Question

我的fastq脚本仍然存在问题。这次我遇到了脚本如何处理输入的问题。

这是我脚本的一部分

while read Sequence_Name && read Sequence && read Quality_name && read Quality_sequence
n=1
do

            if [[ ${#Sequence} != ${#Quality_sequence} ]] ; then
                echo "Length of Sequence $n different from Length of Quality Sequence"
                echo ${#Sequence} #line added to see the ouput
                echo $Sequence #line added to see the ouput 
                echo ${#Quality_sequence} #line added to see the ouput
                echo $Quality_sequence #line added to see the ouput
             fi
n=$((n+1))
done <$1

问题是输出看起来不像输入。比如

这是输入文件中的内容：

@SRR1350630.196.1 HWUSI-EAS753_0012:8:1:7018:1029 length=24
TGTAAACATCCTACACTCTCAGCT
+SRR1350630.196.1 HWUSI-EAS753_0012:8:1:7018:1029 length=24
`__^\\aa_Z_ccccacc[a\cYc
@SRR1350630.197.1 HWUSI-EAS753_0012:8:1:8338:1032 length=24
TTTGGCAATGGTAGAACTCACACC
+SRR1350630.197.1 HWUSI-EAS753_0012:8:1:8338:1032 length=24
acaa^acc^ac[aacY^\`_cccc

但这就是输出给我的东西

Length of Sequence 196 different from Length of Quality Sequence

24 # this is the echo ${#sequence}
TGTAAACATCCTACACTCTCAGCT # this is the echo $Sequence
22 # this is the echo ${#Quality_sequence}
`__^\aa_Z_ccccacc[acYc #this is the echo $Quality_sequence

Length of Sequence 197 different from Length of Quality Sequence
24
TTTGGCAATGGTAGAACTCACACC
23
acaa^acc^ac[aacY^`_cccc

您可能已经注意到脚本会从输入中删除所有\，除了\\它被视为一个\。因此导致quality_sequence的长度发生变化。

再次感谢您的帮助

Answer 1

您错过了-r的{{1}}参数。你基本上总是想要它。它会阻止read解释＆＃34;反斜杠转义序列。

有关如何正确按行/字段正确读取文件的讨论，请参阅http://mywiki.wooledge.org/BashFAQ/001（讨论read）。

＆＃34; \＆＃34;在字符串char中不被视为char

1 个答案: