Skip to content

Instantly share code, notes, and snippets.

View shenwei356's full-sized avatar

Wei Shen shenwei356

1.4k followers · 291 following
View GitHub Profile
@apcamargo
apcamargo / sam2tsv.py
Created March 10, 2025 03:53
Converts alignments stored in the SAM format to a BLAST-like table
#!/usr/bin/env python
"""
This script processes SAM (Sequence Alignment/Map format) inputs from standard
input and extracts alignment information that is then provided in a tab-separated
table. The following fields are produced: query, target, query_length, query_start,
query_end, target_start, target_end, alignment_length, alignment_identity.
This script was designed for use with SAM files produced by minimap2. However,
it will work with any SAM data that:
@pmenzel
pmenzel / rotate_assembly.pl
Created June 18, 2022 14:44
Perl script for rotating a fasta sequence to start a specified gene search by BLAST
#!/usr/bin/env perl
#
# rotates and (if necessary reverse complements) an assembly of a circular genome
# so that it starts with the sequence having the best blast hit to a gene database,
# e.g. dnaA
#
# depends on blastn being installed
#
# Example usage:
# rotate_assembly.pl assembly.fasta dnaA.fa > rotated_assembly.fa
@clausecker
clausecker / mem.s
Created August 4, 2020 18:18
Vectorised positional popcount for Go
#include "textflag.h"
// func PospopcntMem(counts *[8]int32, buf []byte)
TEXT ·PospopcntMem(SB),NOSPLIT,$0-32
MOVQ counts+0(FP), DI
MOVQ buf_base+8(FP), SI // SI = &buf[0]
MOVQ buf_len+16(FP), CX // CX = len(buf)
SUBQ $32, CX // pre-subtract 32 bit from CX
JL scalar
@clausecker
clausecker / harness.c
Last active August 4, 2020 16:00
8 bit positional popcount with AVX2 without too much code
#define _XOPEN_SOURCE 700
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <time.h>
extern void pospopcnt_reg(int accum[8], const char *buf, size_t len);
extern void pospopcnt_mem(int accum[8], const char *buf, size_t len);
extern void
@kbychkov
kbychkov / gh_pages.sh
Last active November 18, 2023 15:30
Working with gh-pages as an orphan branch
# Create `gh-pages` branch from scratch
cd <dir>
git init
git remote add origin <url>
git checkout --orphan gh-pages
git add .
git commit -m "build 1.0.0"
git push origin gh-pages
@shenwei356
shenwei356 / add-timestamp-for-media-file.sh
Last active September 27, 2023 02:59
Adding create time to image/video files
#!/bin/sh
while read file; do
if [[ $string =~ .*=.* ]]; then
continue
fi
t=$(exiftool "$file" \
| grep "^Create Date" | head -n 1 \
| sed -r "s/\s+/ /g" | cut -d " " -f 4 \
@bsmith89
bsmith89 / Makefile
Created February 5, 2016 19:21
Minorly redacted Makefile for a project using mothur to analyze 16S data.
# ====================
# Project Makefile
# ====================
# User Configuration {{{1
# ====================
# Major targets {{{2
.PHONY: figs res
figs:
# [Partially redacted]
@evantoli
evantoli / GitConfigHttpProxy.md
Last active November 2, 2025 09:57
Configure Git to use a proxy

Configure Git to use a proxy

In Brief

You may need to configure a proxy server if you're having trouble cloning or fetching from a remote repository or getting an error like unable to access '...' Couldn't resolve host '...'.

Consider something like:

@petervmeijgaard
petervmeijgaard / todo-vue-example.html
Last active September 13, 2017 05:24
Todo Vue.js Example
<!DOCTYPE html>
<html>
<head>
<meta http-equiv="content-type" content="text/html; charset=UTF-8">
<title>Todo Vue.js Example</title>
<link rel="stylesheet"
type="text/css"
href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css">
<script src="https://cdn.jsdelivr.net/vue/latest/vue.js"></script>
<style type="text/css">
@mfuerstenau
mfuerstenau / zigzag-encoding.README
Last active September 1, 2025 13:16
ZigZag encoding/decoding explained
ZigZag-Encoding
---------------
Maps negative values to positive values while going back and
forth (0 = 0, -1 = 1, 1 = 2, -2 = 3, 2 = 4, -3 = 5, 3 = 6 ...)
(i >> bitlength-1) ^ (i << 1)
with "i" being the number to be encoded, "^" being
XOR-operation and ">>" would be arithemtic shifting-operation