Lineage Specific Differences

In [15]: 
cd /Users/Shared/Apps/bedtools-2.17.0 

/Users/Shared/Apps/bedtools-2.17.0
In [17]: 
cd bin

/Users/Shared/Apps/bedtools-2.17.0/bin
In [18]: 
!intersectBed -a /Volumes/web-1/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_exon.gff -b /Volumes/web-1/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/3xCoverage/methylKit/DMRs_v2/lineage_vs_developmental_differences/Lineage_30percent_diff.bed > /Volumes/web-1/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/3xCoverage/methylKit/DMRs_v2/lineage_vs_developmental_differences/Lineage_developmental_genomicfeatures/lineage_exon.txt -wb
In [19]: 
!intersectBed -a /Volumes/web-1/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_gene.gff -b /Volumes/web-1/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/3xCoverage/methylKit/DMRs_v2/lineage_vs_developmental_differences/Lineage_30percent_diff.bed  > /Volumes/web-1/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/3xCoverage/methylKit/DMRs_v2/lineage_vs_developmental_differences/Lineage_developmental_genomicfeatures/lineage_gene.txt -wb
In [20]: 
!intersectBed -a /Volumes/web-1/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_intron.gff -b /Volumes/web-1/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/3xCoverage/methylKit/DMRs_v2/lineage_vs_developmental_differences/Lineage_30percent_diff.bed  > /Volumes/web-1/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/3xCoverage/methylKit/DMRs_v2/lineage_vs_developmental_differences/Lineage_developmental_genomicfeatures/lineage_intron.txt -wb
In [21]: 
!intersectBed -a /Volumes/web-1/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_TE.gff -b /Volumes/web-1/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/3xCoverage/methylKit/DMRs_v2/lineage_vs_developmental_differences/Lineage_30percent_diff.bed  > /Volumes/web-1/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/3xCoverage/methylKit/DMRs_v2/lineage_vs_developmental_differences/Lineage_developmental_genomicfeatures/lineage_TE.txt -wb
In [22]: 
!intersectBed -a /Volumes/web-1/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_1k5p_gene_promoter.gff -b /Volumes/web-1/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/3xCoverage/methylKit/DMRs_v2/lineage_vs_developmental_differences/Lineage_30percent_diff.bed  > /Volumes/web-1/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/3xCoverage/methylKit/DMRs_v2/lineage_vs_developmental_differences/Lineage_developmental_genomicfeatures/lineage_promoter.txt -wb
In [23]: 
!intersectBed -a /Volumes/web-1/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_COMP_gene_prom_TE.bed -b /Volumes/web-1/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/3xCoverage/methylKit/DMRs_v2/lineage_vs_developmental_differences/Lineage_30percent_diff.bed  > /Volumes/web-1/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/3xCoverage/methylKit/DMRs_v2/lineage_vs_developmental_differences/Lineage_developmental_genomicfeatures/lineage_complement.txt -wb

