而循环错误:接近意外令牌的语法错误“已完成”

Question

我刚开始使用bash脚本。我想逐行读取包含表格的文件。在每一行中，我希望将值赋值给变量。这基本上是我的代码的格式：

#!/bin/bash

while IFS= read -r line; do
    echo $a $b $c $d
    #if statements…
done < test.txt

我得到了这个错误：“而循环错误:接近意外标记‘完成’的语法错误”

知道我的代码有什么问题吗？我尝试过查看与同一错误相关的其他几个问题，但我无法修复我的代码。谢谢你的帮助!

编辑:这是整个代码。它可能有其他错误(我真的是一个初学者)，但我希望它有帮助。

#!/bin/bash

experiment_database="/home/gperron/datasets/ENCODE_tables/final_tables/test_experiment_database.txt"
file_database="/home/gperron/datasets/ENCODE_tables/final_tables/test_file_database.txt"

EXPERIMENT=`cat $experiment_database | head -n $PBS_ARRAYID | tail -n 1 | cut -f1`
echo "EXPERIMENT #$PBS_ARRAYID: $EXPERIMENT"

while IFS= read -r line; do
        echo $file_ID $experiment $target $biological_replicate $technical_replicate $read_number $url $fastq_file $genome
        if [ "$experiment" == "$EXPERIMENT" ]; then
                if [ $biological_replicate == 1 ]; then
                        if [ $technical_replicate == 1 ]; then
                                if [ $read_number == 1 ]; then
                                        ID_111= $file_ID
                                        fastq_111= $fastq_file
                                        url_111= $url
                                        echo "FASTQ file 111 ID: $ID_111"
                                        echo "FASTQ file 111: $fastq_111"
                                        echo "FASTQ file 111 url: $url_111"
                                elif [ $read_number == 2 ]; then
                                        ID_112= $file_ID
                                        fastq_112= $fastq_file
                                        url_112= $url
                                        echo "FASTQ file 112 ID: $ID_112"
                                        echo "FASTQ file 112: $fastq_112"
                                        echo "FASTQ file 112 url: $url_112"
                                fi
                        elif [ $technical_replicate == 2 ]; then
                                if [ $read_number == 1 ]; then
                                        ID_121= $file_ID
                                        fastq_121= $fastq_file
                                        url_121= $url
                                        echo "FASTQ file 121 ID: $ID_121"
                                        echo "FASTQ file 121: $fastq_121"
                                        echo "FASTQ file 121 url: $url_121"
                                elif [ $read_number == 2 ]; then
                                        ID_122= $file_ID
                                        fastq_122= $fastq_file
                                        url_122= $url
                                        echo "FASTQ file 122 ID: $ID_122"
                                        echo "FASTQ file 122: $fastq_122"
                                        echo "FASTQ file 122 url: $url_122"
                                fi
                elif [ $biological_replicate == 2 ]; then
                        if [ $technical_replicate == 1 ]; then
                                if [ $read_number == 1 ]; then
                                        ID_211= $file_ID
                                        fastq_211= $fastq_file
                                        url_211= $url
                                        echo "FASTQ file 211 ID: $ID_211"
                                        echo "FASTQ file 211: $fastq_211"
                                        echo "FASTQ file 211 url: $url_211"
                                elif [ $read_number == 2 ]; then
                                        ID_212= $file_ID
                                        fastq_212= $fastq_file
                                        url_212= $url
                                        echo "FASTQ file 212 ID: $ID_212"
                                        echo "FASTQ file 212: $fastq_212"
                                        echo "FASTQ file 212 url: $url_212"
                                fi
                        elif [ $technical_replicate == 2 ]; then
                                if [ $read_number == 1 ]; then
                                        ID_221= $file_ID
                                        fastq_221= $fastq_file
                                        url_221= $url
                                        echo "FASTQ file 221 ID: $ID_221"
                                        echo "FASTQ file 221: $fastq_221"
                                        echo "FASTQ file 221 url: $url_221"

                                elif [ $read_number == 2 ]; then
                                        ID_222= $file_ID
                                        fastq_222= $fastq_file
                                        url_222= $url
                                        echo "FASTQ file 222 ID: $ID_222"
                                        echo "FASTQ file 222: $fastq_222"
                                        echo "FASTQ file 222 url: $url_222"

                                fi
                        fi
                fi
        fi
done < test_file_database.txt

如果我搞清楚了，请告诉我。

Answer 1

在$biological_replicate == 1接近顶部后，if [ $technical_replicate == 1 ]; then在elif之后没有fi。见下文。

我认为您可能对indirect expansion感兴趣，如下所示。(可能有点笨拙；我最近才发现间接扩张。)

this_id="${biological_replicate}${technical_replicate}${read_number}"   # e.g., 111, 112, ...
declare "ID_${this_id}"=$file_id   # evaluates the left side into, e.g., ID_111, and sets $ID_111=$file_id

我认为这可以大大减少您的if链。

以上编辑的代码：

while IFS= read -r line; do
    echo $file_ID $experiment $target $biological_replicate $technical_replicate $read_number $url $fastq_file $genome
    if [ "$experiment" == "$EXPERIMENT" ]; then
            if [ $biological_replicate == 1 ]; then
                    if [ $technical_replicate == 1 ]; then
                            if [ $read_number == 1 ]; then
                                    ID_111= $file_ID
                                    fastq_111= $fastq_file
                                    url_111= $url
                                    echo "FASTQ file 111 ID: $ID_111"
                                    echo "FASTQ file 111: $fastq_111"
                                    echo "FASTQ file 111 url: $url_111"
                            elif [ $read_number == 2 ]; then
                                    ID_112= $file_ID
                                    fastq_112= $fastq_file
                                    url_112= $url
                                    echo "FASTQ file 112 ID: $ID_112"
                                    echo "FASTQ file 112: $fastq_112"
                                    echo "FASTQ file 112 url: $url_112"
                            fi
                    elif [ $technical_replicate == 2 ]; then
                            if [ $read_number == 1 ]; then
                                    ID_121= $file_ID
                                    fastq_121= $fastq_file
                                    url_121= $url
                                    echo "FASTQ file 121 ID: $ID_121"
                                    echo "FASTQ file 121: $fastq_121"
                                    echo "FASTQ file 121 url: $url_121"
                            elif [ $read_number == 2 ]; then
                                    ID_122= $file_ID
                                    fastq_122= $fastq_file
                                    url_122= $url
                                    echo "FASTQ file 122 ID: $ID_122"
                                    echo "FASTQ file 122: $fastq_122"
                                    echo "FASTQ file 122 url: $url_122"
                            fi
                    fi   # <----- this one was missing
            elif [ $biological_replicate == 2 ]; then
            ...