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#!/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

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# -*- 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

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#!/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:

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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

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>>> 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
>>>

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# 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

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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

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#!/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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FROM ubuntu:xenial

ENV ANVIO_VERSION 5.5

ENV DEBIAN_FRONTEND noninteractive

RUN apt-get update
RUN apt-get install locales
RUN locale-gen en_US.UTF-8
ENV LANG='en_US.UTF-8' LANGUAGE='en_US:en' LC_ALL='en_US.UTF-8'

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#!/usr/bin/env python

# you run this first:
#
#    python 01-gen-nucmer-jobs.py affiliations.txt MAGs_input_dir
#

import os
import sys
import anvio.fastalib as u