Fastq to fasta format with sed/awk command [duplicate]

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Converting FASTQ to FASTA with SED/AWK (13 answers)

Closed 8 years ago.

I have a data with fastq format:

@HISEQ:157:C11RCACXX:6:1101:1522:2491 2:N:0:CGTACG
GTGCCNNNNNNNNNNNNNNNNNNNNNNNTGCGNNNNNNNNNNNNNNCNNGCAGATACTCGTANNNNNNNNNGNNNNNNNN
NNNNNNNNNNNNNNNNNNNNN
+
@BCFF###########################################################################
#####################
@HISEQ:157:C11RCACXX:6:1101:1668:2494 2:N:0:CGTACG
TCTTTNNNNNNNNNNNNNNNNNNNNNNNATTGNNNNNNNNNNNNNNTTNTGTTTTACGGTTTNNNNNNNNGCNNNNNNNN
NNNNNNNNNNNNNNNNNNNNN
+
C@CFF###########################################################################
#####################
@HISEQ:157:C11RCACXX:6:1101:2557:2492 2:N:0:CGTACG
CCTCTNNNNNNNNNNNNNNNNNNNNNNNGTTGNNNNNNNNNNNNNNCNNCAACACACTCCTCNNNNNNNNGCNNNNNNNN
NNNNNNNNNNNNNNNNNNNNN
+
CCCFF###########################################################################
#####################

and I want to split each read with "+" used awk command, but it didnt't work, Is there simple command with see/awk can convert it into fasta format?

The expect output should be

>HISEQ:157:C11RCACXX:6:1101:1522:2491 2:N:0:
CGTACGGTGCCNNNNNNNNNNNNNNNNNNNNNNNTGCGNNNNNNNNNNNNNNCNNGCAGATACTCGTANNNNNNNNNGNNNNNNNN
NNNNNNNNNNNNNNNNNNNNN
>HISEQ:157:C11RCACXX:6:1101:1668:2494 2:N:0:
CGTACGTCTTTNNNNNNNNNNNNNNNNNNNNNNNATTGNNNNNNNNNNNNNNTTNTGTTTTACGGTTTNNNNNNNNGCNNNNNNNN
NNNNNNNNNNNNNNNNNNNNN
>HISEQ:157:C11RCACXX:6:1101:2557:2492 2:N:0:
CGTACGCCTCTNNNNNNNNNNNNNNNNNNNNNNNGTTGNNNNNNNNNNNNNNCNNCAACACACTCCTCNNNNNNNNGCNNNNNNNN
NNNNNNNNNNNNNNNNNNNNN

Thanks a lot!

Answer 1

You may try the following

awk -f conv.awk input.txt

where input.txt is your input data file, and conv.awk is

/@HISEQ/ { p=1; sub(/^@/,">"); sub(/:[^:]*$/,":"); print; next }
/^\+/ {p=0}
p==1 { print }

Answer 2

awk '((/@/&&$0!~/#/)||$0!~/#/)&&$0!~/\+/' your_file

Tested Below:

> cat temp2
@HISEQ:157:C11RCACXX:6:1101:1522:2491 2:N:0:CGTACG
GTGCCNNNNNNNNNNNNNNNNNNNNNNNTGCGNNNNNNNNNNNNNNCNNGCAGATACTCGTANNNNNNNNNGNNNNNNNN
NNNNNNNNNNNNNNNNNNNNN
+
@BCFF###########################################################################
#####################
@HISEQ:157:C11RCACXX:6:1101:1668:2494 2:N:0:CGTACG
TCTTTNNNNNNNNNNNNNNNNNNNNNNNATTGNNNNNNNNNNNNNNTTNTGTTTTACGGTTTNNNNNNNNGCNNNNNNNN
NNNNNNNNNNNNNNNNNNNNN
+
C@CFF###########################################################################
#####################
@HISEQ:157:C11RCACXX:6:1101:2557:2492 2:N:0:CGTACG
CCTCTNNNNNNNNNNNNNNNNNNNNNNNGTTGNNNNNNNNNNNNNNCNNCAACACACTCCTCNNNNNNNNGCNNNNNNNN
NNNNNNNNNNNNNNNNNNNNN
+
CCCFF###########################################################################
#####################
>
> nawk '((/@/&&$0!~/#/)||$0!~/#/)&&$0!~/\+/' temp2
@HISEQ:157:C11RCACXX:6:1101:1522:2491 2:N:0:CGTACG
GTGCCNNNNNNNNNNNNNNNNNNNNNNNTGCGNNNNNNNNNNNNNNCNNGCAGATACTCGTANNNNNNNNNGNNNNNNNN
NNNNNNNNNNNNNNNNNNNNN
@HISEQ:157:C11RCACXX:6:1101:1668:2494 2:N:0:CGTACG
TCTTTNNNNNNNNNNNNNNNNNNNNNNNATTGNNNNNNNNNNNNNNTTNTGTTTTACGGTTTNNNNNNNNGCNNNNNNNN
NNNNNNNNNNNNNNNNNNNNN
@HISEQ:157:C11RCACXX:6:1101:2557:2492 2:N:0:CGTACG
CCTCTNNNNNNNNNNNNNNNNNNNNNNNGTTGNNNNNNNNNNNNNNCNNCAACACACTCCTCNNNNNNNNGCNNNNNNNN
NNNNNNNNNNNNNNNNNNNNN
>