jackkamm

import numpy as np
import pandas as pd
import anndata as ad

adata = ad.read_h5ad("/home/jack/src/zellkonverter/inst/extdata/krumsiek11.h5ad")

# add float column to colData/obs
adata.obs['dummy_num'] = 42.42

# float column with NA

jackkamm

<!--
WARNING: THIS IS AN AUTO-GENERATED FILE. CHANGES TO IT ARE LIKELY TO BE
OVERWRITTEN AND LOST. Changes to this xml configuration should be made using:
  virsh edit win10-gaming
or other application using the libvirt API.
-->

<domain type='kvm'>
  <name>win10-gaming</name>
  <uuid>b562f5ca-4792-4d2d-99be-ece9905ff714</uuid>

jackkamm

Observations from initial testing of ob-session-async-shell.el:

• Didn’t work with zsh
• Worked with bash and sh
• #+RESULTS contains input commands that it shouldn’t, as well as the command printing the end-indicator, for example see the below code block and its #+RESULTS:

  sleep 1
  echo foo
      

jackkamm

[    0.000000] Linux version 5.2.8-arch1-1-ARCH (builduser@heftig-63215) (gcc version 9.1.0 (GCC)) #1 SMP PREEMPT Fri Aug 9 21:36:07 UTC 2019
[    0.000000] Command line: initrd=\initramfs-linux.img cryptdevice=UUID=d837c52a-7aca-4e58-a595-ee22f4518288:cryptroot resume=/dev/mapper/cryptroot resume_offset=94031872 root=/dev/mapper/cryptroot rw
[    0.000000] KERNEL supported cpus:
[    0.000000]   Intel GenuineIntel
[    0.000000]   AMD AuthenticAMD
[    0.000000]   Hygon HygonGenuine
[    0.000000]   Centaur CentaurHauls
[    0.000000] x86/fpu: Supporting XSAVE feature 0x001: 'x87 floating point registers'
[    0.000000] x86/fpu: Supporting XSAVE feature 0x002: 'SSE registers'
[    0.000000] x86/fpu: Supporting XSAVE feature 0x004: 'AVX registers'

jackkamm

# This is a simple script to backup, compress, and encrypt $HOME
set +e

# set recipient for encryption
RECIPIENT="jackkamm@gmail.com"

# To improve I/O, keep $DEST on local filesystem,
# and copy it to external medium afterwards
DEST=/var/tmp/backup_home.tar

jackkamm

from collections import Counter, OrderedDict
import pysam
from Bio import SeqIO
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord

def bam2consensus(
        ref_fname, bam_fname, ac_threshold, af_threshold, out_fname):

    consensus = OrderedDict()

jackkamm

library(taxizedb)
library(dplyr)
library(purrr)
library(sankeyD3)
library(shiny)

df <- read.csv('data/mosquito_reports/cms_040_rna_a_s21.csv', head=T, stringsAsFactors=F)

df %>%
  filter(tax_id > 0, tax_level==1, NT_r > 0) %>%

jackkamm

import os
import urllib
import xml.etree.ElementTree as ET

from Bio import Entrez
Entrez.email = "jack.kamm@czbiohub.org"

uid = ET.parse(Entrez.esearch(db="assembly", term="GCA_000150765.1")).getroot().find("IdList")[0].text
ftp_path = ET.parse(Entrez.esummary(db="assembly", id=uid)).getroot().find("DocumentSummarySet").find("DocumentSummary").find("FtpPath_GenBank").text
basename = os.path.basename(ftp_path)