Jason D Limberis SemiQuant

Molecular Biologist | Bioinfomatician

SemiQuant / bacterial gff to mRNA

Created August 21, 2023 16:32

Convert NCBI gff for bacteria to a usable format for bcftools csq

	import gffutils

	input_gff_file = "Mycobacterium_tuberculosis_H37Rv_gff_v4.gff"
	output_gff_file = input_gff_file.replace('.gff', '_fixed.gff')

	# Create a new GFF database
	db = gffutils.create_db(input_gff_file, dbfn=':memory:', force=True, merge_strategy='replace')

	# Create a new GFF writer
	output_handle = open(output_gff_file, 'w')

SemiQuant / ImpactHunter.py

Last active June 3, 2023 15:57

Summarize the publication of a researcher, and calculate their IFs for first and last authorships in a data range

	#!/bin/python
	from Bio import Entrez
	import subprocess
	import ast
	import statistics
	def search_publications(author_name, start_year, end_year):
	# Search PubMed for publications by the author within the specified date range
	query = f'({author_name}[Author]) AND (Journal Article[Publication Type]) NOT (Clinical Trial[Publication Type]) NOT preprint[pt] NOT review[pt] AND ({start_year}:{end_year}[PDAT])'
	handle = Entrez.esearch(db='pubmed', term=query)
	record = Entrez.read(handle)

SemiQuant / TabbedTabs_Flex

Created May 10, 2019 08:38

Tab box in a flex dashboard with tabbed columns

	---
	title: "Tabbed Tabs"
	author: "SemiQuant"
	date: "5/10/2019"
	output:
	flexdashboard::flex_dashboard:
	orientation: columns
	vertical_layout: fill
	---

SemiQuant / Dave Gist Tutorial

Created October 11, 2018 09:55

This is what you do, Dave.