znorgaard

name

bioinformatics-python

description

Use when writing Python that handles SAM/BAM/CRAM, FASTA/FASTQ, VCF, or BED files; building test fixtures with bioinformatics records; parsing CIGARs or sequencing read structures; doing genomic interval overlap queries; or modeling typed delimited (TSV/CSV) records. Surfaces fgpyo, pybedlite, and fgmetric features so common primitives (SamBuilder, Template, Cigar, Metric, MetricWriter, BedSource, OverlapDetector) are used instead of hand-rolled equivalents. fgmetric.Metric is preferred over fgpyo.util.Metric.

Using fgpyo, pybedlite, and fgmetric

Three Fulcrum Genomics libraries (fgpyo, pybedlite, fgmetric — all on PyPI) cover most Python bioinformatics primitives. Default to them. Do not hand-roll the equivalents.

If they aren't installed in the project, add them. If a project bans them, do not push.

stephenturner

library(tidyverse)

# Get Gene Summary info
gs_orig <- read_tsv("https://ftp.ncbi.nlm.nih.gov/gene/DATA/gene_summary.gz")
gs <- gs_orig |>
  janitor::clean_names() |>
  set_names(str_replace, "number_tax_id", "tax_id") |>
  filter(tax_id==9606) |>
  distinct()
gs

tomsing1

Installing Nextflow on a Mac

• Install JAVA 8

 brew install adoptopenjdk8

• Install Nextflow: curl https://get.nextflow.io | bash in the current directory
• Optional: Move the nextflow binary to a directory that is in the PATH.

naomiajacobs

from dnachisel import *

# Subbed in `CCTCCT` for `AAAGTT` to account for proline substitution
virus = 'ATGTTTGTTTTTCTTGTTTTATTGCCACTAGTCTCTAGTCAGTGTGTTAATCTTACAACCAGAACTCAATTACCCCCTGCATACACTAATTCTTTCACACGTGGTGTTTATTACCCTGACAAAGTTTTCAGATCCTCAGTTTTACATTCAACTCAGGACTTGTTCTTACCTTTCTTTTCCAATGTTACTTGGTTCCATGCTATACATGTCTCTGGGACCAATGGTACTAAGAGGTTTGATAACCCTGTCCTACCATTTAATGATGGTGTTTATTTTGCTTCCACTGAGAAGTCTAACATAATAAGAGGCTGGATTTTTGGTACTACTTTAGATTCGAAGACCCAGTCCCTACTTATTGTTAATAACGCTACTAATGTTGTTATTAAAGTCTGTGAATTTCAATTTTGTAATGATCCATTTTTGGGTGTTTATTACCACAAAAACAACAAAAGTTGGATGGAAAGTGAGTTCAGAGTTTATTCTAGTGCGAATAATTGCACTTTTGAATATGTCTCTCAGCCTTTTCTTATGGACCTTGAAGGAAAACAGGGTAATTTCAAAAATCTTAGGGAATTTGTGTTTAAGAATATTGATGGTTATTTTAAAATATATTCTAAGCACACGCCTATTAATTTAGTGCGTGATCTCCCTCAGGGTTTTTCGGCTTTAGAACCATTGGTAGATTTGCCAATAGGTATTAACATCACTAGGTTTCAAACTTTACTTGCTTTACATAGAAGTTATTTGACTCCTGGTGATTCTTCTTCAGGTTGGACAGCTGGTGCTGCAGCTTATTATGTGGGTTATCTTCAACCTAGGACTTTTCTATTAAAATATAATGAAAATGGAACCATTACAGATGCTGTAGACTGTGCACTTGACCCTCTCTCAGAAACAAAGTGTACGTTGAAATCCTTCAC

upkarlidder

Deep Learning Hands-On Series with Eric Schles

05/22 - Deep Learning Hands-On Series - Data Exploration and API First Design 🎥

05/29 - Deep Learning Hands-On Series - Model Tuning 🎥

06/05 - Deep Learning Hands-On Series - Monitoring [cancelled]

Resources

Notebooks

mikelove

RUNS, = glob_wildcards("fastq/{run}_1.fastq.gz")

SALMON = "/proj/milovelab/bin/salmon-1.4.0_linux_x86_64/bin/salmon"

ANNO = "/proj/milovelab/anno"

rule all:
    input: expand("quants/{run}/quant.sf", run=RUNS)

rule salmon_index:

hannes-brt

# Copyright 2019 Hannes Bretschneider
# 
# Permission is hereby granted, free of charge, to any person
# obtaining a copy of this software and associated documentation
# files (the "Software"), to deal in the Software without
# restriction, including without limitation the rights to use,
# copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the
# Software is furnished to do so, subject to the following
# conditions:

toniher

#!/bin/bash

# Based on https://github.com/sylabs/singularity/issues/1537
# Usage: bash docker2singularity.sh mydockerimg mysingularity.simg

set -ueo pipefail

IMG=$1
FILEOUT=$2
PORT=${3:-5000}

hiraksarkar

## requirement bed tools
BIN='/home/hirak/bedtools2/bin'
## Gencode 
## gencode.v29.chr_patch_hapl_scaff.annotation.gtf
GTF_FILE="gencode.v29.chr_patch_hapl_scaff.annotation.gtf"

# extract transcript boundaries 
cat $GTF_FILE | awk 'BEGIN{OFS="\t";} $3=="transcript" {print $1,$4-1,$5,$12}' | tr -d "\"" | tr -d ";" | $BIN/sortBed > gencode_transcript_intervals.bed

# merge exon boundaris 

ColinFay

snippet module
	${1:name}UI <- function(id){
		ns <- NS(id)
		tagList(
		
		)
	}

	${1:name} <- function(input, output, session){