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Hannah9777
Asked: 2020-03-05 04:16:16 +0800 CST

Filtering for a set of files that start and end with certain characters

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Hi I am new to all of this so any help is appreciated!! I have a list of files that I want my bash script to work on such as

BG2_45TS02.assembled.fast

BG2_45TS02.riboassembled.fastq

BG3_45TS02.assembled.fastq

BG3_45TS02.riboassembled.fastq

BG4_45TS02.assembled.fastq

BG4_45TS02.riboassembled.fastq

If I only want to pick out those starting with BG2 and those ending with .riboassembled.fastq

does this work BG2*.riboassembledfastq so for example my script would be 

for file in $STEP_2/BG2*.riboassembled.fastq
bash find wildcards

2 Answers

  1. Yes, that will work.

    You can simply try with using echo or printf in your loop:

    $ for file in "$STEP_2"/BG2*.riboassembled.fastq; do printf '%s\n' "$file"; done
/BG2*.riboassembled.fastq

    Search for globbing to get more information and tutorials on how it works, e.g. https://www.tldp.org/LDP/abs/html/globbingref.html

    Note, variables containing file names (here $STEP_2) should be put in double quotes, otherwise it will cause problems if the variable contains spaces.

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  2. As pLumo suggested, you could use $file variable to point at your current file

    Run:

    $ for file in ./BG2*; do cat $file; done

    Result:

    ./BG2_45TS02.assembled.fast
date
Wed 04 Mar 2020 02:39:39 PM EET
./BG2_45TS02.riboassembled.fastq
date
Wed 04 Mar 2020 02:39:39 PM EET

    Run:

    $ for file in ./BG2*ribo*q; do cat $file; done

    Result:

    ./BG2_45TS02.riboassembled.fastq
date
Wed 04 Mar 2020 02:39:39 PM EET

    Instead of do cat $file you could use something else. cat $file is only for demonstration.

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