CODEWITHSUNDEEP
bashperl
justaguy
justaguy

Reputation: 3022

calling perl script in bash to execute

Below is how I call the perl script in a bash function: but I am getting: c:\cygwin\home\cmccabe\bashparse.sh: line 156: C:\Users\cmccabe\Desktop\annovar\ matrix.pl: command not found

So I must be calling it incorrectly.

I provide the full path to the .pl , the input and the output

perl -e 'C:\Users\cmccabe\Desktop\annovar\matrix.pl' < "${id}".txt.hg19_multianno.txt >     "L:\NGS\3_BUSINESS\Matrix\Torrent\matrix_"${id}".txt"

The overall goal is use ${id}.txt.hg19_multianno.txt as the input file and after the perl script is run on that file (which adds the columns and text and the new file is saved to the path L:\NGS\3_BUSINESS\Matrix\Torrent\matrix_${id}.txt. That path is a static path and will never change, there is probably a better way but I am not expert enough to know. Thank you :).

Here is the perl script

#!/bin/perl

# format for matrix import

use warnings;
use strict;

my ($debug);
$debug = 0;
$debug = 1;

while (<>) {
chomp;
if ( $. == 1 ) {
s/$/ Index/;
if ( $. == 2 ) {
s/$/ Chromosome Position/;
if ( $. == 3 ) {
s/$/ Gene/;
if ( $. == 4 ) {
s/$/ Inheritance/;
if ( $. == 5 ) {
s/$/ RNA Accession/;
if ( $. == 6 ) {
s/$/ Chr/;
if ( $. == 7 ) {
s/$/ Coverage/;
if ( $. == 8 ) {
s/$/ Score/;
if ( $. == 9 ) {
s/$/ A(#F#R)/;
if ( $. == 10 ) {
s/$/ C(#F#R)/;
if ( $. == 11 ) {
s/$/ G(#F#R)/;
if ( $. == 12 ) {
s/$/ T(#F#R)/;
if ( $. == 13 ) {
s/$/ Ins(#F#R)/;
if ( $. == 14 ) {
s/$/ Del(#F#R)/;
if ( $. == 15 ) {
s/$/ SNP db_xref/;
if ( $. == 16 ) {
s/$/ Mutation Call/;
if ( $. == 17 ) {
s/$/ Mutation Allele Frequency/;
if ( $. == 18 ) {
s/$/ Amino Acid Change/;
if ( $. == 43 ) {
s/$/ HP/;
if ( $. == 44 ) {
s/$/ SPLICE/;
if ( $. == 45 ) {
s/$/ Pseudogene/;
if ( $. == 46 ) {
s/$/ Classification/;
if ( $. == 47 ) {
s/$/ HGMD/;
if ( $. == 48 ) {
s/$/ Disease/;
if ( $. == 49 ) {
s/$/ Sanger/;
if ( $. == 50 ) {
s/$/ References/;
}
print "$_\n";
}

print STDERR " ( Lines read: $. )\n";

exit(0);

Upvotes: 0

Views: 143

Answers (1)

bgoldst
bgoldst

Reputation: 35314

The -e command-line option takes literal Perl code as an argument. It does not take a file name. For example:

perl -e 'print("Hello, World!\n");';

If you want to run a script, just omit the -e:

perl myscript.pl;

Thus, your command will work if you run it as follows:

perl 'C:\Users\cmccabe\Desktop\annovar\matrix.pl' < "${id}".txt.hg19_multianno.txt >     "L:\NGS\3_BUSINESS\Matrix\Torrent\matrix_"${id}".txt"

Upvotes: 2

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