Billy Rowell williamrowell

## openpgp.md

      
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                williamrowell
                / openpgp.md
            
            
              Created
              November 25, 2022 06:30
            
          
    openpgp4fpr:945A28513CB2BE6D67602C0F37BCE34F94A3D0BE

  
## HG002.giabv421.summary.csv

          
            Type
            Filter
            TRUTH.TOTAL
            TRUTH.TP
            TRUTH.FN
            QUERY.TOTAL
            QUERY.FP
            QUERY.UNK
            FP.gt
            METRIC.Recall
            METRIC.Precision
            METRIC.Frac_NA
            METRIC.F1_Score
            TRUTH.TOTAL.TiTv_ratio
            QUERY.TOTAL.TiTv_ratio
            TRUTH.TOTAL.het_hom_ratio
            QUERY.TOTAL.het_hom_ratio

            
              INDEL
              ALL
              525467
              522308
              3159
              1004238
              3119
              456981
              1746
              0.993988
              0.994301
              0.455052
              0.994144
              
              
              1.52827573414
              2.00682078193

            
              INDEL
              PASS
              525467
              522308
              3159
              1004238
              3119
              456981
              1746
              0.993988
              0.994301
              0.455052
              0.994144
              
              
              1.52827573414
              2.00682078193

            
              SNP
              ALL
              3365126
              3362716
              2410
              4365804
              848
              999299
              476
              0.999284
              0.999748
              0.228892
              0.999516
              2.10012756571
              1.78797411801
              1.58119585325
              1.46169126378

            
              SNP
              PASS
              3365126
              3362716
              2410
              4365804
              848
              999299
              476
              0.999284
              0.999748
              0.228892
              0.999516
              2.10012756571
              1.78797411801
              1.58119585325
              1.46169126378

## reduceMPL.sh
#!/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
#

## master_to_main.md

      
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                williamrowell
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              Last active
              November 27, 2021 04:58
            
              
                change default branch from master to main
              
          
Move the ‘master’ branch to ‘main’

git branch -m master main

Push ‘main’ to remote repo

git push -u origin main

  
## 00_README.md

      
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                williamrowell
                / 00_README.md
            
            
              Created
              April 30, 2020 02:54
            
              
                Simplified DeepVariant singularity wrappers for small PacBio datasets
              
          
    Simplified DeepVariant singularity wrappers for small PacBio datasets

Adapted from DeepVariant documentation.
CPU-only

# pull docker image (only need to do this once)
BIN_VERSION=0.10.0
singularity pull docker://google/deepvariant:"${BIN_VERSION}"

  
## depth_mean_stddev.py
#!/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

## dotplot workflow
module load smrtanalysis/mainline jre parallel

# extract fasta from ccs readset
bam2fasta -u -o consensusreadset consensusreadset.bam

# make dotplots with gepard
python split_ccs_fasta.py consensusreadset.fasta
## download gepard and prepare it
wget https://github.com/univieCUBE/gepard/archive/v1.40.0.zip
unzip v1.40.0.zip

## mockingbird.py
#!/usr/bin/env python
"""Download corpus of tweets for user SCREEN_NAME and generate new tweets.

"""
import os
import sys
import json
import argparse
import twitter
import markovify

## error_jitter.m
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 (rowellw@janelia.hhmi.org)

## cellFromTextFile.m
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);
Type	Filter	TRUTH.TOTAL	TRUTH.TP	TRUTH.FN	QUERY.TOTAL	QUERY.FP	QUERY.UNK	FP.gt	METRIC.Recall	METRIC.Precision	METRIC.Frac_NA	METRIC.F1_Score	TRUTH.TOTAL.TiTv_ratio	QUERY.TOTAL.TiTv_ratio	TRUTH.TOTAL.het_hom_ratio	QUERY.TOTAL.het_hom_ratio
INDEL	ALL	525467	522308	3159	1004238	3119	456981	1746	0.993988	0.994301	0.455052	0.994144			1.52827573414	2.00682078193
INDEL	PASS	525467	522308	3159	1004238	3119	456981	1746	0.993988	0.994301	0.455052	0.994144			1.52827573414	2.00682078193
SNP	ALL	3365126	3362716	2410	4365804	848	999299	476	0.999284	0.999748	0.228892	0.999516	2.10012756571	1.78797411801	1.58119585325	1.46169126378
SNP	PASS	3365126	3362716	2410	4365804	848	999299	476	0.999284	0.999748	0.228892	0.999516	2.10012756571	1.78797411801	1.58119585325	1.46169126378
	#!/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
	#
	#!/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
	module load smrtanalysis/mainline jre parallel

	# extract fasta from ccs readset
	bam2fasta -u -o consensusreadset consensusreadset.bam

	# make dotplots with gepard
	python split_ccs_fasta.py consensusreadset.fasta
	## download gepard and prepare it
	wget https://github.com/univieCUBE/gepard/archive/v1.40.0.zip
	unzip v1.40.0.zip
	#!/usr/bin/env python
	"""Download corpus of tweets for user SCREEN_NAME and generate new tweets.

	"""
	import os
	import sys
	import json
	import argparse
	import twitter
	import markovify
	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 (rowellw@janelia.hhmi.org)
	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);