AWK for file .fastq

[WayneSzalinsky]

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!

 

[feherke]

Hi

gawk '[b]ENDFILE[/b][teal]{[/teal][COLOR=FF6600]srand()[/color][teal];[/teal][b]print[/b] [navy]r[/navy][teal]=[/teal][COLOR=FF6600]int[/color][teal]([/teal]NR[teal]/[/teal][purple]4[/purple][teal]*[/teal][COLOR=FF6600]rand()[/color][teal])*[/teal][purple]4[/purple][teal]}[/teal]FNR[teal]!=[/teal]NR[teal]&&[/teal]FNR[teal]>[/teal]r[teal]&&[/teal]FNR[teal]<=[/teal]r[teal]+[/teal][purple]4[/purple]' .fastq .fastq

( Note the input file name specified twice. )

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


Feherke.
feherke.ga