wflynny

# Some universal variables
NCELLS=6000
OUTPUT_NAME="nice-name"
FASTQ_DIR="/path/to/fastqs"
REFERENCE_GENOME="/path/to/reference_dir"
[[ -z "${PBS_NUM_PPN}" ]] && NCORES=20 || NCORES=${PBS_NUM_PPN}

# When reads look like:
# sample-name_S?_L00?_R1_001.fastq.gz
# sample-name_S?_L00?_R2_001.fastq.gz

wflynny

# Visit the Ensembl ftp site.
# ftp://ftp.ensembl.org/pub/release-95/
#
# You want to find data under the following two URLs:
# 1.  ftp://ftp.ensembl.org/pub/release-95/fasta/[YOUR_SPECIES_HERE]/dna/
# 2.  ftp://ftp.ensembl.org/pub/release-95/gtf/[YOUR_SPECIES_HERE]/
#
# The first file of interest is under the fasta URL:
#     [YOUR_SPECIES_HERE].[ASSEMBLY].dna.primary_assembly.fa.gz
# or, if that doesn't exist,

wflynny

#!/usr/bin/env bash
#### PBS preamble

#PBS -N jupyter-server
#PBS -o /path/to/software/logs/jupyter-server.${PBS_JOBID%%.*}.out

#PBS -j oe
#PBS -m n

#PBS -l mem=128GB

wflynny

_grab_ip() {
  jobid=$1
  port=$2
  hostname=$(qstat -f ${jobid} | grep -oP "exec_host = (\K[a-z0-9]+)")
  echo "http://${hostname}:${port}"
}

_submit_job() {
  queue=$1
  port=$2

wflynny

from sklearn.cluster import KMeans
import numpy as np
import pandas as pd
import scanpy as sc

def load_hto_matrix(mtx_dir):
    raw_htos = sc.read_mtx(mtx_dir + "/matrix.mtx.gz").T
    raw_htos.var = pd.read_csv(mtx_dir + "/features.tsv.gz", header=None, index_col=0)
    raw_htos.obs = pd.read_csv(mtx_dir + "/barcodes.tsv.gz", header=None, index_col=0)
    raw_htos = raw_htos[:, ~raw_htos.var_names.isin(["unmapped"])]

wflynny

import re
import argparse

parser = argparse.ArgumentParser()
parser.add_argument("-i", "--infile", required=True)
parser.add_argument("-o", "--outfile", required=True)
args = parser.parse_args()

gene_matcher = re.compile('\tgene\t.*gene_id (".*?");.*Name (".*?");')
parent_matcher = re.compile('gene_id (".*?");.*Parent (".*?");')

wflynny

#!/usr/bin/env bash

TEMP=$(getopt -o hsg --long help,snapshot,gpu -n 'susuage' -- "$@")

if [ $? != 0 ] ; then echo "Terminating..." >&2 ; exit 1 ; fi

# Note the quotes around `$TEMP': they are essential!
eval set -- "$TEMP"

SNAPSHOT=false

wflynny

import re
from pathlib import Path
from xml.etree import ElementTree as ET

import numpy as np
from skimage import exposure
from skimage.io import imread, imsave, imshow
from skimage.filters import threshold_otsu, gaussian

wflynny

from matplotlib.text import Annotation
from matplotlib.legend_handler import HandlerBase
from matplotlib import patheffects
from matplotlib.colors import CSS4_COLORS, hex2color

class AnnotationHandler(HandlerBase):
    def create_artists(self, legend, artist, xdescent, ydescent,
                       width, height, fontsize, trans):
        a = Annotation(
            artist.get_text(), [width/2, height/2],

wflynny

###################
# chord diagram
import matplotlib.pyplot as plt
from matplotlib.path import Path as mplPath
import matplotlib.patches as patches

import numpy as np
import pandas as pd

LW = 0.3