#SR edits - html embeds not working on html so generatinv nbviewer linke
!date

filename='BiGo_larvae_2'

#ipynb viewer format:
!echo 'http://nbviewer.ipython.org/github/sr320/ipython_nb/blob/master/''{filename}''.ipynb'

#ipynb file:
!echo 'https://github.com/sr320/ipython_nb/blob/master/''{filename}''.ipynb'





! /Volumes/Bay3/Software/BSMAP/bsmap-2.74/bsmap -a /Volumes/web/trilobite/Crassostrea_gigas_HTSdata/FCC3ATL/BS_CgF_ACAGTG_L004_R1_001.fastq.gz -d /Volumes/web/cnidarian/oyster.v9.fa -o /Volumes/web/cnidarian/BiGo_egg_redo.sam -p 4

#FEB 13 redux looking at  R1 AND R2
! /Volumes/Bay3/Software/BSMAP/bsmap-2.74/bsmap -a /Volumes/web/trilobite/Crassostrea_gigas_HTSdata/batterbox/FCC3ATL/BS_CgF_ACAGTG_L004_R1_001.fastq.gz -b /Volumes/web/trilobite/Crassostrea_gigas_HTSdata/batterbox/FCC3ATL/BS_CgF_ACAGTG_L004_R2_001.fastq.gz  -d /Volumes/web/cnidarian/oyster.v9.fa -o /Volumes/web/cnidarian/BiGo_egg_redo4.sam -p 4

#FEB 13 redux looking at filtered R1
! /Volumes/Bay3/Software/BSMAP/bsmap-2.74/bsmap -a /Volumes/web/trilobite/Crassostrea_gigas_HTSdata/batterbox/FCC3ATL/filtered_BS_CgF_ACAGTG_L004_R1.fastq.gz -d /Volumes/web/cnidarian/oyster.v9.fa -o /Volumes/web/cnidarian/BiGo_egg_redo3.sam -p 4

from IPython.display import Image
Image(url= 'http://eagle.fish.washington.edu/cnidarian/skitch/BiGo_larvae_1892C389.png')

#Lets run good sperm sample with only one end...
#M3
! /Volumes/Bay3/Software/BSMAP/bsmap-2.74/bsmap -a /Volumes/NGS\ Drive/NGS\ Raw\ Data/Cg_larvae_BSseq/filtered_BS_CgM3_GATCAG_L007_R1.fastq.gz -d /Volumes/web/cnidarian/oyster.v9.fa -o /Volumes/web/cnidarian/BiGo_lar_M3_1side.sam -p 3
Total number of aligned reads: 3707307 (67%)
Done.
Finished at Fri Jan 24 08:09:52 2014
Total time consumed:  933 secs
#stop
#issue with files
from IPython.display import Image
Image(url= 'http://eagle.fish.washington.edu/cnidarian/skitch/trilobite_and_BiGo_Larvae_and_Mackenzie_Gavery_1892E4D6.png')

Only 1 filtered fasta
Code from core - FCD2CA8
Lets QC in IPlant DE

!ils

!imkdir BiGo_larvae

!ils

!icd BiGo_larvae

!iput -f -V -r /Volumes/web/trilobite/Crassostrea_gigas_HTSdata/batterbox/BiGo_Larvae

!ils

!iget -r FastQC_0.10.1__multi-file__analysis1-2014-02-03-09-29-30.603

cd /Volumes/web/cnidarian

from IPython.display import HTML
HTML('<iframe src=http://eagle.fish.washington.edu/cnidarian/FastQC_0.10.1_020314/filtered_BS_CgF_TTAGGC_L007_R1_fastqc/fastqc_report.html width=100% height=550></iframe>')

from IPython.display import HTML
HTML('<iframe src=http://eagle.fish.washington.edu/cnidarian/FastQC_0.10.1_020314/filtered_BS_CgF_TTAGGC_L007_R2_fastqc/fastqc_report.html width=100% height=550></iframe>')

from IPython.display import HTML
HTML('<iframe src=http://eagle.fish.washington.edu/cnidarian/FastQC_0.10.1_020314/filtered_Bs_CgLarve_T3D3_GCCAAT_L007_R1_fastqc/fastqc_report.html width=100% height=550></iframe>')

