jkobject

jkobject

openjdk
ca-certificates
rbenv
git-lfs
samtools
sqlite
htop
htslib
kubernetes
shai

jkobject

[
  {
    "type": "escape",
    "width": 64,
    "align": "left"
  },
  { "type": "brightnessDown", "width": 62, "bordered": false, "align": "left" },
  { "type": "brightnessUp", "width": 62, "bordered": false, "align": "left" },
  {
    "type": "play",

jkobject

def vcf_to_df(path):
    def read_comments(f):
        fields = {}
        description = {}
        for l in f: 
            l = l.decode("utf-8")
            if l.startswith('##'):
                if 'FORMAT' in l[:20]:
                    res = l.split('ID=')[1].split(',')[0]
                    desc = l.split('Description=')[1][:-2]

jkobject

bubble{
	render{
		<View id=top
			onLayout={(event) => this.props.getHeight(event.nativeEvent.layout.height+this.state.posY)
	}}

weave{
	// One line in one branch (example of 1 message)
	
	updateDisplayList(newcurrent){

jkobject

SMs= {}
for i, bam in enumerate(versions):
    print(i,end='\r')
    data = os.popen('export GCS_OAUTH_TOKEN=`gcloud auth application-default print-access-token` && samtools view -H '+bam +' | grep "^@RG"')
    if data == signal.SIGINT:
        print('Awakened')
        break
    else:
        res = data.read()
        SMs[bam] = re.findall("(?<=\tSM:).+?\t", res)[0]

jkobject

    for k, rowinfo in samples.iterrows():
      # check for broken bam files; if broken, then remove from consideration
      # need to check for broken filepaths before checking if the sample is in Terra so that we don't add a broken file path for a new participant
      pdb.set_trace()
      filepath = rowinfo[extract['bam']]
      sample_to_check = os.popen('gsutil -m ls -al ' + filepath).read().split('\n')
      if sample_to_check == ['']:
        # this bam file doesn't exist at this filepath
        print("The bam file path we have in data workspace is broken, so we will remove it from consideration:\n " + str(filepath))
        broken_bams += [filepath]

jkobject

def accessAndChange(func, wmfrom, wmto=None, name index_func=None):
  data = {}
  try:
    a = wmfrom.get_participants()
    data.update({'participants': a})
  except:
    print('no participants')
  try:
    a = wmfrom.get_samples()
    data.update({'samples': a})

jkobject

command <<<
    # Function call depends on whether sample has match normal or not
    if [ ${normal_id} != NA ]; then
      echo "Filtering variants with match normal"
      match_normal_variants="--match_normal_filtered_variants ${match_normal_variants}"
    else
      echo "Filtering variants with no match normal"
    fi
    python /TSCA/filter_variants.py \
      --sample_type Tumor \

jkobject

cat urls.txt | parallel -j 10 'curl -L -s {} | gsutil cp - "gs://BUCKETNAME/GCPFOLDER"$(echo {} | cut -d \/ -f -1)'
#need to have parallel installed (brew, apt)