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nightknight87 — Mon, 30 Nov 2015 10:46:08 +0800

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regex noob question

nightknight87 — Sat, 01 Oct 2011 14:12:26 +0800

Dear sifus,
i am pretty new to regex, now starting to learn..

i have a situation where i want to find anypattern1|anypattern2|anypattern3 which must have the 2 vertical tab in between for example:

JAT|JJAT|JcCB0060211.10
CUSA|Cucsa.032480JAT|JcCA0008551.10

i tried \w+\|*\w+\|*\w+

but it didnt work...hope you guys can shed me some light....... thanks!

updates1:
further explaination on situation:

i have a ~80gb file which should have look like this for further processing :

PATENS|Pp1s223_20V6.1 PATENS|Pp1s210_96V6.1 54.51 754 270 8 48 754 201 928 0.0 813
PATENS|Pp1s223_20V6.1 PATENS|Pp1s122_9V6.1 52.62 781 272 10 48 754 178 934 0.0 785
PATENS|Pp1s223_20V6.1 SEMO|SMO78743 52.88 730 261 9 60 753 1 683 0.0 719
PATENS|Pp1s223_20V6.1 ZMA|zmaGRMZM2G071518_T01 43.84 730 338 8 63 754 5 700 6e-170 599

but there are some irregularites lines that combine these separates ids causing them to look like:
CUSA|Cucsa.032480JAT|JcCA0008551.10 52.62 781 272 10 48 754 178 934 0.0 785 (where you can see the 2 columns which are
CUSA|Cucsa.032480 and JAT|JcCA0008551.10 are joined becoming CUSA|Cucsa.032480JAT|JcCA0008551.10

several others of the same example where the two columns are joined :

JAT|JJAT|JcCB0060211.10 43.84 730 338 8 63 754 5 700 6e-170 599

hntu|bada33|das 43.84 730 338 8 63 754 5 700 6e-170 599

so i want to remove these line such mentioned above containing combined pattern and have only the normal separated columns such as:

PATENS|Pp1s223_20V6.1 SEMO|SMO78743 52.88 730 261 9 60 753 1 683 0.0 719
PATENS|Pp1s223_20V6.1 ZMA|zmaGRMZM2G071518_T01 43.84 730 338 8 63 754 5 700 6e-170 599

tq

update 2:

thanks to everbody, i have come out with this regex

CODE

.*\|[^\s]*\|\w+

CODE

cat testfile |sed -r '/.*\|[^\s]*\|\w+/d' >outfile

and it has remove these kind of pattern such as:
JAT|JJAT|JcCB0060211.10 43.84 730 338 8 63 754 5 700 6e-170 599

hntu|bada33|das 43.84 730 338 8 63 754 5 700 6e-170 599

but there is another one that suppose to be remove but wasnt remove which is:

CUSA|Cucsa.032480JAT|JcCA0008551.10 54.51 754 270 8 48 754 201 928 0.0 813

your ideas will be much appreciated tq

update3-SOLVED by isolatedSH33P thanks man!

CODE

cat testfile | sed -r '/[a-zA-Z0-9.]*\|[a-zA-Z0-9.]*\|[^\s]+/d' > outfile

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(WTS)Bioinformatics Consultation/Analysis/Services

regex noob question