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) |
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 | |
>>> |
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 |
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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