使用if和else检查目录名并在linux bash脚本中分配变量

Question

I am creating (what I thought was) a simple script to check through my current directory which contains more directories with the names;

SAMPLE_ANN-A10, SAMPLE_ANN-B4 etc.
SAMPLE_NEM-E7, SAMPLE_NEM-H2, etc.
SAMPLE_TODE-H02 etc. etc.

I would like to assign a QUERY variable for each SAMPLE and run a command. All TODEs will use the same variable, all NEMs will use the same and all ANNs the same.

Here is my current script with the error message. Thanks for looking.

---

#!/bin/bash

for dir in $@
do
QUERY=''
    if $dir == SAMPLE_ANN*/
        then
            $QUERY=annelids.fasta
    elif $dir == SAMPLE_NEM*/
        then
            $QUERY=nemertea.fasta
    else
        $QUERY=nematode.fasta
    fi

    echo $QUERY #used to check if the variable was set correctly

nohup blastn -query $QUERY -subject $dir/spades_output/contigs.fasta -out $dir/spades_output/mito_blast

done

---

#command from linux --> ./auto_mito_blast.sh SAMPLE_ANN-B4

---

#error message : 

#./auto_mito_blast.sh: line 7: Sample_ANN-B4/: Is a directory
#./auto_mito_blast.sh: line 10: Sample_ANN-B4/: Is a directory
#./auto_mito_blast.sh: line 14: =nematode.fasta: command not found

Thanks, Joe

Answer 1

Double brackets [[ should do the work. =>

for dir in $@
do
    QUERY=''
    if [[ $dir == SAMPLE_ANN* ]]
        then
            QUERY=annelids.fasta
    elif [[ $dir == SAMPLE_NEM* ]]
        then
            QUERY=nemertea.fasta
    else
        QUERY=nematode.fasta
    fi
    echo $QUERY #used to check if the variable was set correctly
done

ATM: you are just iterating over all given parameter, but as far as i understand you want to iterate over all directories in the current directory, which would be something like:

for dir in ./*

Still need some is dir check. Another way would be using find like

find . -type d -depth 1 --execute yourscript {} \;