The terminal output of the perl command is attached: it basically matches two separate files and combines them into one and excludes non-unique values. I am not sure I follow what you are saying about the syntax of the perl function, but made some changes.
I am using cygwin on a windows 7 machine Thank you very much
The cd line as is works if the shells are run separate but not when they are combined.
Code:
#!/bin/bash
printf "What is the id of the patient to be matched : "; read id
printf "What panel: "; read panel
case "$id" in
cd 'C:\Users\cmccabe\Desktop\annovar'
OMR=Output_Mutation_Report
perl -aF/\\t/ -lne 'BEGIN{%m=map{chomp;s/\cM|\cJ//g;$p=join("\t",(split/\t/)[4,5]);($p,$_)} <>;$m{"#CHROM\tINFO"}=$m{"Chr\tSegment Position"}};/SEGPOS=(\d+)/ || /\t(INFO)\t/ or next;$p=$F[0]."\t".$1;exists $m{$p} and print join("\t",$_,$m{$p})' ${id}_${panel}_${OMR}.txt < ${id}_${panel}_${OMR}_Filtered.vcf > ${id}_matched.vcf
;;
show_menu=true
menu=( [yY] [nN] )
func_show() { # "MESSAGE STRING"
# Prints passed argument
# Returns nothing
printf '\n\t%s\n\n' "$1"
}
#
# Display & Action
#
clear
while $show_menu
do printf '#----------------------#\n%s\n' "Are there additonal patients to be matched"
select entry in "${menu[@]}" Back
do case "$entry" in
Back) show_menu=false
;;
[yY]) perl -aF/\\t/ -lne 'BEGIN{%m=map{chomp;s/\cM|\cJ//g;$p=join("\t",(split/\t/)[4,5]);($p,$_)} <>;$m{"#CHROM\tINFO"}=$m{"Chr\tSegment Position"}};/SEGPOS=(\d+)/ || /\t(INFO)\t/ or next;$p=$F[0]."\t".$1;exists $m{$p} and print join("\t",$_,$m{$p})' ${id}_${panel}_${OMR}.txt < ${id}_${panel}_${OMR}_Filtered.vcf > ${id}_matched.vcf (index id 0) :: $entry
;;
[nN]) func_show "printf "Does the file need to be converted : " ; read id :: ${menu[${#menu[@]}-1]}"
while true
do
printf "Enter ID : " ; read id
cd 'C:\Users\cmccabe\Desktop\annovar'
[ -z "$id" ] && break
[ "$id" = "end" ] && break
perl convert2annovar.pl -includeinfo -format vcf4old ${id}_matched.vcf > ${id}_matched.avinput
done
;;
*)
esac
break
done
done
Hi :
I have a file containing the print queues with their IP address. I wanted to combine the 'lpstat' output with their respective IP address.
For example :
zebhtrmb-6078 lgonzale priority 0 Mar 17 11:50 on zebhtrmb
with
zebhtrmb-6078 lgonzale priority 0 ... (1 Reply)
Is there any way to combine 3 excel files into one comma separated file, after removing the header row from all the three files. Is this possible? I have looked in FAQ and I did not find anything.
Appreciate any suggestions or links to resources.
Radhika. (11 Replies)
I have multiple files; each file contains a certain data in a column view
simply i want to combine all those files into one file in columns
example
file1:
a
b
c
d
file 2:
1
2
3
4
file 3:
G (4 Replies)
I need to combine two files based on the content in first column and combine it into one file . For example :
file1:
A 10
B 20
C 30
D 40
File2:
B 200
E 500
A 100
D 400
Need the output in this format:
file 3 :
column 1 Column 2 Column 3
A 10 100
B 20 ... (4 Replies)
i have 3 files: file1, file2 and file3
file1 has this content:
#!/bin/ksh
sqlplus username/password@Servername << EOF
file2 has this content:
drop table dropme cascade constraints;
file3 has this content:
EOF
all said and done, file1, file2 and file2 will look like... (1 Reply)
I have n of files with ending with _ZERO.txt
need to combine all file ending with _ZERO.txt into 1 file
ex:
A_ZERO.txt
1
2
B_ZERO.txt
3
4
Output:
FINAL.txt
1
2 (3 Replies)
The script below is an attempt to combine 3 shells into 1.
The first part: match.sh
prompts the user for an id of a patient and runs a match script based on the response of "y" or "n". After completing the user is asked if there are additional patients, and based on "y" or "n" a certain action... (2 Replies)
Hello All , I am new to this Forum,
I am trying to write a script to combine two data files with 1 column in common and others columns are different .
File1
Apple 29
tomatao 4
grapes 25
File2
Apple fruit
tomatao veg
grapes fruit
other (3 Replies)
i use the split command to split a one terabyte backup file into 10 chunks of 100 GB each. The files are split one after the other. While the files is being split, I will like to scp the files one after the other as soon as the previous one completes, from server A to Server B. Then on server B ,... (2 Replies)
Discussion started by: malaika
2 Replies
LEARN ABOUT OPENSOLARIS
shell
shell(1F) FMLI Commands shell(1F)NAME
shell - run a command using shell
SYNOPSIS
shell command [command] ...
DESCRIPTION
The shell function concatenate its arguments, separating each by a space, and passes this string to the shell ($SHELL if set, otherwise
/usr/bin/sh).
EXAMPLES
Example 1 A sample output of shell command.
Since the Form and Menu Language does not directly support background processing, the shell function can be used instead.
`shell "build prog > /dev/null &"`
If you want the user to continue to be able to interact with the application while the background job is running, the output of an exe-
cutable run by shell in the background must be redirected: to a file if you want to save the output, or to /dev/null if you don't want to
save it (or if there is no output), otherwise your application may appear to be hung until the background job finishes processing.
shell can also be used to execute a command that has the same name as an FMLI built-in function.
NOTES
The arguments to shell will be concatenate using spaces, which may or may not do what is expected. The variables set in local environments
will not be expanded by the shell because "local" means "local to the current process."
ATTRIBUTES
See attributes(5) for descriptions of the following attributes:
+-----------------------------+-----------------------------+
| ATTRIBUTE TYPE | ATTRIBUTE VALUE |
+-----------------------------+-----------------------------+
|Availability |SUNWcsu |
+-----------------------------+-----------------------------+
SEE ALSO sh(1), attributes(5)SunOS 5.11 5 Jul 1990 shell(1F)
11-08-2014
