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Full Discussion: Help with generating a script
Top Forums Shell Programming and Scripting Help with generating a script Post 302555116 by kellywilliams on Wednesday 14th of September 2011 01:29:05 AM
Old 09-14-2011
So the files all come in this format below:

There is a heading line at the top of each file, and each subsequent line starts with chr. For this example, I would be wanting to identify the lines containing WASH7P in file1.txt and file2.txt (or if this would work with .csv files?)

file1.txt
Code:
chr_name	chr_start	chr_end	ref_base	alt_base	hom_het	snp_quality	tot_depth	alt_depth	dbSNP	dbSNP131	region	gene	change	annotation	dbSNP132	1000genomes	allele freq
chr01	14907	14907	A	G	het	108	52	39	snp131	rs6682375	ncRNA	WASH7P	.	.	rs6682375	.	.
chr01	14930	14930	A	G	het	148	62	44	snp131	rs6682385	ncRNA	WASH7P	.	.	rs6682385	1000g2010nov_all	0.71
chr01	761752	761752	C	T	hom	225	69	69	snp131	rs1057213	ncRNA	NCRNA00115	.	.	rs1057213	1000g2010nov_all	0.544
chr01	761800	761800	A	T	hom	42	11	11	snp131	rs1064272	ncRNA	NCRNA00115	.	.	rs1064272	1000g2010nov_all	0.114

file2.txt
Code:
chr_name	chr_start	chr_end	ref_base	alt_base	hom_het	snp_quality	tot_depth	alt_depth	dbSNP	dbSNP131	region	gene	change	annotation	dbSNP132	1000genomes	allele freq
chr01	17556	17556	C	T	het	43	30	9	.	.	ncRNA	WASH7P	.	.	.	.	.
chr01	69511	69511	A	G	hom	225	106	106	snp131	rs2691305	exonic	OR4F5	nonsynonymous SNV	"OR4F5:NM_001005484:exon1:c.A421G:p.T141A,"	rs2691305	1000g2010nov_all	0.789
chr01	761732	761732	C	T	hom	225	103	102	snp131	rs2286139	ncRNA	NCRNA00115	.	.	rs2286139	1000g2010nov_all	0.537


I would like be asked to type in GeneName (i.e. WASH7P) and the output in a .txt file to be something like:
Code:
file1.txt:chr01	14907	14907	A	G	het	108	52	39	snp131	rs6682375	ncRNA	WASH7P	.	.	rs6682375	.	.
file1.txt:chr01	14930	14930	A	G	het	148	62	44	snp131	rs6682385	ncRNA	WASH7P	.	.	rs6682385	1000g2010nov_all	0.71
file2.txt:chr01	17556	17556	C	T	het	43	30	9	.	.	ncRNA	WASH7P	.	.	.	.	.

Many thanks,

Kelly
Last edited by Franklin52; 09-14-2011 at 04:00 AM.. Reason: Please use code tags for code and data samples, thank you
 

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LEARN ABOUT REDHAT

mac2unix

dos2unix(1)						      General Commands Manual						       dos2unix(1)

NAME

       dos2unix - DOS/MAC to UNIX text file format converter

SYNOPSYS

       dos2unix [options] [-c convmode] [-o file ...] [-n infile outfile ...]

       Options:

       [-hkqV] [--help] [--keepdate] [--quiet] [--version]

DESCRIPTION

       This manual page documents dos2unix, the program that converts plain text files in DOS/MAC format to UNIX format.

OPTIONS

       The following options are available:

       -h --help
	      Print online help.

       -k --keepdate
	      Keep the date stamp of output file same as input file.

       -q --quiet
	      Quiet mode. Suppress all warning and messages.

       -V --version
	      Prints version information.

       -c --convmode convmode
	      Sets conversion mode. Simulates dos2unix under SunOS.

       -o --oldfile file ...
	      Old file mode. Convert the file and write output to it. The program default to run in this mode. Wildcard names may be used.

       -n --newfile infile outfile ...
	      New  file  mode.	Convert the infile and write output to outfile. File names must be given in pairs and wildcard names should NOT be
	      used or you WILL lost your files.

EXAMPLES

       Get input from stdin and write output to stdout.

	      dos2unix

       Convert and replace a.txt. Convert and replace b.txt.

	      dos2unix a.txt b.txt

	      dos2unix -o a.txt b.txt

       Convert and replace a.txt in ASCII conversion mode.  Convert and replace b.txt in ISO conversion mode.  Convert	c.txt  from  Mac  to  Unix
       ascii format.

	      dos2unix a.txt -c iso b.txt

	      dos2unix -c ascii a.txt -c iso b.txt

	      dos2unix -c mac a.txt b.txt

       Convert and replace a.txt while keeping original date stamp.

	      dos2unix -k a.txt

	      dos2unix -k -o a.txt

       Convert a.txt and write to e.txt.

	      dos2unix -n a.txt e.txt

       Convert a.txt and write to e.txt, keep date stamp of e.txt same as a.txt.

	      dos2unix -k -n a.txt e.txt

       Convert and replace a.txt. Convert b.txt and write to e.txt.

	      dos2unix a.txt -n b.txt e.txt

	      dos2unix -o a.txt -n b.txt e.txt

       Convert c.txt and write to e.txt. Convert and replace a.txt.  Convert and replace b.txt. Convert d.txt and write to f.txt.

	      dos2unix -n c.txt e.txt -o a.txt b.txt -n d.txt f.txt

DIAGNOSTICS

BUGS

       The program does not work properly under MSDOS in stdio processing mode.  If you know why is that so, please tell me.

AUTHORS

       Benjamin Lin - <blin@socs.uts.edu.au>

       Bernd Johannes Wuebben (mac2unix mode) <wuebben@kde.org>

MISCELLANY

       Tested environment:

	      Linux 1.2.0 with GNU C 2.5.8

	      SunOS 4.1.3 with GNU C 2.6.3

	      MS-DOS 6.20 with Borland C++ 4.02

       Suggestions and bug reports are welcome.

SEE ALSO

       unix2dos(1) mac2unix(1)

1995.03.31							   dos2unix v3.0						       dos2unix(1)
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