In [6]:

tr ',' "\t" </Volumes/web/Mollusk/174gm_analysis/RNAseq/MethandUnmeth_Over5xCoverage.csv> /Volumes/web/Mollusk/174gm_analysis/RNAseq/MethandUnmeth_Over5xCoverage.txt

  File "<ipython-input-6-5709b0c950e9>", line 1
    tr ',' "\t" </Volumes/web/Mollusk/174gm_analysis/RNAseq/MethandUnmeth_Over5xCoverage.csv> /Volumes/web/Mollusk/174gm_analysis/RNAseq/MethandUnmeth_Over5xCoverage.txt
         ^
SyntaxError: invalid syntax

In [14]:

!intersectBed -a /Volumes/web/Mollusk/174gm_analysis/RNAseq/MethandUnmeth_Over5xCoverage.txt -b /Volumes/web/Mollusk/174gm_analysis/RNAseq/Cgigas_v9_gene.gff > /Volumes/web/Mollusk/174gm_analysis/RNAseq/Genemethylation_CGI.txt

Differing number of GFF fields encountered at line: 2146459.  Exiting...

In [13]:

!head /Volumes/web/Mollusk/174gm_analysis/RNAseq/Genemethylation_CGI.txt

In [20]:

!tr '=' "\t" </Volumes/web/Mollusk/174gm_analysis/RNAseq/MethScoreperGene.txt> /Volumes/web/Mollusk/174gm_analysis/RNAseq/MethScoreperGene_Modified.txt

In [21]:

!head /Volumes/web/Mollusk/174gm_analysis/RNAseq/MethScoreperGene_Modified.txt

ID	CGI_10000003;	0.125

ID	CGI_10000005;	0.036

ID	CGI_10000011;	0.014

ID	CGI_10000013;	1

ID	CGI_10000013;	1

ID	CGI_10000013;	0.917

ID	CGI_10000013;	0.938

ID	CGI_10000013;	0.75

ID	CGI_10000013;	1

ID	CGI_10000013;	0.889

In [22]:

!tr ';' "\t" </Volumes/web/Mollusk/174gm_analysis/RNAseq/MethScoreperGene_Modified.txt> /Volumes/web/Mollusk/174gm_analysis/RNAseq/MethScoreperGene_Modified2.txt

In [23]:

!head /Volumes/web/Mollusk/174gm_analysis/RNAseq/MethScoreperGene_Modified2.txt

ID	CGI_10000003		0.125

ID	CGI_10000005		0.036

ID	CGI_10000011		0.014

ID	CGI_10000013		1

ID	CGI_10000013		1

ID	CGI_10000013		0.917

ID	CGI_10000013		0.938

ID	CGI_10000013		0.75

ID	CGI_10000013		1

ID	CGI_10000013		0.889

In []: