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grepping using the "|" alternative operator

Tags:

regex

linux

grep

The following is a sample of a large file named AT5G60410.gff:

Chr5    TAIR10  gene    24294890    24301147    .   +   .   ID=AT5G60410;Note=protein_coding_gene;Name=AT5G60410 Chr5    TAIR10  mRNA    24294890    24301147    .   +   .   ID=AT5G60410.1;Parent=AT5G60410;Name=AT5G60410.1;Index=1 Chr5    TAIR10  protein 24295226    24300671    .   +   .   ID=AT5G60410.1-Protein;Name=AT5G60410.1;Derives_from=AT5G60410.1 Chr5    TAIR10  exon    24294890    24295035    .   +   .   Parent=AT5G60410.1 Chr5    TAIR10  five_prime_UTR  24294890    24295035    .   +   .   Parent=AT5G60410.1 Chr5    TAIR10  exon    24295134    24295249    .   +   .   Parent=AT5G60410.1 Chr5    TAIR10  five_prime_UTR  24295134    24295225    .   +   .   Parent=AT5G60410.1 Chr5    TAIR10  CDS 24295226    24295249    .   +   0   Parent=AT5G60410.1,AT5G60410.1-Protein; Chr5    TAIR10  exon    24295518    24295598    .   +   .   Parent=AT5G60410.1

I am having some trouble extracting specific lines from this using grep. I wanted to extract all lines that are of type "gene" or type "exon", specified in the third column. I was suprised when this did not work:

grep 'gene|exon' AT5G60410.gff

No results are returned. Where have I gone wrong?

like image 915
MattLBeck Avatar asked Jul 21 '11 12:07

MattLBeck

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1 Answers

You need to escape the |. The following should do the job.

grep "gene\|exon" AT5G60410.gff
like image 138
Jeff Foster Avatar answered Oct 11 '22 22:10

Jeff Foster
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