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Edit $args within a command

 
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# 1  
Old 11-06-2014
Edit $args within a command
Hi,
I'm using a while loop for a given command "bowtie2" with several parameters.

Code:
mkdir clean
paste <(ls --quote-name ./qc/sg_*_R1_val_1.fq.gz) <(ls --quote-name ./qc/sg_*_R2_val_2.fq.gz) |sed 's/"./-1 ./' | sed 's/gz"\t/gz\t -2 /' | sed 's/"//g' |\
      while read args ; do
                           bowtie2  -x ./MrBean_genome_final/dl_mt -p 4 -k 1 -N 1 -L 25 $args --un-conc-gz ./clean/{$args | sed -e 's/.fq.gz.*$//' -e 's/-1 .\/qc\///' -e 's/_R1_val_1//' }.gz -S a.sam

done

so the $args is actually edited to feed two parameters "-1" and "-2"
Code:
 paste <(ls --quote-name ./qc/sg_*_R1_val_1.fq.gz) <(ls --quote-name ./qc/sg_*_R2_val_2.fq.gz) |sed 's/"./-1 ./' | sed 's/gz"\t/gz\t -2 /' | sed 's/"//g'
-1 ./qc/sg_21_L001_R1_val_1.fq.gz        -2 ./qc/sg_21_L001_R2_val_2.fq.gz
-1 ./qc/sg_21_L002_R1_val_1.fq.gz        -2 ./qc/sg_21_L002_R2_val_2.fq.gz
-1 ./qc/sg_22_L001_R1_val_1.fq.gz        -2 ./qc/sg_22_L001_R2_val_2.fq.gz
-1 ./qc/sg_22_L002_R1_val_1.fq.gz        -2 ./qc/sg_22_L002_R2_val_2.fq.gz
-1 ./qc/sg_23_L001_R1_val_1.fq.gz        -2 ./qc/sg_23_L001_R2_val_2.fq.gz
-1 ./qc/sg_23_L002_R1_val_1.fq.gz        -2 ./qc/sg_23_L002_R2_val_2.fq.gz
-1 ./qc/sg_25_L001_R1_val_1.fq.gz        -2 ./qc/sg_25_L001_R2_val_2.fq.gz

For the parameter "--un-conc-gz" I was trying to feed it by editing with sed the $arg,

Code:
--un-conc-gz ./clean/{$args | sed -e 's/.fq.gz.*$//' -e 's/-1 .\/qc\///' -e 's/_R1_val_1//' }.gz

to feed iteratively "--un-conc-gz" with this
Code:
sg_21_L001
sg_21_L002
sg_22_L001
sg_22_L002
sg_23_L001
sg_23_L002
sg_25_L001

Can I do this? Do I need a loop within the loop, if so how?

P.S. the sed editing is OK, no need to focus there.

Many thanks in advance.

---------- Post updated at 04:15 PM ---------- Previous update was at 10:37 AM ----------

Update, I added the echo,
Code:
--un-conc-gz ./clean/{echo "$args" | sed 's/.fq.gz.*$//' |sed 's/-1 .\/qc\///' |sed 's/_R1_val_1//'}.gz

but I get an error message
Quote:
sed: invalid option -- S
.
# 2  
Old 11-06-2014
Perhaps you could simplify this and show us what you are trying to achieve for the call to bowtie and describe the inputs (file list etc.) and what you want it to end up calling it with. It is a little hard work to decipher your code without any design or comments and I worry about missing something vital.

Can you just explain the logic you use to get the bowtie calls?


Thanks, in advance,
Robin
# 3  
Old 11-06-2014
OK, I'll try to simplify with an example and remove the non essential for the question.
Thanks.

