conchoecia

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conchoecia

#!/usr/bin/env python3

# script: make_notebooks.py
# author: darrin t schultz
# date  : 20161004

# make_notebooks.py is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.

conchoecia

import glob
import os


"""
snakemake interprets some output files as being ambiguous since the processing pipeline is not a DAG.
as a results you must use --allow-ambiguity
example usage:
snakemake --cores 90
"""

conchoecia

import os
from pathlib import Path
import yaml

configfile: "directories.yaml"

# The yaml file should look like this below. Just an object called "directories"
#  and a list of directories in which the pipeline should look for things.
#
#  directories:

conchoecia

# The goal of this script is to map reads to a region and to assemble it de novo.
# This is useful for scenarios in which there are gaps between known homologous sequence,
#  like what one might encounter when doing a de novo mitochondrial genome assembly
#  or assembling a gene locus from a transcript.
#

#The steps for this assembly process are.
# 1) Map all of the reads to the scaffold
# 2) Extract all of the read pairs from the original fastq files and make new fastqs.
# 3) Use the new Fastq files in a de novo Spades assembly.

conchoecia

#!/bin/bash
# this script makes plots of positions of linker sequences in HiC/Chicago libraries

#!/bin/bash

function processthis {
    OUT1="${LIB}fpos.txt"
    IN1="${LIB}_f.fastq.gz"
    OUT2="${LIB}rpos.txt"
    IN2="${LIB}_r.fastq.gz"

conchoecia

"""
fraction	lum	NaCl_Conc	type
1	4213	0.06	step
2	5123	0.06	step
3	7813	0.06	step
4	12988	0.06	step
5	24373	0.06	step
6	24843	0.1	slope
7	7513	0.1	slope
8	5358	0.2	step

conchoecia

"""
Author: Darrin Schultz @conchoecia
File: Transcriptome assembly, annotation, and db creation

Instructions:
  - To run this script and all of its analyses: make sure that python 3,
    snakemake, and biopython are installed on your Unix computer.
  - Execute the following command: `snakemake --cores 45`, replacing `45`
    with the number of threads available on your machine.
"""

conchoecia

#!/usr/bin/env python

myseq = "ACNNNNNNNNNNNNNCATGTACTTGGATCTATCGGTGATCGGATCGGTATGCGTACGAGTGTCAGTCNNNNNNNNNNNNNNNACGTGGTATGCGGCATGCGTAGCGTCAGCTAGCTGATATTGCGTAGCNNNNNNNNNNGGTATGCGTG"

def contig_ranges(seq, sub):
    indices = list(find_all(seq, sub))
    gap_starts = []
    gap_stops  = []
    gap_ranges = []
    prev = -1