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AWK for file .fastq

AWK for file .fastq

AWK for file .fastq

(OP)
Hi folks!
this is a .fastq file example:

@IRIS:7:1:17:800#0/1
GGAAACACTACTTAGGCTTATAAGATCNGGTTGCGG
+IRIS:7:1:17:800#0/1
ababbaaabaaaaa`]`ba`]`aaaaYD\\_a``XT
@IRIS:7:1:17:150#0/1
TGATGTACTATGCATATGAACTTGTATGCAAAGTGG
+IRIS:7:1:17:150#0/1
abaabaa`aaaaaaa^ba_]]aaa^aaaaa_^][aa
@IRIS:7:1:18:16#0/1
AGGTTCGTGTTGAGTGTTGCCTCTTTTTCTGTTAAT
+IRIS:7:1:18:16#0/1
abb`bbbabbbaWa`baba_Z``babaa[_aa`\X_
@IRIS:7:1:19:1343#0/1
GGCATCTCCAGAGGAGGCTGTACCTGTGGAATAGCA
+IRIS:7:1:19:1343#0/1
abbbbbbbbababaaba_a\FXQXNVKO^F[RWYSQ

and so on for thousand of record
Each record is made of four line i.e

@IRIS:7:1:17:800#0/1
GGAAACACTACTTAGGCTTATAAGATCNGGTTGCGG
+IRIS:7:1:17:800#0/1
ababbaaabaaaaa`]`ba`]`aaaaYD\\_a``XT

Now,
I was wondering if anyone knows how to get through AWK or SED, RANDOM records from a fastq file.
thanks!

RE: AWK for file .fastq

Hi

CODE --> command-line

gawk 'ENDFILE{srand();print r=int(NR/4*rand())*4}FNR!=NR&&FNR>r&&FNR<=r+4' .fastq .fastq 
( Note the input file name specified twice. )

Tested with GNU awk, requires version 4.0.0. ( If necessary, is possible to replace the ENDFILE pattern with a workaround. )

Feherke.
feherke.ga

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