---------- Post updated at 05:19 PM ---------- Previous update was at 04:50 PM ----------

Using while loop for a given command with several parameters,

Code:
arguments |\
      while read args ; do
                           command  $args --un-conc-gz {echo $args | sed 'editing' } --several --others --parameters
done

so the arguments is actually edited to feed two parameters "-1" and "-2"
Code:
 
-1 ./path/file_a_1        -2 ./path/file_a_2
-1 ./path/file_b_1        -2 ./path/file_b_2
-1 ./path/file_c_1        -2 ./path/file_c_2

For the command parameter "--un-conc-gz" I was trying to feed it by reediting the $arg with sed,

Code:
echo $args | sed 'editing'
file_a
file_b
file_c

and I manage to get, file_a, file_b and file_c but I guess is not doing it iteratively with the $args.


So it would perfom the following commands
Code:
command -1 ./path/file_a_1 -2 ./path/file_a_2 --un-conc-gz file_a --several --others --parameters
command -1 ./path/file_b_1 -2 ./path/file_b_2 --un-conc-gz file_b --several --others --parameters
command -1 ./path/file_c_1 -2 ./path/file_c_2 --un-conc-gz file_c --several --others --parameters

Hope this is more clear!
# 4  
Old 11-06-2014
If all the commands to run are based with the 1 and 2 effectively being literal, could you do this:-
Code:
find . -type f | while read path_file         # Or however you generate your file list
do
   file="${path_file##*/}"                    # Get just the file bit, dropping the path
   echo "command -1 ${path_file}_1 -2 ${path_file}_2 --un-conc-gz $file --several --others --parameters"
done

If it displays what you want, take out the echo and double quotes.

If I've missed the point, let me know where I've gone wrong and I will have another think.


Regards,
Robin
This User Gave Thanks to rbatte1 For This Post:
sargotrons
# 5  
Old 11-06-2014
You may want to write a Perl wrapper with the YAML library. Perl and YAML are really good at reading configuration files. You would then have a configuration file with all of the parameters that you need to make the bowtie2 call, you can parse all of the inputs and more simply change the inputs to what you need and make it work. It would probably be easier to read and understand then the approach you are taking. etc..etc..

Here is the install page for YAML. I am using Perl and YAML to build a software installer. The customer will only need to provide the response file to make it work. Which is much easier than handling each parameter separately. And I can directly reference any parameter as $yaml_hash->{field_name}.

YAML - search.cpan.org
This User Gave Thanks to gandolf989 For This Post:
sargotrons
# 6  
Old 11-07-2014
@rbatte1
Seems perfect, I'll try it later on.
Update you on the results later on.

Many thanks!

---------- Post updated 07-11-14 at 11:46 AM ---------- Previous update was 06-11-14 at 05:51 PM ----------
@rbatte1
It works! After some slight changes (in bold) because of my files names
Code:
find ./path/ -type f | sed -e 's/_R.*$//' -e 's/_R//'|sort -u | while read path_file         # Or however you generate your file list
do
    file="${path_file##*/}"                    # Get just the file bit, dropping the path
  echo "command -1 ${path_file}_R1_val_1.fq.gz -2 ${path_file}_R2_val_2.fq.gz --un-conc-gz $file --several --others --parameters"
done

it gives this expected output:

Quote:
command -1 ./path/fileA_R1_val_1.fq.gz -2 ./path/fileA_R2_val_2.fq.gz --un-conc-gz fileA --several --others --parameters
command -1 ./path/fileB_R1_val_1.fq.gz -2 ./path/fileB_R2_val_2.fq.gz --un-conc-gz fileB --several --others --parameters
command -1 ./path/fileC_R1_val_1.fq.gz -2 ./path/fileC_R2_val_2.fq.gz --un-conc-gz fileC --several --others --parameters
command -1 ./path/fileD_R1_val_1.fq.gz -2 ./path/fileD_R2_val_2.fq.gz --un-conc-gz fileD --several --others --parameters
Many thanks for your help! Smilie

@gandolf989
Thanks for the suggestion, actually the command is already a perl wrapper.
That is away ahead for my state of knowledge, hope to get there some day...
This User Gave Thanks to sargotrons For This Post:
rbatte1
 
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