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Perl command in bash

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Top Forums Shell Programming and Scripting Perl command in bash
# 29  
Old 03-31-2015
The set -x is below: things appear to ok?

I will investigate how the script is called. Thank you Smilie.

Code:
NOTICE: Multianno output file is written to del.txt.hg19_multianno.txt
+ printf 'The annotation is complete, would you like analyze additional target g
ene patients? Y/N '
The annotation is complete, would you like analyze additional target gene patien
ts? Y/N + read match_choice
n
+ case "$match_choice" in
+ id=del
+ remove
+ printf '\n\n'


+ printf 'Removing old files, please wait '
Removing old files, please wait + rm 'C:\Users\cmccabe\Desktop\annovar\out_posit
ion.txt'
+ rm 'C:\Users\cmccabe\Desktop\annovar\out_parse.txt'
+ cd C:
+ rm c:/Users/cmccabe/Desktop/Python27/del.txt
+ cd C:
+ rm c:/Users/cmccabe/Desktop/Python27/out_name.txt
+ printf '\n Old files removed, formatting for matrix '

 Old files removed, formatting for matrix + matrix
+ cd 'C:\Users\cmccabe\Desktop\annovar'
+ perl matrix.pl
Can't open : No such file or directory at matrix.pl line 44.
+ printf 'Process complete and new file saved in L:NGS3_BUSINESSMatrixTorrentmat
rix_del.txt, Are there additional target gene patients? Y/N '
Process complete and new file saved in L:NGS3_BUSINESSMatrixTorrentmatrix_del.tx
t, Are there additional target gene patients? Y/N + read match_choice

# 30  
Old 03-31-2015
Quote:
Originally Posted by cmccabe
The set -x is below: things appear to ok?...
Do they appear ok to you?

Quote:
Originally Posted by cmccabe
...I will investigate how the script is called. ...
That's a good approach. I can tell you the problem but it will be better if you find it out yourself.
# 31  
Old 03-31-2015
Another set -x Part of the problem was the entire path was needed and that fixed the output, but the input is not being read (in bold). Thank you Smilie.

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


Code:
NOTICE: Multianno output file is written to snp.txt.hg19_multianno.txt
+ printf 'The annotation is complete, would you like analyze additional target g
ene patients? Y/N '
The annotation is complete, would you like analyze additional target gene patien
ts? Y/N + read match_choice
n
+ case "$match_choice" in
+ id=snp
+ remove
+ printf '\n\n'


+ printf 'Removing old files, please wait '
Removing old files, please wait + rm 'C:\Users\cmccabe\Desktop\annovar\out_posit
ion.txt'
+ rm 'C:\Users\cmccabe\Desktop\annovar\out_parse.txt'
+ cd C:
+ rm c:/Users/cmccabe/Desktop/Python27/snp.txt
+ cd C:
+ rm c:/Users/cmccabe/Desktop/Python27/out_name.txt
+ printf '\n Old files removed, formatting for matrix '

 Old files removed, formatting for matrix + matrix
+ perl 'C:\Users\cmccabe\Desktop\annovar\matrix.pl'
c:\cygwin\home\cmccabe\bashparse.sh: line 215: C:\Users\cmccabe\Desktop\annovar\
"${id}".txt.hg19_multianno.txt: No such file or directory
+ printf 'Process complete and new file saved in L:/NGS/3_BUSINESS/Matrix/Torren
t/matrix_snp.txt, Are there additional target gene patients? Y/N '

# 32  
Old 03-31-2015
Not quite sure about the linebreaks, if they were caused by a small terminal window, or by 'string-generation'...
Code:
+ perl 'C:\Users\cmccabe\Desktop\annovar\matrix.pl'
c:\cygwin\home\cmccabe\bashparse.sh: line 215: C:\Users\cmccabe\Desktop\annovar\
"${id}".txt.hg19_multianno.txt: No such file or directory

It states that it is looking for a literal "${id}".
Seems there is too much escaped or wrongly quoted.

Is the filename supposed to have <str>.txt.<str>.txt?

hth
# 33  
Old 03-31-2015
Is the filename supposed to have <str>.txt.<str>.txt?
Yes this is correct.
# 34  
Old 03-31-2015
Quote:
Originally Posted by cmccabe
...but the input is not being read (in bold). ...
...
You'll need to do more investigation for that one.
Pay very close attention to the little details in all my previous posts in this thread and you should be able to find the problem.
# 35  
Old 04-01-2015
I am reading all of your threads and not having any luck, I am still investigating but it appears to be the way that the input file is being read by the perl script. Is that right? Thank you Smilie.


Code:
 perl matrix.pl < "${id}".txt.hg19_multianno.txt > L:/NGS/3_BUSINESS/Matrix/Torrent/matrix_"${id}".txt


It was the way it was called... I see now that the < input and > output are not needed:

Code:
 perl matrix.pl "${id}".txt.hg19_multianno.txt L:/NGS/3_BUSINESS/Matrix/Torrent/matrix_"${id}".txt

However, the new file that is created only has the headers in it and doesn't carry over the data in the multianno.txt.
Maybe
Code:
 chomp;
          if ($.input) {

Thank you Smilie
matrix_del.txt (569 Bytes) 
matrix_del - desired.txt (750 Bytes) 
Last edited by cmccabe; 04-01-2015 at 12:56 PM..
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