Conrad Stack ConradStack

Criollo (B97 CIRAD)

ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF_000208745.1_Criollo_cocoa_genome_V2 ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000208745.2_Criollo_cocoa_genome_V2

SAM and BAM filtering one-liners

@author: David Fredman, [email protected] (sans poly-A tail)
@dependencies: http://sourceforge.net/projects/bamtools/ and http://samtools.sourceforge.net/

Please extend with additional/faster/better solutions via a pull request!

BWA mapping (using piping for minimal disk I/O)

	#!/usr/bin/env perl

	use warnings;use strict;

	my ($header,$sequence);
	$header = <>;
	chomp $header;
	while(my $line = <>){
	chomp $line;
	if($line =~ /^>/){


	# Create a new fasta file given a fasta file and list of sequence names
	# - outputting the long_name does/did not seem to work properly in the faidx script that is packaged with pyfaidx


	from pyfaidx import *

	# read fasta file
	fa = Fasta('test.fa')

	/*
	From [this stackover post](https://stackoverflow.com/questions/2418527/sql-server-query-to-get-the-list-of-columns-in-a-table-along-with-data-types-no)
	*/

	SELECT
	c.name 'Column Name',
	t.Name 'Data type',
	c.max_length 'Max Length',
	c.precision ,
	c.scale ,


	# Derived from https://towardsdatascience.com/how-to-fine-tune-gpt-2-for-text-generation-ae2ea53bc272

	import os
	import pandas as pd
	from transformers import GPT2LMHeadModel, GPT2Tokenizer
	import numpy as np
	import random
	import torch
	from torch.utils.data import Dataset, DataLoader


	# From [this tutorial](https://www.tecmint.com/clear-ram-memory-cache-buffer-and-swap-space-on-linux/)
	sync; echo 1 > /proc/sys/vm/drop_caches