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  • JQL
    replied
    Thanks!

    I have all the fastq files in the dir of /fastq. but I don't need /fastq, only need P1, P2...
    Is there an easy way to pick up what the * stands for?

    John

    for f in fastq/*.fastq.gz; do echo ${f%.fastq.gz}; done


    Originally posted by GenoMax View Post
    Code:
    $ ls *.fastq.gz
    P1.fastq.gz  P2.fastq.gz  Pdot1.fastq.gz  Pdot2.fastq.gz
    Compare the list above to the output below. Can you see what f% is doing?

    Code:
    $ for f in *.fastq.gz; do echo ${f%.fastq.gz}; done
    
    P1
    P2
    Pdot1
    Pdot2

    Leave a comment:


  • GenoMax
    replied
    Code:
    $ ls *.fastq.gz
    P1.fastq.gz  P2.fastq.gz  Pdot1.fastq.gz  Pdot2.fastq.gz
    Compare the list above to the output below. Can you see what f% is doing?

    Code:
    $ for f in *.fastq.gz; do echo ${f%.fastq.gz}; done
    
    P1
    P2
    Pdot1
    Pdot2

    Leave a comment:


  • JQL
    started a topic books for linux shell scripting and python?

    books for linux shell scripting and python?

    Can you guys recommend a good introductory book for shell scripting, and maybe python? I'm going to have to learn it better.

    e.g. what does the % mean here?

    for f in *.fasta.gz
    do
    metaphlan2.py $f --input_type fasta --nproc 4 > ${f%.fasta.gz}_profile.txt
    done

    thanks
    John

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