I'm going to concatonate the Sept and Nov runs from my Larvae data (R1 and R2 separately)

F_R1

In [1]: 
!cat /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Nov/filtered_BS_CgF_TTAGGC_L004_R1.fastq /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Sept/filtered_BS_CgF_TTAGGC_L007_R1.fastq > /Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/F_R1.fastq

M1_R1

In [2]: 
!cat /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Nov/filtered_BS_CgM1_ACTTGA_L004_R1.fastq /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Sept/filtered_BS_CgM1_ACTTGA_L007_R1.fastq > /Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/M1_R1.fastq

M3_R1

In [3]: 
!cat /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Nov/filtered_BS_CgM3_GATCAG_L004_R1.fastq /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Sept/filtered_BS_CgM3_GATCAG_L007_R1.fastq > /Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/M3_R1.fastq

T1D3_R1

In [4]: 
!cat /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Nov/filtered_BS_CgLarv_T1D3_TGACCA_L004_R1.fastq /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Sept/filtered_BS_CgLarv_T1D3_TGACCA_L007_R1.fastq > /Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T1D3_R1.fastq

T1D5_R1

In [5]: 
!cat /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Nov/filtered_BS_CgLarv_T1D5_ACAGTG_L004_R1.fastq /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Sept/filtered_BS_CgLarv_T1D5_ACAGTG_L007_R1.fastq >  /Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T1D5_R1.fastq

T3D3_R1

In [6]: 
!cat /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Nov/filtered_Bs_CgLarve_T3D3_GCCAAT_L004_R1.fastq /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Sept/filtered_Bs_CgLarve_T3D3_GCCAAT_L007_R1.fastq > /Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T3D3_R1.fastq

T3D5_R1

In [7]: 
!cat /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Nov/filtered_BS_CgLarv_T3D5_CAGATC_L004_R1.fastq /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Sept/filtered_BS_CgLarv_T3D5_CAGATC_L007_R1.fastq > /Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T3D5_R1.fastq

F_R2

In [8]: 
!cat /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Nov/filtered_BS_CgF_TTAGGC_L004_R2.fastq /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Sept/filtered_BS_CgF_TTAGGC_L007_R2.fastq > /Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/F_R2.fastq

M1_R2

In [9]: 
!cat /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Nov/filtered_BS_CgM1_ACTTGA_L004_R2.fastq /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Sept/filtered_BS_CgM1_ACTTGA_L007_R2.fastq > /Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/M1_R2.fastq

M3_R2

In [10]: 
!cat /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Nov/filtered_BS_CgM3_GATCAG_L004_R2.fastq /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Sept/filtered_BS_CgM3_GATCAG_L007_R2.fastq >  /Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/M3_R2.fastq

T1D3_R2

In [11]: 
!cat /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Nov/filtered_BS_CgLarv_T1D3_TGACCA_L004_R2.fastq /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Sept/filtered_BS_CgLarv_T1D3_TGACCA_L007_R2.fastq >  /Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/T1D3_R2.fastq

T1D5_R2

In [12]: 
!cat /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Nov/filtered_BS_CgLarv_T1D5_ACAGTG_L004_R2.fastq /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Sept/filtered_BS_CgLarv_T1D5_ACAGTG_L007_R2.fastq > /Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/T1D5_R2.fastq

T3D3_R2

In [13]: 
!cat /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Nov/filtered_Bs_CgLarve_T3D3_GCCAAT_L004_R2.fastq /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Sept/filtered_Bs_CgLarve_T3D3_GCCAAT_L007_R2.fastq > /Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/T3D3_R2.fastq

T3D5_R2

In [14]: 
!cat /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Nov/filtered_BS_CgLarv_T3D5_CAGATC_L004_R2.fastq /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Sept/filtered_BS_CgLarv_T3D5_CAGATC_L007_R2.fastq > /Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/T3D5_R2.fastq

Script to take html snapshot of IPython notebook

Notes from Steven's notebook: http://nbviewer.ipython.org/urls/dl.dropboxusercontent.com/u/115356/ip/nbview/_IPsnapshot.ipynb
In [9]: 
#NOTEBOOK NAME
nb='Concatenate_Larvae_Files'

#NOTEBOOK LOCATION
nbloc='/Users/claireolson/Dropbox/Lab\ \(1\)/IPython_nbs/Claire/'



#TIMESTAMP
date=!date +%m%d_%H%M
#LOCATION OF POST DIRECTORY
post='/Volumes/web/Mollusk/iPython_Posts/'
In [10]: 
cd {post}

/Volumes/web/Mollusk/iPython_Posts
In [11]: 
!ipython nbconvert {nbloc}{nb} --to html --template full --output {nb}{date}

[NbConvertApp] Using existing profile dir: u'/Users/claireolson/.ipython/profile_default'
[NbConvertApp] Converting notebook /Users/claireolson/Dropbox/Lab (1)/IPython_nbs/Claire/Concatenate_Larvae_Files.ipynb to html
[NbConvertApp] Support files will be in Concatenate_Larvae_Files[0331_1048]_files/
[NbConvertApp] Loaded template html_full.tpl
[NbConvertApp] Writing 212215 bytes to Concatenate_Larvae_Files[0331_1048].html
In []: