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

#!/usr/bin/env python
from __future__ import print_function
import yaml, sys
from os import path, makedirs, listdir, remove
from time import sleep
from shutil import copy2
from pyppl import commands, utils
from subprocess import list2cmdline

commands._desc             = 'A set of utilities for JupyterLab.'

pwwang

{"lastUpload":"2020-04-09T18:01:08.444Z","extensionVersion":"v3.4.3"}

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

pwwang

{"lastUpload":"2017-06-14T22:41:49.796Z","extensionVersion":"v2.8.1"}