Po-E Li poeli

poeli / rmSeqFromFastaByPtnFile.sh

Created June 10, 2020 05:27

remove sequences from FASTA in pattern file

	#!/usr/bin/bash

	awk '{ if ((NR>1)&&($0~/^>/)) { printf("\n%s", $0); } else if (NR==1) { printf("%s", $0); } else { printf("\t%s", $0); } }' \
	\| grep -vwf $1 - \
	\| tr "\t" "\n"

poeli / convert_sam_to_fasta

Created April 3, 2020 15:58

awk '{OFS="\t"; print ">"$1"\n"$10}'

poeli / python_http_server.sh

Created March 25, 2020 05:25

python3 -m http.server $1

poeli / add_env_to_jupyter.sh

Created March 24, 2020 21:54

	conda install -c anaconda ipykernel
	python -m ipykernel install --user --name=$1

poeli / vim

Created March 20, 2020 19:40

DOS format to UNIX

	:e ++ff=dos
	:set ff=unix

poeli / after_update.sh

Created March 20, 2020 16:26

sudo xcode-select -switch /Library/Developer/CommandLineTools/

poeli / sacct2json.jq

Last active March 12, 2020 05:07

	# USAGE: jq -R -s -f sacct2json.jq
	# objectify/1 takes an array of string values as inputs, converts
	# numeric values to numbers, and packages the results into an object
	# with keys specified by the "headers" array

	def objectify(headers):
	# For jq 1.4, replace the following line by: def tonumberq: .;
	def tonumberq: tonumber? // .;
	. as $in
	\| reduce range(0; headers\|length) as $i ({}; .[headers[$i]] = ($in[$i] \| tonumberq) );

poeli / multifasta_to_singlefasta.sh

Last active February 20, 2020 00:14

Split multiFASTA to singleFASTA and use seq id as filenames

 awk -F ' ' '{ if(/^>/){F=sprintf("%s.fasta", substr($1,2)); print > F;next;} else {print >> F}}'

poeli / extract_reads_from_fastq_by_desc.pl

Created May 17, 2018 21:40

poeli / fasta_u2t.sh

Created May 9, 2018 19:43

Convert Us to Ts in FASTA file

	#!/bin/sh
	awk '$0~/^>/{print $0;next}; {gsub("U","T");print $0}'