wckdouglas

wckdouglas

# using starship: https://starship.rs/
eval "$(starship init zsh)"

# never beep
setopt NO_BEEP

# auto completion: https://dev.to/rossijonas/how-to-set-up-history-based-autocompletion-in-zsh-k7o
zstyle ':completion:*' matcher-list '' 'm:{a-zA-Z}={A-Za-z}' 'r:|=*' 'l:|=* r:|=*'
autoload -U compinit && compinit

wckdouglas

#!/usr/bin/env python

import subprocess
from pathlib import Path

import numpy as np
import pandas as pd
import luigi
from luigi.contrib.sge import SGEJobTask # fixed SGE in this branch https://github.com/wckdouglas/luigi
from luigi.mock import MockTarget

wckdouglas

# load libraries

from keras import backend as K
from keras.models import Sequential, model_from_json
from keras.layers import Dense, Conv1D,\
                         Flatten, MaxPool1D,  \
                         Dropout, LSTM, \
                         Bidirectional
from sequencing_tools.fastq_tools import reverse_complement, \
                    onehot_sequence_encoder

wckdouglas

chr1    566309  566361  -       GTGATT
chr1    568081  568136  +       TTGAAA,TTGAAA,TTGAAA
chr1    16840712        16840773        -       TACTTA
chr1    17067025        17222642        +       TGGCAG
chr1    45196732        45196802        -       TCGCCT
chr1    161424755       161432231       -       GCGTTG
chr1    161493635       161493697       -       TGGTGG
chr1    173834762       173834818       -       TTGTAA
chr1    173835773       173835846       -       TCCACA
chr1    204475714       204475737       +       TCAAGT

wckdouglas

I have reused the code enough to make a package out of it.

The python package is deposited at Github. with an example in Jupyter notebook.

⚠️ this gist is out-of-date, please see the diffexpr package for a maintained version of the code

wckdouglas

def make_regions(chromosome_length, how_many_bases_to_look_at):
    start = 0
    end = start + leap
    while end < chromosome_length:
        yield (start, end)
        start = end
        end = end + how_man_bases_to_look_at
    yield (start, chromosome_length)

wckdouglas

>PrefixPE/1
AATGATACGGCGACCACCGAGATCTACACGTTCAGAGTTCTACAGTCCGACGATC
>PrefixPE/2
CAAGCAGAAGACGGCATACGAGATNNNNNNGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT
>PCR_Primer1
AATGATACGGCGACCACCGAGATCTACACGTTCAGAGTTCTACAGTCCGACGATC
>PCR_Primer1_rc
GATCGTCGGACTGTAGAACTCTGAACGTGTAGATCTCGGTGGTCGCCGTATCATT
>PCR_Primer2
CAAGCAGAAGACGGCATACGAGATNNNNNNGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT

wckdouglas

library(grid)

# http://stackoverflow.com/questions/23588127/match-legend-text-color-in-geom-text-to-symbol
coloring_legend_text <- function(p){
    g <- ggplotGrob(p)
    names.grobs <- grid.ls(grid.force(g))$name 
    labels <- names.grobs[which(grepl("label", names.grobs))]

    # Get the colours
    # The colours are the same as the colours of the plotted points.

wckdouglas

/* Solarized Dark 

For use with Jekyll and Pygments

http://ethanschoonover.com/solarized

SOLARIZED HEX      ROLE
--------- -------- ------------------------------------------
base03    #002b36  background
base01    #586e75  comments / secondary content