Don't 100% understand what you're doing, but fixed a few things. Try below
#!/bin/bash
for sample in *.fastq; do
name="${sample/.fastq/}"
while read -r line; do
if [[ $line == '@'* ]]; then
head="$line" && echo "$head" >> "${name}_new.fq"
elif [[ -n $head && ${#line} == 51 && $line =~ (CTG|TTG)$ ]]; then
sequence="${line:0:49}" && echo "$sequence" >> "${name}_new.fq"
elif [[ $line == '+'* ]]; then
plus="$line" && echo "$line" >> "${name}_new.fq"
else
quality="$line" && echo "$quality" >> "${name}_new.fq"
fi
done < "$sample"
done
Example output
> cat sample_new.fq
> cat sample.fastq
@HWI-ST1072:187:C35YUACXX:7:1101:1609:1983 1:N:0:ACAGTG
NGGAGAAAGAGAGTGTGTTTTTAGGGGGAGATTTTTAAAATGGTTGTTTTG
+
#0<BFFFFFFFFF<BFFFIIFFFFFIIIBFFFFFIIFIIIIIFFBFFFFFF
@HWI-ST1072:187:C35YUACXX:7:1101:1747:1995 1:N:0:ACAGTG
NGGTTGTGGTGGTGGGTATTTGTAGTTTTATTTATTCGGGAGGTTGAGCTG
+
#0<BFFFFFFFFFFIIBFFIIIIIIFIIIFFIIFIIIFIIFIIFFFFIIFF
@HWI-ST1072:187:C35YUACXX:7:1101:9351:2210 1:N:0:ACAGTG
CGGTTTTGTTTTATTTTGTATGATTAGGAGGGTTTTGGAGGTTTAGTTACC
+
BBBFFFFFFFFFFIIIIIFFIIFIIIIIIIIIFFIIFIFIIFFIIIFIIII
@HWI-ST1072:187:C35YUACXX:7:1101:1747:1995 1:N:0:ACAGTG
NGGTTGTGGTGGTGGGTATTTGTAGTTTTATTTAT
+
#0<BFFFFFFFFFFIIBFFIIIIIIFIIIFFIIFI
> ./abovescript
> cat sample_new.fq
@HWI-ST1072:187:C35YUACXX:7:1101:1609:1983 1:N:0:ACAGTG
NGGAGAAAGAGAGTGTGTTTTTAGGGGGAGATTTTTAAAATGGTTGTTT
+
@HWI-ST1072:187:C35YUACXX:7:1101:1747:1995 1:N:0:ACAGTG
NGGTTGTGGTGGTGGGTATTTGTAGTTTTATTTATTCGGGAGGTTGAGC
+
@HWI-ST1072:187:C35YUACXX:7:1101:9351:2210 1:N:0:ACAGTG
CGGTTTTGTTTTATTTTGTATGATTAGGAGGGTTTTGGAGGTTTAGTTACC
+
BBBFFFFFFFFFFIIIIIFFIIFIIIIIIIIIFFIIFIFIIFFIIIFIIII
@HWI-ST1072:187:C35YUACXX:7:1101:1747:1995 1:N:0:ACAGTG
NGGTTGTGGTGGTGGGTATTTGTAGTTTTATTTAT
+