I have a file like entries like this:
@HWI-ST750:151:C1C6AACXX:8:1101:10000:14114/1
AAACATACCATTGCATATTTCGTATAATTCGAATTTAAGCAAGTTGTATTGCCAACAGCTCAGATCAATTAAGAATCTTTTCAAATTTATCAATTTA
+/1
DDHBFHHIAHHJEGJFGICHG;CGHGIJIIAIHHIJIGAGIE9FDFHGHG:4???BBC@8=;@FHI:DACHE>>AEAA@;B@;)6(>AC@>35@DDC
@HWI-ST750:151:C1C6AACXX:8:1101:10000:37802/1
GTTCCTTTACTTGCTCCCATGTCCCAATCTAACACACATGAGTCGTCGCACGCCAGTAAATCTAAAGATTTCAGACACTCAGACTCGTACAGTGAAA
+/1
FHHHHHJJIJJJJJJJJJJJJIJJJIJJJJJJJJJJJIHJIJ@GIHIIJJJIJHGHFFFFFFEEDEEEEDDDDDDDDDCDDCCCDDDABBDD>CC>A
I want to cut every 2nd line, from 1st to 45th word. So I used the following command:
sed "0~2p" BT8_A.fastq | cut -c1-45 | head -n 12
It worked properly but after cutting 1st 45 words th same line is getting appended to next line.Like this -
@HWI-ST750:151:C1C6AACXX:8:1101:10000:14114/1
AAACATACCATTGCATATTTCGTATAATTCGAATTTAAGCAAGTT
AAACATACCATTGCATATTTCGTATAATTCGAATTTAAGCAAGTT
+/1
DDHBFHHIAHHJEGJFGICHG;CGHGIJIIAIHHIJIGAGIE9FD
DDHBFHHIAHHJEGJFGICHG;CGHGIJIIAIHHIJIGAGIE9FD
@HWI-ST750:151:C1C6AACXX:8:1101:10000:37802/1
GTTCCTTTACTTGCTCCCATGTCCCAATCTAACACACATGAGTCG
GTTCCTTTACTTGCTCCCATGTCCCAATCTAACACACATGAGTCG
+/1
FHHHHHJJIJJJJJJJJJJJJIJJJIJJJJJJJJJJJIHJIJ@GI
FHHHHHJJIJJJJJJJJJJJJIJJJIJJJJJJJJJJJIHJIJ@GI
I am not able to solve this. Where I am going wrong here. Help me.
Thank you.
My desired output is:
@HWI-ST750:151:C1C6AACXX:8:1101:10000:14114/1
AAACATACCATTGCATATTTCGTATAATTCGAATTTAAGCAAGTT
+/1
DDHBFHHIAHHJEGJFGICHG;CGHGIJIIAIHHIJIGAGIE9FD
@HWI-ST750:151:C1C6AACXX:8:1101:10000:37802/1
GTTCCTTTACTTGCTCCCATGTCCCAATCTAACACACATGAGTCG
+/1
FHHHHHJJIJJJJJJJJJJJJIJJJIJJJJJJJJJJJIHJIJ@GI
如果只想每隔第二行剪切一次,而其余各行保持不变,则使用awk
可能会更容易:
awk 'NR % 2 == 0 { print substr($0, 0, 45) } NR % 2 == 1 { print }' BT8_A.fastq
单程:
$ sed 'n;s/\(.\{45\}\).*/\1/' file
here is a sed one-liner:
sed -r '2~2s/^(.{45}).*/\1/' file
output:
kent$ sed -r '2~2s/^(.{45}).*/\1/' file │drwxr-xr-x 4 kent kent 160 Feb 15 16:48 pkg/
@HWI-ST750:151:C1C6AACXX:8:1101:10000:14114/1 │-rw-r--r-- 1 kent kent 19 Feb 15 14:06 status.xml
AAACATACCATTGCATATTTCGTATAATTCGAATTTAAGCAAGTT │-rw-r--r-- 1 kent kent 18K Feb 15 16:44 tinyswitch.tgz
+/1 │-rw-r--r-- 1 kent kent 73 Feb 15 14:06 t.sh
DDHBFHHIAHHJEGJFGICHG;CGHGIJIIAIHHIJIGAGIE9FD │-rw-r--r-- 1 kent kent 18K Feb 15 16:24 tsw.tgz
@HWI-ST750:151:C1C6AACXX:8:1101:10000:37802/1 │-rw-r--r-- 1 kent kent 7.5K Feb 19 18:44 vimod.zsh
GTTCCTTTACTTGCTCCCATGTCCCAATCTAACACACATGAGTCG │-rw-r--r-- 1 kent kent 23K Feb 19 22:09 vimrd
+/1 │-rw-r--r-- 1 kent kent 42 Feb 17 16:00 x.txt
FHHHHHJJIJJJJJJJJJJJJIJJJIJJJJJJJJJJJIHJIJ@GI
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