🐝

Rodrigo O. Polo ropolomx

🐝

https://about.me/ropolo

ropolomx / screen_cheatsheet.markdown

Created October 7, 2020 15:15 — forked from jctosta/screen_cheatsheet.markdown

Screen Cheatsheet

Screen Quick Reference

Description	Command
Start a new session with session name	`screen -S <session_name>`
List running sessions / screens	`screen -ls`
Attach to a running session	`screen -x`
Attach to a running session with name	`screen -r <session_name>`

ropolomx / conda_export.sh

Created September 6, 2019 19:23

conda env export --no-builds

ropolomx / extract_fasta_samtools.sh

Created April 12, 2019 01:43

Extract sequences from FASTA file by name

samtools faidx Trinity.fasta -r PL_transcript_id.csv > PL_extract.fasta

ropolomx / colors.csv

Created March 31, 2019 04:40 — forked from lokeb/colors.csv

Color names with Hex Code obtained from https://en.wikipedia.org/wiki/List_of_colors:_A%E2%80%93F

ropolomx / qiime_manifest.sh

Last active February 4, 2019 19:03

Create QIIME manifest in command line

	# Send filenames to manifest file

	ls *.fastq.gz > manifest.txt

	# Duplicate first column and add comma separation

	awk -F',' '{$1=$1","$1}1' OFS=',' manifest.txt > tmp && mv tmp manifest.txt

	# If necessary remove text information from first column in Vim visual mode

ropolomx / extract_ribo.py

Created January 11, 2019 07:43

	#!/usr/bin/env python3
	from Bio import SeqIO
	from Bio.SeqRecord import SeqRecord
	import sys

	gbank = SeqIO.parse(open(sys.argv[1], "r"), "genbank")
	output_handle=open("rRNAs.fa","w")

	rRNAs = []
	for genome in gbank :

ropolomx / fosmid_assembly.smk

Last active November 13, 2018 23:44

	import os
	import glob

	SAMPLE = ['FC-F1', 'FC-H1', 'FC-I1']

	FWD = expand('{sample}/{sample}_unmapped_fwd.fastq', sample=SAMPLE)
	REV = expand('{sample}/{sample}_unmapped_rev.fastq', sample=SAMPLE)

	rule all:
	input:

ropolomx / nullarbor_sample_files.sh

Last active October 24, 2018 00:09

Prepare sample files for Nullarbor

	# send file names of R1s to a file
	ls *_R1_001.fastq.gz > samples.tab

	# depending on which version of awk/gawk we can do inplace changes
	awk -F'\t' '{$1=$1"\t"$1}1' OFS='\t' samples.tab > tmp && mv tmp samples.tab

	# Extract sample name
	sed -i 's/$[0-9+]$$[A-Z+]$.*\.fastq\.gz\t/\1\2\t/g' samples.tab

	# Copy file names

ropolomx / kraken.smk

Created May 25, 2018 19:55

Snakefile for running Kraken

	import os
	import glob

	KRAKEN_DB = 'fmdv_kraken_db'

	FILTER = ["0.05","0.2"]

	SAMPLE = [os.path.basename(f).split('_')[0] for f in glob.glob('../fmdv_fastq/_1_.fastq')]

	rule all:

ropolomx / make_amr_analytic_matrix.R

Last active May 25, 2018 17:59

Create analytic matrix from AMR Plus Plus results


	# Load packages -----------------------------------------------------------

	library(tidyverse)

	# library(stringr)
	# Need to load if using tidyverse version 1.1.1. Not necessary to load separately if using tidyverse 1.2.1

	library(here)