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@pwwang
pwwang / sift4g_annotator
Created Jun 11, 2020
Wrapper script for SIFT4G_Annotator
View sift4g_annotator
#!/usr/bin/env python
#
# Wrapper script for SIFT4G_annotator
#
#
# Program Parameters
#
import os
import subprocess
@pwwang
pwwang / Makefile
Created Sep 28, 2019
A proxy Makefile to subdirectory's Makefile
View Makefile
# 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
pwwang / vcf2maf.pl
Created Sep 24, 2018
vcf2maf.pl with logs
View vcf2maf.pl
#!/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 );
View jlab.py
#!/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
pwwang / cloudSettings
Last active Apr 9, 2020
Visual Studio Code Settings Sync Gist
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{"lastUpload":"2020-04-09T18:01:08.444Z","extensionVersion":"v3.4.3"}
@pwwang
pwwang / __fish_move_last.fish
Last active Jul 5, 2018
Fish cd with symbolic path kept.
View __fish_move_last.fish
# 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
View Add_Open_Command_Window_Here_as_Administrator.reg
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
pwwang / qst
Last active Jul 12, 2017
qstat with full job name
View qst
#!/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
pwwang / testPE1.sam
Last active Jul 10, 2017
Testing reads
View testPE1.sam
This file has been truncated, but you can view the full file.
@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
View cloudSettings
{"lastUpload":"2017-06-14T22:41:49.796Z","extensionVersion":"v2.8.1"}