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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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SCRIPT(1)						    BSD General Commands Manual 						 SCRIPT(1)

NAME
script -- make typescript of terminal session SYNOPSIS
script [-a] [-c COMMAND] [-f] [-q] [-t] [file] DESCRIPTION
Script makes a typescript of everything printed on your terminal. It is useful for students who need a hardcopy record of an interactive session as proof of an assignment, as the typescript file can be printed out later with lpr(1). If the argument file is given, script saves all dialogue in file. If no file name is given, the typescript is saved in the file typescript. Options: -a Append the output to file or typescript, retaining the prior contents. -c COMMAND Run the COMMAND rather than an interactive shell. This makes it easy for a script to capture the output of a program that behaves differently when its stdout is not a tty. -f Flush output after each write. This is nice for telecooperation: One person does `mkfifo foo; script -f foo' and another can super- vise real-time what is being done using `cat foo'. -q Be quiet. -t Output timing data to standard error. This data contains two fields, separated by a space. The first field indicates how much time elapsed since the previous output. The second field indicates how many characters were output this time. This information can be used to replay typescripts with realistic typing and output delays. The script ends when the forked shell exits (a control-D to exit the Bourne shell (sh(1)), and exit, logout or control-d (if ignoreeof is not set) for the C-shell, csh(1)). Certain interactive commands, such as vi(1), create garbage in the typescript file. Script works best with commands that do not manipulate the screen, the results are meant to emulate a hardcopy terminal. ENVIRONMENT
The following environment variable is utilized by script: SHELL If the variable SHELL exists, the shell forked by script will be that shell. If SHELL is not set, the Bourne shell is assumed. (Most shells set this variable automatically). SEE ALSO
csh(1) (for the history mechanism), scriptreplay(1). HISTORY
The script command appeared in 3.0BSD. BUGS
Script places everything in the log file, including linefeeds and backspaces. This is not what the naive user expects. AVAILABILITY
The script command is part of the util-linux-ng package and is available from ftp://ftp.kernel.org/pub/linux/utils/util-linux-ng/. Linux July 30, 2000 Linux
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