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Shell Programming and Scripting

User prompt for perl

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# 1  
Old 09-25-2014
User prompt for perl
Code:
 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})' 12345_Marfan20_Output_Mutation_Report.txt < 12345_Marfan20_Output_Mutation_Report_Filtered.vcf > 12345_matched.vcf

The above perl script is used to merge two large data sets into 1 file. Is it possible to prompt the user to enter in the ID and panel? The same format is used each time and the only 3 things that change are the ID in italic and the panel in bold.

For example, the user would be prompted "Enter ID" = 12345, then asked "What panel" = Marfan20

the answers to the questions would be placed in the indicated places in the script. Thanks Smilie.
# 2  
Old 09-25-2014
Is it allowed to not be a one-liner? (Something 3 screens wide should not have been a 1-liner...)
# 3  
Old 09-25-2014
When I open the code using linux it is three lines, not sure why its one on here (maybe windows).

Code:
 
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})'
W34903_Noonan14_Output_Mutation_Report.txt < W34903_Noonan14_Output_Mutation_Report_Filtered.vcf > W34903_matched.vcf

Thanks.
# 4  
Old 09-25-2014
Of course it is possible to prompt the user for some input in perl, but it's somehow hard to use this input outside of the script, especially in the case of this one-liner, thus following bash script might be a viable workaround:
Code:
#!/bin/bash

echo -n "Enter ID  : "; read id
echo -n "What panel: "; read panel

OMR=Output_Mutation_Report

perl -aF/\\t/ -lne 'BEGIN ... ' $id_$panel_$OMR.txt < $id_$panel_$OMR_Filtered.vcf > $id_matched.vcf

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