picard-tools-current/picard.jar SamToFastq I=$1.unmapped.bam F=$1.unmapped.bam.fastq
	/home/ionadmin/bin/bbmap/reformat.sh in=$1.unmapped.bam.fastq out=$1.unmapped.bam.fastq.fasta
	gzip $1.unmapped.bam.fastq.fasta

kevin3 / cool-python.py

Created October 10, 2017 08:16

	The following tricks I find pretty useful in my daily Python work. I also added a few I stumbled upon lately.

	1. Use collections

	This really makes your code more elegant and less verbose, a few examples I absorbed this week:

	Named tuples:

	>>> Point = collections.namedtuple('Point', ['x', 'y'])
	>>> p = Point(x=1.0, y=2.0)

kevin3 / rsync-files.sh

Created March 1, 2017 07:30

rsync -ahP --times --owner --group /mnt/external/exportedReports/Auto_user_S5-00333-1 /media/USB

kevin3 / plot-pd-gantt-offline.py

Created February 7, 2017 05:01

	import plotly
	from plotly.tools import FigureFactory as FF

	import pandas as pd

	df = pd.read_csv('https://raw.githubusercontent.com/plotly/datasets/master/gantt_example.csv')

	fig = FF.create_gantt(df, colors=['#333F44', '#93e4c1'], index_col='Complete', show_colorbar=True,
	bar_width=0.2, showgrid_x=True, showgrid_y=True)
	plotly.offline.plot(fig, filename='gantt-use-a-pandas-dataframe')

kevin3 / transaction.sql

Created March 22, 2013 18:10

trial sql create table for a record of stock transactions

	Create Table "main"."transactions"
	CREATE TABLE IF NOT EXISTS "main"."transactions" ("tid" INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL ,
	"stkcode" TEXT NOT NULL ,
	"stkname" TEXT, "qty" INTEGER NOT NULL ,
	"broker" TEXT NOT NULL ,
	"price" REAL NOT NULL ,
	"targetprice" REAL,
	"stoploss" REAL,
	"longshort" TEXT NOT NULL ,
	"date" TEXT NOT NULL ,

kevin3 / parseSCBtrans.py

Created March 18, 2013 19:49

Simple python script to join every 4 lines and also misc formatting to get SCB transactions auto formatted as a csv file

	#!/usr/bin/python
	"""simple python script to join every 4 lines into one from a plain text file"""
	data = open("SCBtransactions2013-03-19.orig.csv").readlines()
	data = [ i.strip() for i in data ] #get rid of newlines
	data = [ i.replace("\t \t","\t") for i in data ] #get rid of double tabs
	data = [ i.replace("SGD","") for i in data ] #get rid of SGD
	fourlines = range(0,len(data),4)
	for num,line in enumerate(data):
	if num in fourlines:
	print ' '.join(data[num:num+4])