Alex Reynolds alexpreynolds

## README.md

      
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                alexpreynolds
                / README.md
            
            
              Created
              February 5, 2024 08:28
                — forked from manzt/README.md
            
              
                minimal higlass + vite
              
          
    minimal higlass vite

pnpm install
pnpm dev

  
## example.bed
chr7	5563000	5573000	TxFlnk	10.26175	+
chr17	39843800	39853800	TxFlnk	10.16751	+
chr6	32935400	32945400	TxFlnk	10.10112	+
chr22	39915200	39925200	TxFlnk	10.02993	+
chr17	79475800	79485800	TxFlnk	9.96371	+
chr11	65264200	65274200	TxFlnk	9.72111	+
chr19	3977800	3987800	TxFlnk	9.71104	+
chr12	56551000	56561000	TxFlnk	9.69233	+
chr1	234739400	234749400	TxFlnk	9.66319	+
chr20	42085400	42095400	TxFlnk	9.66160	+

## index.html
<!DOCTYPE html>
<html lang="en">

<head>
  <meta charset="UTF-8" />
  <meta http-equiv="X-UA-Compatible" content="IE=edge" />
  <meta name="viewport" content="width=device-width, initial-scale=1.0" />
  <title>Client-side BED file upload test</title>
</head>

## app.js
const PORT_NUMBER = 3000;

// Requiring express for routing
const express = require('express');

// Creating app from express
const app = express();

// Requiring in-built file system
const fs = require('fs');

## blog.pl
#!/usr/bin/perl -w
use strict;

# Utility to help format my notes, progress, results etc in atomic chunks,
# so they can be organized by project, data, technology, "todo" lists, etc.

if (@ARGV < 1) {
    die " Usage:   $0 <new | parse> \n";
    # Hidden optional arguments, not tested lately:   [tag-list or +/-days]\n";
}

## blog0.css
p.todo { color:red; margin:0; padding:0; font-size:0.8em; }
p.done { color:green; margin:0; padding:0; font-size:0.7em; }
p.info { color:gray; margin:0; padding:0; font-size:0.8em; }
p.tags { color:gray; margin:0; padding:0; font-size:0.7em; }
p.cwd{ color:gray; margin:0; padding:0; font-size:0.8em; }
p.src { color:gray; margin:0; padding:0; font-size:0.8em; }
p.subject { color:black; margin:0; padding:0; font-size:1.5em; font-weight:bolder; }
.novel { color:green; font-weight:bolder; }
.xfac { color:#B80000; font-weight:bolder; }
.jaspar { color:#3399FF; font-weight:bolder; }

## .textblogrc
weblocal /home/areynolds/public_html
webroot /~areynolds
blogdir blog

## split_scores_by_chr.py
#!/usr/bin/env python

import gzip

ASSEMBLY = "hg38"
chromosome_sizes = { "hg38" :
    [
        {
            "name": 1,
            "size": 248956422

## aggregate_scores.py
#!/usr/bin/env python

import sys
import math
import pandas as pd
import numpy as np
from scipy import stats
import json
from json import JSONEncoder
import zipfile

## crop_and_stitch.py
#!/usr/bin/env python

import subprocess
import sys
from os import listdir
from os.path import isfile, join
import time

# image, crop dimensions
img_dir = sys.argv[1]
	chr7 5563000 5573000 TxFlnk 10.26175 +
	chr17 39843800 39853800 TxFlnk 10.16751 +
	chr6 32935400 32945400 TxFlnk 10.10112 +
	chr22 39915200 39925200 TxFlnk 10.02993 +
	chr17 79475800 79485800 TxFlnk 9.96371 +
	chr11 65264200 65274200 TxFlnk 9.72111 +
	chr19 3977800 3987800 TxFlnk 9.71104 +
	chr12 56551000 56561000 TxFlnk 9.69233 +
	chr1 234739400 234749400 TxFlnk 9.66319 +
	chr20 42085400 42095400 TxFlnk 9.66160 +
	<!DOCTYPE html>
	<html lang="en">

	<head>
	<meta charset="UTF-8" />
	<meta http-equiv="X-UA-Compatible" content="IE=edge" />
	<meta name="viewport" content="width=device-width, initial-scale=1.0" />
	<title>Client-side BED file upload test</title>
	</head>
	const PORT_NUMBER = 3000;

	// Requiring express for routing
	const express = require('express');

	// Creating app from express
	const app = express();

	// Requiring in-built file system
	const fs = require('fs');
	#!/usr/bin/perl -w
	use strict;

	# Utility to help format my notes, progress, results etc in atomic chunks,
	# so they can be organized by project, data, technology, "todo" lists, etc.

	if (@ARGV < 1) {
	die " Usage: $0 <new \| parse> \n";
	# Hidden optional arguments, not tested lately: [tag-list or +/-days]\n";
	}
	p.todo { color:red; margin:0; padding:0; font-size:0.8em; }
	p.done { color:green; margin:0; padding:0; font-size:0.7em; }
	p.info { color:gray; margin:0; padding:0; font-size:0.8em; }
	p.tags { color:gray; margin:0; padding:0; font-size:0.7em; }
	p.cwd{ color:gray; margin:0; padding:0; font-size:0.8em; }
	p.src { color:gray; margin:0; padding:0; font-size:0.8em; }
	p.subject { color:black; margin:0; padding:0; font-size:1.5em; font-weight:bolder; }
	.novel { color:green; font-weight:bolder; }
	.xfac { color:#B80000; font-weight:bolder; }
	.jaspar { color:#3399FF; font-weight:bolder; }
	weblocal /home/areynolds/public_html
	webroot /~areynolds
	blogdir blog
	#!/usr/bin/env python

	import gzip

	ASSEMBLY = "hg38"
	chromosome_sizes = { "hg38" :
	[
	{
	"name": 1,
	"size": 248956422
	#!/usr/bin/env python

	import sys
	import math
	import pandas as pd
	import numpy as np
	from scipy import stats
	import json
	from json import JSONEncoder
	import zipfile
	#!/usr/bin/env python

	import subprocess
	import sys
	from os import listdir
	from os.path import isfile, join
	import time

	# image, crop dimensions
	img_dir = sys.argv[1]