Developmental Differences

In [24]: 
!intersectBed -a /Volumes/web-1/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_exon.gff -b /Volumes/web-1/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/3xCoverage/methylKit/DMRs_v2/lineage_vs_developmental_differences/Developmental_differences/comparisons/Developmental_differences_MalesvDay5_30p.bed > /Volumes/web-1/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/3xCoverage/methylKit/DMRs_v2/lineage_vs_developmental_differences/Lineage_developmental_genomicfeatures/developmental_MalesvDay5_exon.txt -wb
In [25]: 
!intersectBed -a /Volumes/web-1/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_gene.gff -b /Volumes/web-1/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/3xCoverage/methylKit/DMRs_v2/lineage_vs_developmental_differences/Developmental_differences/comparisons/Developmental_differences_MalesvDay5_30p.bed > /Volumes/web-1/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/3xCoverage/methylKit/DMRs_v2/lineage_vs_developmental_differences/Lineage_developmental_genomicfeatures/developmental_MalesvDay5_gene.txt -wb
In [26]: 
!intersectBed -a /Volumes/web-1/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_intron.gff -b /Volumes/web-1/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/3xCoverage/methylKit/DMRs_v2/lineage_vs_developmental_differences/Developmental_differences/comparisons/Developmental_differences_MalesvDay5_30p.bed > /Volumes/web-1/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/3xCoverage/methylKit/DMRs_v2/lineage_vs_developmental_differences/Lineage_developmental_genomicfeatures/developmental_MalesvDay5_intron.txt -wb
In [27]: 
!intersectBed -a /Volumes/web-1/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_TE.gff -b /Volumes/web-1/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/3xCoverage/methylKit/DMRs_v2/lineage_vs_developmental_differences/Developmental_differences/comparisons/Developmental_differences_MalesvDay5_30p.bed > /Volumes/web-1/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/3xCoverage/methylKit/DMRs_v2/lineage_vs_developmental_differences/Lineage_developmental_genomicfeatures/developmental_MalesvDay5_TE.txt -wb
In [28]: 
!intersectBed -a /Volumes/web-1/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_1k5p_gene_promoter.gff -b /Volumes/web-1/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/3xCoverage/methylKit/DMRs_v2/lineage_vs_developmental_differences/Developmental_differences/comparisons/Developmental_differences_MalesvDay5_30p.bed > /Volumes/web-1/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/3xCoverage/methylKit/DMRs_v2/lineage_vs_developmental_differences/Lineage_developmental_genomicfeatures/developmental_MalesvDay5_promoter.txt -wb
In [29]: 
!intersectBed -a /Volumes/web-1/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_COMP_gene_prom_TE.bed -b /Volumes/web-1/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/3xCoverage/methylKit/DMRs_v2/lineage_vs_developmental_differences/Developmental_differences/comparisons/Developmental_differences_MalesvDay5_30p.bed > /Volumes/web-1/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/3xCoverage/methylKit/DMRs_v2/lineage_vs_developmental_differences/Lineage_developmental_genomicfeatures/developmental_MalesvDay5_complement.txt -wb
In [30]: 
!intersectBed -a /Volumes/web-1/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_exon.gff -b /Volumes/web-1/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/3xCoverage/methylKit/DMRs_v2/lineage_vs_developmental_differences/Developmental_differences/comparisons/Developmental_differences_MalesvDay3_30p.bed > /Volumes/web-1/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/3xCoverage/methylKit/DMRs_v2/lineage_vs_developmental_differences/Lineage_developmental_genomicfeatures/developmental_MalesvDay3_exon.txt -wb
In [31]: 
!intersectBed -a /Volumes/web-1/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_gene.gff -b /Volumes/web-1/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/3xCoverage/methylKit/DMRs_v2/lineage_vs_developmental_differences/Developmental_differences/comparisons/Developmental_differences_MalesvDay3_30p.bed > /Volumes/web-1/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/3xCoverage/methylKit/DMRs_v2/lineage_vs_developmental_differences/Lineage_developmental_genomicfeatures/developmental_MalesvDay3_gene.txt -wb
In [32]: 
!intersectBed -a /Volumes/web-1/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_intron.gff -b /Volumes/web-1/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/3xCoverage/methylKit/DMRs_v2/lineage_vs_developmental_differences/Developmental_differences/comparisons/Developmental_differences_MalesvDay3_30p.bed > /Volumes/web-1/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/3xCoverage/methylKit/DMRs_v2/lineage_vs_developmental_differences/Lineage_developmental_genomicfeatures/developmental_MalesvDay3_intron.txt -wb
In [33]: 
