pwwang

# ~/.config/fish/functions/whichpy.fish
function whichpy --description 'Print python package information'
    set -l whichpy_script_url "https://gist.githubusercontent.com/pwwang/879966128b0408c2459eb0a0b413fa69/raw/4e3d29ffc580f62182f45f50d4feee3b58c6b633/whichpy.py"
    set -l whichpy_script /tmp/whichpy.py
    if not test -f "$whichpy_script"
        echo "Downloading: $whichpy_script_url"
        command curl -sS "$whichpy_script_url" -o "$whichpy_script"
    end
    if test (count $argv) -eq 0
        echo "Usage: whichpy <package> [python]"

pwwang

function poetry-editable --description 'Do editable install for poetry project'
    echo "= RUN poetry build"
    poetry build
    set ver (poetry version -s)
    pushd dist/
    tar zxvf *-$ver.tar.gz
    popd
    mv setup.py setup.py.bak

    function on_premature_exit

pwwang

#!/usr/bin/env python
#
# Wrapper script for SIFT4G_annotator
#

#
# Program Parameters
#
import os
import subprocess

pwwang

# get all targets from subdirectory
SUBDIR := subdir
TARGETS := $(shell make -C $(SUBDIR) -rpn | sed -n -e "/^$$/ { n ; /^[^ .\#%][^ ]\*:/ { s/:.\*$$// ; p ; } ; }" )

# default target
all:

# pass all targets to subdirectory
%:

pwwang

#!/usr/bin/env perl

# vcf2maf - Convert a VCF into a MAF by mapping each variant to only one of all possible gene isoforms

use strict;
use warnings;
use IO::File;
use Getopt::Long qw( GetOptions );
use Pod::Usage qw( pod2usage );
use File::Path qw( mkpath );

pwwang

# for prevd and nextd, cd -
function __fish_move_last -d "Move the last element of a directory history from src to dest"
	set -l src $argv[1]
	set -l dest $argv[2]

	set -l size_src (count $$src)

	if test $size_src = 0
		# Cannot make this step

pwwang

Windows Registry Editor Version 5.00

; Created by: Shawn Brink
; http://www.sevenforums.com
; Tutorial: http://www.sevenforums.com/tutorials/47415-open-command-window-here-administrator.html


 
[-HKEY_CLASSES_ROOT\Directory\shell\runas]

pwwang

#!/usr/bin/env python

from subprocess import check_output
from re import search
cmd    = ['qstat', '-xml']
# get the xml output
output = check_output (cmd)
keys   = [] # the feature names
vals   = [] # the jobs including all features
job    = [] # the features

pwwang

@HD	VN:1.4	SO:coordinate
@SQ	SN:chrPhage	LN:48502
@RG	ID:testPE1.L1	PU:unit1	LB:lib1	SM:testPE1	PL:Illumina
@PG	ID:bwa	PN:bwa	VN:0.7.15-r1140	CL:bwa mem -t 1 -R @RG\tID:testPE1.L1\tPU:unit1\tLB:lib1\tSM:testPE1\tPL:Illumina ./data/lambda_virus.fa /data2/junwenwang/panwen/tools/bioprocs/tests/workdir/PyPPL.pFastqPE2SamData.sambam.20pe9DUu/1/input/testPE1_1.fq /data2/junwenwang/panwen/tools/bioprocs/tests/workdir/PyPPL.pFastqPE2SamData.sambam.20pe9DUu/1/input/testPE1_2.fq
@PG	ID:bamsort	PN:bamsort	CL:bamsort I=/data2/junwenwang/panwen/tools/bioprocs/tests/workdir/PyPPL.pSam2BamData.sambam.hl9sPcM2/1/input/testPE1.sam O=/data2/junwenwang/panwen/tools/bioprocs/tests/workdir/PyPPL.pSam2BamData.sambam.hl9sPcM2/1/output/testPE1.bam SO=coordinate blockme=16384 tmpfile=/tmp/pSam2BamData.testPE1.1/tmp. inputformat=sam outformat=bam inputthreads=1 outputthreads=1 markduplicates=0 rmdup=0	PP:bwa	VN:2.0.72
r92	2145	chrPhage	1	60	273H42M	=	43	244	GGGCGGCGACCTCGCGGGTTTTCGCTATTTATGAAAATTTTC	A5)?.3E8,=E*1F4/"F50>9/#H'=A:/$G9)