Cory cory-weller

Overview

script_specific.sh is an example for extracting sequences between two anchors.

The output is a three-column tab-delimited table in the format

| anchor1 | insert | anchor2 |

Only lines that match the pattern are included.

min_insert is the minimum number of characters needed to be a match.

Instructions based on those from the Biowulf team

You must be on the NIH network on campus, or connected to VPN.

Then, start an interactive session from the command-line on Biowulf:

# On BIOWULF:
sinteractive --mem 20G --time 8:00:00 --gres lscratch:20 --tunnel

	@HD VN:1.5 SO:unsorted
	@SQ SN:chr1 LN:248956422 M5:6aef897c3d6ff0c78aff06ac189178dd AS:20 UR:/seq/references/kendrix/v0/kendrix.fasta SP:Homo sapiens
	@SQ SN:chr2 LN:242193529 M5:f98db672eb0993dcfdabafe2a882905c AS:20 UR:/seq/references/kendrix/v0/kendrix.fasta SP:Homo sapiens
	@SQ SN:chr3 LN:198295559 M5:76635a41ea913a405ded820447d067b0 AS:20 UR:/seq/references/kendrix/v0/kendrix.fasta SP:Homo sapiens
	@SQ SN:chr4 LN:190214555 M5:3210fecf1eb92d5489da4346b3fddc6e AS:20 UR:/seq/references/kendrix/v0/kendrix.fasta SP:Homo sapiens
	@SQ SN:chr5 LN:181538259 M5:a811b3dc9fe66af729dc0dddf7fa4f13 AS:20 UR:/seq/references/kendrix/v0/kendrix.fasta SP:Homo sapiens
	@SQ SN:chr6 LN:170805979 M5:5691468a67c7e7a7b5f2a3a683792c29 AS:20 UR:/seq/references/kendrix/v0/kendrix.fasta SP:Homo sapiens
	@SQ SN:chr7 LN:159345973 M5:cc044cc2256a1141212660fb07b6171e AS:20 UR:/seq/references/kendrix/v0/kendrix.fasta SP:Homo sapiens
	@SQ SN:chr8 LN:145138636 M5:c67955b5f7815a9a1edfaa15893d3616 AS:20 UR:/seq/references/kendrix/v0/kendrix.fasta S

	#!/usr/bin/env bash

	# DETAILS: Functions by setting the field separator to a regular expression capturing ">", tab, and space.
	# For each row in the file, if it is a header (begins with ">"), update the value of variable s
	# to be equal to the first word in the header, and write a header line only containing that first word.
	# Every line is written to a file <first_word_in_header>.fa, splitting the file into separate contigs.

	awk -F "(^>\|\t\| )" '{if($0 ~ /^>/) {s=$2".fa"; print ">"$2 > s} else print > s}' ${inFasta}

	#!/usr/bin/env bash

	# Installs singularity

	sudo apt-get update

	sudo apt-get install -y --no-install-recommends \
	build-essential \
	libssl-dev \
	uuid-dev \

	#!/usr/bin/env bash

	echo "Running ampliconsplit.sh $@"

	## convenience functions for arg parsing
	usage_error () { echo >&2 "ERROR: $1"; exit 2; }
	assert_argument () { test "$1" != "$EOL" \|\| usage_error "$2 requires an argument. Try --help"; }

	# Parse Arguments
	## import $@

	SYMBOL ENSEMBL seqnames start end width strand
	ENSG00000243485 chr1 29554 31109 1556 +
	FAM138A ENSG00000237613 chr1 34554 36081 1528 -
	OR4F5 ENSG00000186092 chr1 65419 71585 6167 +
	ENSG00000238009 chr1 89295 133723 44429 -
	ENSG00000239945 chr1 89551 91105 1555 -
	ENSG00000239906 chr1 139790 140339 550 -
	ENSG00000241860 chr1 141474 173862 32389 -
	ENSG00000241599 chr1 160446 161525 1080 +
	ENSG00000286448 chr1 266855 268655 1801 +


	#!/usr/bin/env Rscript
	library(Seurat)
	library(DoubletFinder)

	## Standard pre-processing
	seurat_obj <- CreateSeuratObject(kidney.data)
	seurat_obj <- NormalizeData(seurat_obj)
	seurat_obj <- FindVariableFeatures(seurat_obj, selection.method = "vst", nfeatures = 2000)

	#!/usr/bin/env python
	'''finds a header within a given fasta file, then prints the desired nucleotide ranges to STDOUT'''

	import sys
	import argparse
	import regex as re

	def wrap_fasta(seq):
	'''wraps sequence every 80 characters with newlines'''
	return '\n'.join([seq[x:x+80] for x in range(0,len(seq),80)])