CODEWITHSUNDEEP
shell
Papy
Papy

Reputation: 41

"\" not considered as char in string char

I am still having issue with my fastq script. This time I have an issue with how the script handle input.

this is part of my script

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

the issue is that the ouput does not look like the input. such as

this is what is in the input file :

@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

but this is what the output gave me

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

You may have noticed that the script remove all \ from the input except \\ that it is considered as one \. So inducing a shift in the lenght of the quality_sequence.

thanks for your help again

Upvotes: 1

Views: 40

Answers (1)

Etan Reisner
Etan Reisner

Reputation: 80931

You are missing the -r argument to read. You basically always want it. It prevents read from "interpreting" backslash escape sequences.

See http://mywiki.wooledge.org/BashFAQ/001 for discussion about how to properly read files by line/field correctly (which discusses -r).

Upvotes: 1

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