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janxkoci avatar janxkoci commented on July 17, 2024 1

What is your locale? I noticed awks other than gawk are failing in mysterious ways under some locales, see e.g. #34 (especially the last comment).

Try to run export LC_ALL=C and then rerun your bioawk command.

Edit: Btw I can get a match with this, but it's not perfect:

bioawk -c fastx 'match($seq, /[[:alpha:]]+GCCCAGGTGCAGCTGCAG/) {print "@"$name" "$comment"\n"$seq"\n+\n"$qual}' sampleR1.fq

Note the double square brackets in [[:alpha:]] - gawk tells you loud and clear if you use only single brackets.

from bioawk.

splaisan avatar splaisan commented on July 17, 2024 1

thanks @janxkoci, the issue is with {7} which is not interpreted as exactly 7 times, it works with + instead

from bioawk.

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