williamrowell

HANDY ONE-LINE SCRIPTS FOR AWK                               30 April 2008
Compiled by Eric Pement - eric [at] pement.org               version 0.27

Latest version of this file (in English) is usually at:
   http://www.pement.org/awk/awk1line.txt

This file will also be available in other languages:
   Chinese  - http://ximix.org/translation/awk1line_zh-CN.txt   

USAGE:

williamrowell

#!/bin/bash
# for all files in folder, remove newlines

for FILE in `ls`
do
    tr -d '\n' < $FILE > ${FILE}.tmp
    mv ${FILE}.tmp $FILE
done

williamrowell

#!/bin/sh

mkdir mp3
for I in *.flac; do
    flac -d --stdout "$I" | lame -V0 --vbr-new - mp3/"$I"
done

for J in *.flac; do
    id3cp -2 "$J" mp3/"$J"
done

williamrowell

function cellArray = cellFromTextFile(fileName)
% Loads cell array of strings, 1xN character arrays, from the given text
% file.
if exist(fileName, 'file') == 0
    error('unable to read file, %s, does not exist', fileName);
end
try
    cellArray = textread(fileName, '%s');
catch ME
    error('unable to read file, %s: %s', ME.message);

williamrowell

function error_jitter(xvals, yvals, errvals)
%%ERROR_JITTER(xvals, yvals)
%
% xvals -> array of x positions
% yvals -> cell array of multiple y positions for each x position
% errvals -> cell array of multiple std/sem for each x position
% TODO: allow yvals/errvals to be ragged array
%
% author: William Rowell ([email protected])

williamrowell

#!/usr/bin/env python3
"""Coverage mean and standard deviation of autosomes

Estimate the mean and standard deviation from a mosdepth coverage BED for
positions with coverage in the range (0, 2 * non-zero mode). This estimate
behaves well for PacBio HiFi WGS of human germline aligned to either hs37d5 and
GRCh38, and may be useful for other situations as well.

$ bash mosdepth --threads 3 --no-per-base --by 500 -m "${BAM%.*}.median" "${BAM}"
$ tabix ${BAM%.*}.median.regions.bed.gz {1..22} | python depth_mean_stddev.py

williamrowell

#!/usr/bin/env bash

# from https://leancrew.com/all-this/2022/01/reducing-the-size-of-large-pdfs/

# Reduces the size of PDF plots created by Matplotlib.
# Assumes that the files to be reduced are named mpl[Something].pdf
# and that it's called via
#
#     reduceMPL mpl*.pdf
#

williamrowell

openpgp4fpr:945A28513CB2BE6D67602C0F37BCE34F94A3D0BE