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  • 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

  • #2
    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

    Comment


    • #3
      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

      Comment

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