Simple script to write new lines in a text file


 
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# 15  
Quote:
Originally Posted by bartus11
Can you post output of:
Code:
cat -e file | head

Yea something weird is going on...file is fine when I open in excel. This is what the cat looks like

Code:
jonathon-torchias-macbook-pro:Desktop torchiaj$ cat -e test2.txt | head
Gene Name	sdfad	ATRT prev seen (formatted)	UniProt ID	sdfs	NCBI Accession	UCSC Link	Cosmic Gene	Variation	Position	Ref	Alt	AA Length^MA1BG	P04217	ATRT_SP192	P04217	NM_130786	NM_130786	UCSC link	CosLink	nonsynonymous SNV	chr19:58861808	A	G	495^MA1CF	Q9NQ94	"ATRT47B,ATRT47"	Q9NQ94	NM_014576	NM_014576	UCSC link	CosLink	nonsynonymous SNV	chr10:52573772	C	T	594^MA1CF	Q9NQ94	ATRT41	Q9NQ94	NM_014576	NM_014576	UCSC link	CosLink	nonsynonymous SNV	chr10:52566611	C	T	594^MA2M	P01023	ATRT41	P01023	NM_000014	NM_000014	UCSC link	CosLink	nonsynonymous SNV	chr12:9258857	C	T	1474^MA2M	P01023	"ATRT12B,ATRT12"	P01023	NM_000014	NM_000014	UCSC link	CosLink	nonsynonymous SNV	chr12:9254209	T	C	1474^MA2M	P01023	ATRT64	P01023	NM_000014	NM_000014	UCSC link	CosLink	nonsynonymous SNV	chr12:9222373	T	G	1474^MA2M	P01023	ATRT63	P01023	NM_000014	NM_000014	UCSC link	CosLink	nonsynonymous SNV	chr12:9260170	C	T	1474^MA2M	P01023	"ATRT2B,ATRT2,ATRT39,ATRT40"	P01023	NM_000014	NM_000014	UCSC link	CosLink	nonsynonymous SNV	chr12:9243017	G	A	1474^MA2ML1	A8K2U0	ATRT67	A8K2U0	NM_144670	NM_144670	UCSC link	CosLink	nonsynonymous SNV	chr12:8976358	C	G	1454^MA2ML1	A8K2U0	ATRT63	A8K2U0	NM_144670	NM_144670	UCSC link	CosLink	nonsynonymous SNV	chr12:9027033	A	G	1454^MA2ML1	A8K2U0	ATRT33	A8K2U0	NM_144670	NM_144670	UCSC link	CosLink	nonsynonymous SNV	chr12:9004388	G	A	1454^MA2ML1	A8K2U0	"ATRT8B,ATRT8"	A8K2U0	NM_144670	NM_144670	UCSC link	CosLink	nonsynonymous SNV	chr12:9000236	G	A	1454^MA2ML1	A8K2U0	ATRT34	A8K2U0	NM_144670	NM_144670	UCSC link	CosLink	nonsynonymous SNV	chr12:9013737	A	G	1454jonathon-torchias-macbook-pro:Desktop torchiaj$

# 16  
You have to get rid of the Windows newline characters:
Code:
tr '\r' '\n' < file > file.fixed

# 17  
In addition to transforming the classic Mac line breaks, there needs to be a space between -v and OFS, and field 3 contains double quotes that need to be removed and FS is best also set to "\t" in this TAB-delimited file...

Last edited by Scrutinizer; 05-26-2012 at 07:40 PM..
# 18  
Try this:
Code:
awk '$3~/,/{n=split($3,T,/[,"]*/); for (i=2;i<n;i++) {$3=T[i]; print}next}1' FS='\t' OFS='\t' infile


Instead of a separate conversion step (with tr '\r' '\n') it could also be done by setting RS:
Code:
awk '$3~/,/{n=split($3,T,/[,"]*/); for (i=2;i<n;i++) {$3=T[i]; print}next}1' RS='\r' FS='\t' OFS='\t' infile

# 19  
That looks like it worked! Thanks guys for the help.
Much appreciated!!
 

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