!intersectBed -a /Volumes/web-1/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_TE.gff -b /Volumes/web-1/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/3xCoverage/methylKit/DMRs_v2/lineage_vs_developmental_differences/Developmental_differences/comparisons/Developmental_differences_MalesvDay3_30p.bed > /Volumes/web-1/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/3xCoverage/methylKit/DMRs_v2/lineage_vs_developmental_differences/Lineage_developmental_genomicfeatures/developmental_MalesvDay3_TE.txt -wb
In [34]: 
!intersectBed -a /Volumes/web-1/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_1k5p_gene_promoter.gff -b /Volumes/web-1/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/3xCoverage/methylKit/DMRs_v2/lineage_vs_developmental_differences/Developmental_differences/comparisons/Developmental_differences_MalesvDay3_30p.bed > /Volumes/web-1/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/3xCoverage/methylKit/DMRs_v2/lineage_vs_developmental_differences/Lineage_developmental_genomicfeatures/developmental_MalesvDay3_promoter.txt -wb
In [35]: 
!intersectBed -a /Volumes/web-1/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_COMP_gene_prom_TE.bed -b /Volumes/web-1/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/3xCoverage/methylKit/DMRs_v2/lineage_vs_developmental_differences/Developmental_differences/comparisons/Developmental_differences_MalesvDay3_30p.bed > /Volumes/web-1/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/3xCoverage/methylKit/DMRs_v2/lineage_vs_developmental_differences/Lineage_developmental_genomicfeatures/developmental_MalesvDay3_complement.txt -wb
In [36]: 
!intersectBed -a /Volumes/web-1/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_exon.gff -b /Volumes/web-1/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/3xCoverage/methylKit/DMRs_v2/lineage_vs_developmental_differences/Developmental_differences/comparisons/Developmental_differences_Day3vDay5_30p.bed > /Volumes/web-1/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/3xCoverage/methylKit/DMRs_v2/lineage_vs_developmental_differences/Lineage_developmental_genomicfeatures/developmental_Day3vDay5_exon.txt -wb
In [37]: 
!intersectBed -a /Volumes/web-1/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_gene.gff -b /Volumes/web-1/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/3xCoverage/methylKit/DMRs_v2/lineage_vs_developmental_differences/Developmental_differences/comparisons/Developmental_differences_Day3vDay5_30p.bed > /Volumes/web-1/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/3xCoverage/methylKit/DMRs_v2/lineage_vs_developmental_differences/Lineage_developmental_genomicfeatures/developmental_Day3vDay5_gene.txt -wb
In [38]: 
!intersectBed -a /Volumes/web-1/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_intron.gff -b /Volumes/web-1/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/3xCoverage/methylKit/DMRs_v2/lineage_vs_developmental_differences/Developmental_differences/comparisons/Developmental_differences_Day3vDay5_30p.bed > /Volumes/web-1/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/3xCoverage/methylKit/DMRs_v2/lineage_vs_developmental_differences/Lineage_developmental_genomicfeatures/developmental_Day3vDay5_intron.txt -wb
In [39]: 
!intersectBed -a /Volumes/web-1/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_TE.gff -b /Volumes/web-1/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/3xCoverage/methylKit/DMRs_v2/lineage_vs_developmental_differences/Developmental_differences/comparisons/Developmental_differences_Day3vDay5_30p.bed > /Volumes/web-1/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/3xCoverage/methylKit/DMRs_v2/lineage_vs_developmental_differences/Lineage_developmental_genomicfeatures/developmental_Day3vDay5_TE.txt -wb
In [40]: 
!intersectBed -a /Volumes/web-1/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_1k5p_gene_promoter.gff -b /Volumes/web-1/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/3xCoverage/methylKit/DMRs_v2/lineage_vs_developmental_differences/Developmental_differences/comparisons/Developmental_differences_Day3vDay5_30p.bed > /Volumes/web-1/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/3xCoverage/methylKit/DMRs_v2/lineage_vs_developmental_differences/Lineage_developmental_genomicfeatures/developmental_Day3vDay5_promoter.txt -wb
In [41]: 
!intersectBed -a /Volumes/web-1/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_COMP_gene_prom_TE.bed -b /Volumes/web-1/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/3xCoverage/methylKit/DMRs_v2/lineage_vs_developmental_differences/Developmental_differences/comparisons/Developmental_differences_Day3vDay5_30p.bed > /Volumes/web-1/Mollusk/bs_larvae_exp/AdapterTrimmed_FilteredFiles/3xCoverage/methylKit/DMRs_v2/lineage_vs_developmental_differences/Lineage_developmental_genomicfeatures/developmental_Day3vDay5_complement.txt -wb
In [3]: 
#NOTEBOOK NAME
nb='Lineage_Developmental_diff_GenomicFeatures'

