adelq

from biom import parse_table
with open('otu_table_hunter.biom') as f:
    table = parse_table(f)
    
print table
table.ids()
table.ids(axis='observation')
table.nnz
normed = table.norm(axis='sample', inplace=False)
phylum_idx = 1

adelq

Labs Coding Challenge

Write a concise piece of code that sends an HTTP POST request to labs.yef.im with the following pieces of data:

• javascript: Your level of comfort with JavaScript, as an integer 0–4, with 0 being no experience and 4 being very comfortable.
• python: Your level of comfort with Python, as an integer 0–4, with 0 being no experience and 4 being very comfortable.
• coffeescript: Your level of comfort with Coffeescript, as an integer 0–4, with 0 being no experience and 4 being very comfortable.
• frameworks: Your level of comfort with web frameworks, as an integer 0–4, with 0 being no experience and 4 being very comfortable.
• url: The URL of a GitHub Gist with the code that does this.(Meta! Note that you might have to edit the Gist a few times)

adelq

replicates = ["rep3", "rep4"]
proteins = ["protein", 
"noprotein"]
cutadapt = '''cutadapt -a TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACnnnnnnATCTCGTATGCCGTCTTCTGCTTG -e 0.06 -O 6 -m 14 \
  data/fastqFiles/totalArab_nuc_rep3_dsRNase_noprotein.raw.fastq \
  -o data/fastqFiles/totalArab_nuc_rep3_dsRNase_noprotein.trimmed.fastq \
  --discard-untrimmed &'''
cutadapt
print cutadapt
cutadapt1 = """cutadapt -a TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACnnnnnnATCTCGTATGCCGTCTTCTGCTTG -e 0.06 -O 6 -m 14 \