Pasted from IPython

file1.py

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 \
  data/fastqFiles/totalArab_nuc_{replicate}_{rnase}_{protein}.raw.fastq \
  -o data/fastqFiles/totalArab_nuc_{replicate}_{rnase}_{protein}.trimmed.fastq \
  --discard-untrimmed &"""
cutadapt = "cutadapt -a TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACnnnnnnATCTCGTATGCCGTCTTCTGCTTG -e 0.06 -O 6 -m 14 \
  data/fastqFiles/totalArab_nuc_{replicate}_{rnase}_{protein}.raw.fastq \
  -o data/fastqFiles/totalArab_nuc_{replicate}_{rnase}_{protein}.trimmed.fastq \
  --discard-untrimmed &"
cutadapt
cutadapt.format(replicate=replicates[1], protein=proteins[1], rnase="dsRnase"
)
ls
rnases = ["dsRNase", "ssRNase"]
from itertools import product
product(replicates, proteins, rnases)
list(product(replicates, proteins, rnases))
f = raw_input()
f
import sys
message = sys.stdin.readlines()
message
"".join(message)
message = sys.stdin.readlines()
m = "".join(message)
print m
m
print m,
m = "".join(sys.stdin.readlines())
print m,
for i in product(replicates, rnases, proteins):
print m.format(*i),
for i in product(replicates, rnases, proteins):
    print m.format(*i),
for i in product(replicates, rnases, proteins):
    print m.format(*i)
%quickref