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Using multiple pipe output

 
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# 1  
Old 08-06-2012
Using multiple pipe output
I have a script that finds all sffs and extracts them into .fastq file types. What I need to do is change the .fastq to .fasta using the below script. How can I change the input.fastq and output.fasta to mirror the file's name? Would I use an array and use the default iterator?

Code:
#!/bin/bash

find . -type f -name \*.sff | xargs python /usr/local/bin/sff_extract.py

find . -type f -name \*.fastq | xargs awk 'BEGIN{P=1}{if(P==1||P==2){gsub(/^[@]/,">");print}; if(P==4)P=0; P++}' input.fastq > output.fasta

# 2  
Old 08-06-2012
Code:
#!/bin/bash
find . -type f -name \*.sff |
while read fname 
do
  python /usr/local/bin/sff_extract.py $fname
  iname=${fname/.sff/.fastq/}
  oname=${fname/.sff/.fasta/}
  awk 'BEGIN{P=1}
     {if(P==1||P==2){gsub(/^[@]/,">");print}; if(P==4)P=0; P++}' $iname > $oname

try that
# 3  
Old 08-06-2012
It did not work. When I run sff extract I get something like file.MID38.fastq which is why I think it did not work, at first I was getting an error saying that it was not a directory. I removed the
Code:
iname=${fname/.sff/.fastq/}   oname=${fname/.sff/.fasta/}

and I did not get any error but it still did not change the fastq to a fasta.
Last edited by jrymer; 08-06-2012 at 03:01 PM.. Reason: forgot code tags
# 4  
Old 08-06-2012
Those are bash substitutions. There is a typo in what I gave you:
Code:
iname=${fname/.sff/.fastq/}   
oname=${fname/.sff/.fasta/}

Remove the trailing / (red)
 
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