#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 [4]: 
cd {post}

[Errno 2] No such file or directory: '/Volumes/web-1/Mollusk/iPython_Posts/'
/Users/claireolson/Dropbox/Lab (1)/IPython_nbs/Claire
/Volumes/web/Mollusk/iPython_Posts
In [47]: 
!ipython nbconvert {nbloc}{nb} --to html --template full --output {nb}{date}

[NbConvertApp] Using existing profile dir: u'/Users/claireellis/.ipython/profile_default'
[NbConvertApp] WARNING | pattern u'/Users/claireolson/Dropbox/Lab (1)/IPython_nbs/Claire/Lineage_Developmental_diff_GenomicFeatures' matched no files
This application is used to convert notebook files (*.ipynb) to various other
formats.

WARNING: THE COMMANDLINE INTERFACE MAY CHANGE IN FUTURE RELEASES.

Options
-------

Arguments that take values are actually convenience aliases to full
Configurables, whose aliases are listed on the help line. For more information
on full configurables, see '--help-all'.

--debug
    set log level to logging.DEBUG (maximize logging output)
--init
    Initialize profile with default config files.  This is equivalent
    to running `ipython profile create <profile>` prior to startup.
--quiet
    set log level to logging.CRITICAL (minimize logging output)
--stdout
    Write notebook output to stdout instead of files.
--profile=<Unicode> (BaseIPythonApplication.profile)
    Default: u'default'
    The IPython profile to use.
--reveal-prefix=<Unicode> (RevealHelpPreprocessor.url_prefix)
    Default: 'reveal.js'
    The URL prefix for reveal.js. This can be a a relative URL for a local copy
    of reveal.js, or point to a CDN.
    For speaker notes to work, a local reveal.js prefix must be used.
--ipython-dir=<Unicode> (BaseIPythonApplication.ipython_dir)
    Default: u''
    The name of the IPython directory. This directory is used for logging
    configuration (through profiles), history storage, etc. The default is
    usually $HOME/.ipython. This options can also be specified through the
    environment variable IPYTHONDIR.
--writer=<DottedObjectName> (NbConvertApp.writer_class)
    Default: 'FilesWriter'
    Writer class used to write the  results of the conversion
--log-level=<Enum> (Application.log_level)
    Default: 30
    Choices: (0, 10, 20, 30, 40, 50, 'DEBUG', 'INFO', 'WARN', 'ERROR', 'CRITICAL')
    Set the log level by value or name.
--to=<CaselessStrEnum> (NbConvertApp.export_format)
    Default: 'html'
    Choices: ['custom', 'html', 'latex', 'markdown', 'python', 'rst', 'slides']
    The export format to be used.
--template=<Unicode> (TemplateExporter.template_file)
    Default: u'default'
    Name of the template file to use
--output=<Unicode> (NbConvertApp.output_base)
    Default: ''
    overwrite base name use for output files. can only  be use when converting
    one notebook at a time.
--post=<DottedOrNone> (NbConvertApp.postprocessor_class)
    Default: u''
    PostProcessor class used to write the  results of the conversion
--config=<Unicode> (BaseIPythonApplication.extra_config_file)
    Default: u''
    Path to an extra config file to load.
    If specified, load this config file in addition to any other IPython config.
--profile-dir=<Unicode> (ProfileDir.location)
    Default: u''
    Set the profile location directly. This overrides the logic used by the
    `profile` option.

To see all available configurables, use `--help-all`

Examples
--------

    The simplest way to use nbconvert is
    
    > ipython nbconvert mynotebook.ipynb
    
    which will convert mynotebook.ipynb to the default format (probably HTML).
    
    You can specify the export format with `--to`.
    Options include ['custom', 'html', 'latex', 'markdown', 'python', 'rst', 'slides']
    
    > ipython nbconvert --to latex mynotebook.ipynb
    
    Both HTML and LaTeX support multiple output templates. LaTeX includes
    'base', 'article' and 'report'.  HTML includes 'basic' and 'full'. You
    can specify the flavor of the format used.
    
    > ipython nbconvert --to html --template basic mynotebook.ipynb
    
    You can also pipe the output to stdout, rather than a file
    
    > ipython nbconvert mynotebook.ipynb --stdout
    
    A post-processor can be used to compile a PDF
    
    > ipython nbconvert mynotebook.ipynb --to latex --post PDF
    
    You can get (and serve) a Reveal.js-powered slideshow
    
    > ipython nbconvert myslides.ipynb --to slides --post serve
    
    Multiple notebooks can be given at the command line in a couple of 
    different ways:
    
    > ipython nbconvert notebook*.ipynb
    > ipython nbconvert notebook1.ipynb notebook2.ipynb
    
    or you can specify the notebooks list in a config file, containing::
    
        c.NbConvertApp.notebooks = ["my_notebook.ipynb"]
    
    > ipython nbconvert --config mycfg.py
In []: