samesense

def get_dbsnp_unknown():
    snvs = {}
    with open('/vol/Users/yk336/database/human/dbsnp/hg19/snp.txt') as f:
        for line in f:
            sp = line.strip().split('\t')
            chrom = sp[1]
            pos = sp[3]
            status = sp[12]
            snv_type = sp[11]
            if status == 'unknown' and snv_type == 'single':

samesense

// Use Gists to store code you would like to remember later on
console.log(window); // log the "window" object to the console

samesense

###Assuming python3 is not on your server and you are not sudo

1. Download python source, compile  
```
wget http://python.org/ftp/python/3.3.4/Python-3.3.4.tgz
gunzip Python-3.3.4.tgz && tar -xvf Python-3.3.4.tar
cd Python-3.3.4
./configure --prefix=/home/me/mypython && make && make install
cd /home/me/mypython
```

samesense

sourceID: description
2000DanishExomes: http://www.ncbi.nlm.nih.gov/pubmed?term=24290377
63000exomes: ExAC
ADNI: Alzheimer's Disease Neuroimaging Initiative
!Ai: Five Khoisan and Bantu genomes from southern Africa, http://www.ncbi.nlm.nih.gov/pubmed?term=20164927
D#kgao: Five Khoisan and Bantu genomes from southern Africa, http://www.ncbi.nlm.nih.gov/pubmed?term=20164927
dbSNP: dbSNP v 144
Geuvadis: Genetic European Variation in Disease, http://www.ebi.ac.uk/eva/?eva-study=PRJEB6042
gonl: GoNL (Founders from 250 Dutch trios, http://www.ncbi.nlm.nih.gov/pubmed?term=24974849)
GS* (ex GS000009929): PGP, 152 individual genomes sequenced by the Personal Genome Project

samesense

# broken, but expresses idea
rule parseMvar:
    input:  DATA + 'collapseCalls_snvs/{sample}.tab',
            expand(DATA + 'bedIntr/{{sample}}_{sample2}.bed', \
                   sample2 = n2t['{wildcards.sample}'])
    output: DATA + 'snv_tumorStatus/{sample}.tab'
    shell:  'python parseTumorStatus.py {input} {output}'
    
# correct syntax    
def getTumor(wc):

samesense

/mnt/isilon/cbmi/variome/bin/java -Xmx32g -Xms16g -jar /mnt/isilon/cbmi/variome/bin/GenomeAnalysisTK-1.6-2-gc2b74ec/3.3-0/GenomeAnalysisTK.jar -l DEBUG -variant_index_type LINEAR -variant_index_parameter 128000 --emitRefConfidence GVCF -T HaplotypeCaller -R /mnt/isilon/cbmi/variome/reference/mm9.fa -I ~/me/projects/blobel/download_encode/data/bam_group/ENCFF001NTS.bam --genotyping_mode DISCOVERY -stand_emit_conf 10 -stand_call_conf 30 -o /home/evansj/me/projects/blobel/download_encode/data/gvars/ENCFF001NTS.g.vcf

samesense

* Data checksums
* Collapse variants by chrom
* Pull reads of all variant positions across bam files
* Pull mapping qualities
* Apply cutoffs
* Annotate collapsed variants w/ function and pop info
* Mk tables

samesense

Copy to local machine clipboard from iteractive remote session

• Works with macOS and remote linux machine
• On local machine, make this plist file to use with launchclt
• On local machine launchctl load local.pbcopy.9999.plist. This must remain running for remote copy to work.
• On remote machine cat "message or file" | nc localhost 9997 -w1
• nc is at /mnt/isilon/cbmi/variome/perry/bin/nc
• On local machine, use paste or pbpaste as usual

Extra

• On my locate machine, p is aliased to the launchctl command

samesense

<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE plist PUBLIC "-//Apple//DTD PLIST 1.0//EN" "http://www.apple.com/DTDs/PropertyList-1.0.dtd">
<plist version="1.0">
<dict>
    <key>Label</key>
    <string>local.pbcopy.9999</string>
    <key>UserName</key>
    <string>joe</string>
    <key>Program</key>
    <string>/usr/bin/pbcopy</string>

samesense

import argparse

def main(args):
    giabBaseCounts(d, args.giabCountFile)
    
if __name__ == "__main__":
    desc = 'Pull data for report.'
    parser = argparse.ArgumentParser(description=desc)
    argLs = ('giabCountFile', 'outFile',)
    for param in argLs: