#!/usr/bin/env python
# coding: utf-8

# In[7]:


cd /Volumes/Data/Sam/scratch/


# ###Quality trim & remove first 39bp from single FASTQ file

# Code explanation:
# 
#     java -jar /usr/local/bioinformatics/Trimmomatic-0.30/trimmomatic-0.30.jar
# This line above initiates Trimmomatic and uses the following arguments to specify order of execution:
# 
# -single end reads (SE)
#     
# -number of threads (-threads 16),
#     
# -type of quality score (-phred33),
# 
# -input file location (/Volumes/nightingales/C_gigas/2212_lane2_CTTGTA_L002_R1_001.fastq.gz),
# 
# -output file name/location (20150506_trimmed_2212_lane2_CTTGTA_L002_R1_001.fastq.gz),
# 
# -single end Illumina TruSeq adaptor trimming (ILLUMINACLIP:/usr/local/bioinformatics/Trimmomatic-0.30/adapters/TruSeq3-SE.fa:2:30:10),
# 
# -cut number of bases at beginning of each read (HEADCROP:39)
# 
# -cut number of bases at beginning of read if below quality threshold (LEADING:3)
# 
# -cut number of bases at end of read if below quality threshold (TRAILING:3)
# 
# -cut if average quality within 4 base window falls below 15 (SLIDINGWINDOW:4:15)

# In[4]:


get_ipython().run_cell_magic('bash', '', 'java -jar /usr/local/bioinformatics/Trimmomatic-0.30/trimmomatic-0.30.jar \\\nSE \\\n-threads 16 \\\n-phred33 \\\n/Volumes/nightingales/C_gigas/2212_lane2_CTTGTA_L002_R1_001.fastq.gz \\\n/Volumes/Data/Sam/scratch/20150506_trimmed_2212_lane2_CTTGTA_L002_R1_001.fastq.gz \\\nILLUMINACLIP:/usr/local/bioinformatics/Trimmomatic-0.30/adapters/TruSeq3-SE.fa:2:30:10 \\\nHEADCROP:39 \\\nLEADING:3 \\\nTRAILING:3 \\\nSLIDINGWINDOW:4:15\n')


# ###FASTQC on trimmed file

# In[5]:


get_ipython().run_cell_magic('bash', '', 'fastqc /Volumes/Data/Sam/scratch/20150506_trimmed_2212_lane2_CTTGTA_L002_R1_001.fastq.gz \\\n--outdir=/Volumes/Eagle/Arabidopsis/\n')


# ###Copy files to Eagle for web-based access

# In[6]:


cp 20150506_* /Volumes/Eagle/Arabidopsis/


# ###Unzip FASTQC output

# In[12]:


get_ipython().run_cell_magic('bash', '', 'unzip /Volumes/Eagle/Arabidopsis/20150506_trimmed_2212_lane2_CTTGTA_L002_R1_001_fastqc.zip\n')


# ###Move unzipped folder to Eagle

# In[13]:


get_ipython().run_cell_magic('bash', '', 'mv 20150506_trimmed_2212_lane2_CTTGTA_L002_R1_001_fastqc/ /Volumes/Eagle/Arabidopsis/\n')