Colelyman

import random

simulate_deletion_lens = range(30) #deletions to simulate - here, 0 to 30bp deletions. The longer the deletion, the more adapter will be included in the read
simulate_mismatch_counts = range(3) #number of mismatches to simulate - her, 0, 1, and 2 mismatches between r1 and r2. The higher the number of mismatches, the less likely the read will be merged.
read_len = 210 #length of reads to generate

read        = '                                 CGGATGTTCCAATCAGTACGCAGAGAGTCGCCGTCTCCAAGGTGAAAGCGGAAGTAGGGCCTTCGCGCACCTCATGGAATCCCTTCTGCAGCACCTGGATCGCTTTTCCGAGCTTCTGGCGGTCTCAAGCACTACCTACGTCAGCACCTGGGACCCCGCCACCGTGCGCCGGGCCTTGCAGTGGGCGCGCTACCTGCGCCACATCCATCGGCGCTTTGGTCGG                                 '
readthrough = 'ACACTCTTTCCCTACACGACGCTCTTCCGATCTCGGATGTTCCAATCAGTACGCAGAGAGTCGCCGTCTCCAAGGTGAAAGCGGAAGTAGGGCCTTCGCGCACCTCATGGAATCCCTTCTGCAGCACCTGGATCGCTTTTCCGAGCTTCTGGCGGTCTCAAGCACTACCTACGTCAGCACCTGGGACCCCGCCACCGTGCGCCGGGCCTTGCAGTGGGCGCGCTACCTGCGCCACATCCATCGGCGCTTTGGTCGGAGATCGGAAGAGCACACGTCTGAACTCCAGTC

Colelyman

"""Discover an Eulerian Path from a graph."""

import argparse
from collections import Counter
from typing import Dict, List, Optional


def construct_graph_from_adjacency(
    graph_file_path: str,
) -> Dict[str, List[str]]:

Colelyman

"""Discover an Eulerian Cycle from a graph."""

import argparse
from typing import Dict, List


def construct_graph_from_adjacency(
    graph_file_path: str,
) -> Dict[str, List[str]]:
    """Construct a graph from an adjacency list in `graph_file_path`.

Colelyman

#!/bin/sh

TEMP_BIB_PATH=".mybib.bib"
TEMP_MD_PATH=".mybib.md"
TEMP_CITATION_PATH=".mycitation.md"

clean() {
    rm -rf $TEMP_BIB_PATH $TEMP_MD_PATH $TEMP_CITATION_PATH
}

Colelyman

d_grimshawi
d_virilis
d_mojavensis
d_willistoni
d_persimilis
d_pseudoobscura
d_ananassae
d_erecta
d_yakuba
d_melanogaster

Colelyman

(defmacro open-file-defer-close (file-path file-handle &body body)
  "Opens FILE-PATH as FILE-HANDLE, executes BODY and finally closes FILE-HANDLE."
  `(let ((,file-handle ,(open file-path)))
     ,@body
     (close ,file-handle)))

Colelyman

Keybase proof

I hereby claim:

• I am colelyman on github.
• I am colelyman (https://keybase.io/colelyman) on keybase.
• I have a public key ASDSxAqaZq-uEWXfjlA7FumgaGXm47CeKWxqphX0ITlVMQo

To claim this, I am signing this object:

Colelyman

# to be run within your project that is built with autotools (aka has a configure script)
# replace the text within '<...>' with the respective paths
export LD_LIBRARY_PATH=<lib directory of the library>:$LD_LIBRARY_PATH

./configure CPPFLAGS="-I<include directory of the library> -L<lib directory of the library>"

make CPPFLAGS="-I<include directory of the library> -L<lib directory of the library>" LDFLAGS="-I<include directory of the library> -L<lib directory of the library>"

Colelyman

# start a job after another job succeeds
JOBID=$(sbatch --parsable job1.sh) && sbatch --dependency=afterok:$JOBID job2.sh

# start a job after another job fails
JOBID=$(sbatch --parsable job1.sh) && sbatch --dependency=afternotok:$JOBID job2.sh

# get the time and memory of a running node
sstat --format="CPUTime,Elapsed,MaxRSS" -j $SLURM_JOB_ID

Colelyman

library(tibble)

# create a tibble with no rows, but defined columns
tbl <- tibble(name=character(), age=numeric(), gender=factor())

# add a row to the tibble. The values can even be vectors!!
tbl <- add_row(tbl, name='Steve', age='24', gender='male')