from IPython.display import HTML
HTML('<iframe src=http://eagle.fish.washington.edu/cnidarian/FastQC_0.10.1_020314/filtered_Bs_CgLarve_T3D3_GCCAAT_L007_R2_fastqc/fastqc_report.html width=100% height=550></iframe>')

pwd

!iget -r FastQC_0.10.1__multi-file__analysis1-2014-02-03-11-29-22.343

from IPython.display import HTML
HTML('<iframe src=http://eagle.fish.washington.edu/cnidarian/FastQC_0.10.1_020314b/Bs_CgLarve_T3D3_GCCAAT_L007_R1_001_fastqc/fastqc_report.html width=100% height=550></iframe>')

from IPython.display import HTML
HTML('<iframe src=http://eagle.fish.washington.edu/cnidarian/FastQC_0.10.1_020314b/Bs_CgLarve_T3D3_GCCAAT_L007_R2_001_fastqc/fastqc_report.html width=100% height=550></iframe>')

from IPython.display import HTML
HTML('<iframe src=http://eagle.fish.washington.edu/cnidarian/FastQC_0.10.1_020314/filtered_BS_CgLarv_T1D3_TGACCA_L007_R1_fastqc/fastqc_report.html width=100% height=550></iframe>')

from IPython.display import HTML
HTML('<iframe src=http://eagle.fish.washington.edu/cnidarian/FastQC_0.10.1_020314/filtered_BS_CgLarv_T1D3_TGACCA_L007_R2_fastqc/fastqc_report.html width=100% height=550></iframe>')

from IPython.display import HTML
HTML('<iframe src=http://eagle.fish.washington.edu/cnidarian/FastQC_0.10.1_020314/filtered_BS_CgLarv_T1D5_ACAGTG_L007_R1_fastqc/fastqc_report.html width=100% height=550></iframe>')

from IPython.display import HTML
HTML('<iframe src=http://eagle.fish.washington.edu/cnidarian/FastQC_0.10.1_020314/filtered_BS_CgLarv_T1D5_ACAGTG_L007_R2_fastqc/fastqc_report.html width=100% height=550></iframe>')

from IPython.display import HTML
HTML('<iframe src=http://eagle.fish.washington.edu/cnidarian/FastQC_0.10.1_020314/filtered_BS_CgLarv_T3D5_CAGATC_L007_R1_fastqc/fastqc_report.html width=100% height=550></iframe>')

from IPython.display import HTML
HTML('<iframe src=http://eagle.fish.washington.edu/cnidarian/FastQC_0.10.1_020314/filtered_BS_CgLarv_T3D5_CAGATC_L007_R2_fastqc/fastqc_report.html width=100% height=550></iframe>')

from IPython.display import HTML
HTML('<iframe src=http://eagle.fish.washington.edu/cnidarian/FastQC_0.10.1_020314/filtered_BS_CgM1_ACTTGA_L007_R1_fastqc/fastqc_report.html width=100% height=550></iframe>')

from IPython.display import HTML
HTML('<iframe src=http://eagle.fish.washington.edu/cnidarian/FastQC_0.10.1_020314/filtered_BS_CgM1_ACTTGA_L007_R2_fastqc/fastqc_report.html width=100% height=550></iframe>')

from IPython.display import HTML
HTML('<iframe src=http://eagle.fish.washington.edu/cnidarian/FastQC_0.10.1_020314/filtered_BS_CgM3_GATCAG_L007_R1_fastqc/fastqc_report.html width=100% height=550></iframe>')

from IPython.display import HTML
HTML('<iframe src=http://eagle.fish.washington.edu/cnidarian/FastQC_0.10.1_020314/filtered_BS_CgM3_GATCAG_L007_R2_fastqc/fastqc_report.html width=100% height=550></iframe>')
Core ID FCC39EM
Issue is only 1 filtered file for PE data....
What does filtered mean?
first need to de compress 
!head /Volumes/web/trilobite/Crassostrea_gigas_HTSdata/BiGo_Larvae/filtered_BS_CgM1_ACTTGA_L007_R1.fastq.gz