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meren / get_genes.py
Created Aug 11, 2020
Get gene calls and their sequences from an anvi'o contigs database
View get_genes.py
from anvio.dbops import ContigsSuperclass
# if your args object contains a `contigs_db` entry in its
# namespace all you don't need the following two lines and
# you can directly pass it to the ContigsSuperclass.
import argparse
args = argparse.Namespace(contigs_db="INFANT-GUT-TUTORIAL/SPLITAH/E_facealis/CONTIGS.db")
# get an instance of the contigs super:
contigs_db = ContigsSuperclass(args)
@meren
meren / gff_parser.py
Last active Jul 21, 2020
An update to Antti Karkman's GFF parser. Find the latest version here: https://github.com/karkman/gff_parser
View gff_parser.py
#!/usr/bin/env python
## Antti Karkman
## University of Gothenburg
## antti.karkman@gmail.com
## 2017
import gffutils
import argparse
View anvi-script-gen-alluvial
#!/usr/bin/env python
# lousy script that works with the outputs of `anvi-export-collection`
# to reconcstruct the fate of contigs for a given algorithm and bin and
# spit out some text to be visualized on https://app.rawgraphs.io/
import sys
from collections import OrderedDict
View fastalib.py
# -*- coding: utf-8 -*-
# pylint: disable=line-too-long
# v.140713
"""A very lightweight FASTA I/O library"""
import io
import sys
import gzip
import numpy
import hashlib
View summarize_blast_results.py
#!/usr/bin/env python
# Click 'Download > Multiple-file JSON' from NCBI search results page,
# unzip it, run this script in it without any parameters, get the
# markdown formatted table.
import json
import glob
# poor man's whatever:
View Oligotyping_Dockerfile_v2.1.sh
FROM ubuntu:xenial
ENV OLIGOTYPING_VERSION 2.1
ENV DEBIAN_FRONTEND noninteractive
RUN apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9
RUN apt-get update
RUN apt-get install locales
RUN locale-gen en_US.UTF-8
View for_steve.py
>>> n = 21
>>> (n * n - n) / 2
210
>>>
>>> l = ['Cys', 'Asp', 'Ser', 'Gln', 'Lys', 'Trp', 'Pro', 'Thr', 'Ile', 'Ala', 'Phe', 'Gly', 'His', 'STP', 'Leu', 'Arg', 'Met', 'Glu', 'Asn', 'Tyr', 'Val']
>>> len(l)
21
>>> len(set(sorted([''.join(sorted([t[0], t[1]])) for t in list(itertools.product(l, l)) if t[0] != t[1]])))
210
>>>
@meren
meren / gen_primer_match_report.py
Last active Jun 19, 2020
Generate a report for primer matching statistics (here you will find the Python program, two example input files (nifH gene primers and full-length nifH genes), and an example terminal output). You will need to have anvi'o installed on your system to run it. For questions: meren at uchicago.edu or tdelmont at uchicago.edu.
View gen_primer_match_report.py
# run this script like this:
#
# python gen_primer_match_report.py primers.txt sequences.txt
#
# it will generate a report file called `primer_matches_report.txt`
#
# example primers file (TAB-delimited, no spaces):
#
# name pair direction sequence
# PolF P1 F TGCGAYCCSAARGCBGACTC
@meren
meren / external-genomes.txt
Last active Jun 8, 2017
Phylogenomic tutorial helper files
View external-genomes.txt
name contigs_db_path
Bacteroides_fragilis_2334 Bacteroides_fragilis_2334.db
Bacteroides_fragilis_2346 Bacteroides_fragilis_2346.db
Bacteroides_fragilis_2347 Bacteroides_fragilis_2347.db
Escherichia_albertii_6917 Escherichia_albertii_6917.db
Escherichia_coli_6920 Escherichia_coli_6920.db
Escherichia_coli_9038 Escherichia_coli_9038.db
Prevotella_dentalis_19591 Prevotella_dentalis_19591.db
Prevotella_denticola_19594 Prevotella_denticola_19594.db
Prevotella_intermedia_19600 Prevotella_intermedia_19600.db
View boxes.R
#!/usr/bin/env Rscript
library(reshape)
library(ggplot2)
# set the work directory
setwd('~/Downloads')
# matrix-boxplots.txt should be a three-column, TAB-delimited matrix with a header for 'region', 'haplotype', and 'ratio'.
m <- data.frame(read.table('matrix-boxplots.txt', header = TRUE, sep="\t"))
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