intersect two file
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11 months ago
harry ▴ 30

I have 2 transcript file - one contain only transcript id and other file contain transcript id, gene name and gene description.

1st file looks like----

ENST00000009589.8
ENST00000084795.9
ENST00000196551.8
ENST00000202773.13
ENST00000211372.9
ENST00000216146.9
ENST00000222247.10
ENST00000225430.9
ENST00000225655.6

2nd file looks like ----

ENST00000387314.1   MT-TF   mitochondrially encoded tRNA-Phe (UUU/C) [Source:HGNC Symbol;Acc:HGNC:7481]
ENST00000389680.2   MT-RNR1 mitochondrially encoded 12S rRNA [Source:HGNC Symbol;Acc:HGNC:7470]
ENST00000387342.1   MT-TV   mitochondrially encoded tRNA-Val (GUN) [Source:HGNC Symbol;Acc:HGNC:7500]
ENST00000387347.2   MT-RNR2 mitochondrially encoded 16S rRNA [Source:HGNC Symbol;Acc:HGNC:7471]
ENST00000386347.1   MT-TL1  mitochondrially encoded tRNA-Leu (UUA/G) 1 [Source:HGNC Symbol;Acc:HGNC:7490]
ENST00000361390.2   MT-ND1  mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 1 [Source:HGNC Symbol;Acc:HGNC:7455]
ENST00000387365.1   MT-TI   mitochondrially encoded tRNA-Ile (AUU/C) [Source:HGNC Symbol;Acc:HGNC:7488]
ENST00000387372.1   MT-TQ   mitochondrially encoded tRNA-Gln (CAA/G) [Source:HGNC Symbol;Acc:HGNC:7495]
ENST00000387377.1   MT-TM   mitochondrially encoded tRNA-Met (AUA/G) [Source:HGNC Symbol;Acc:HGNC:7492]

the 2nd file is download from biomart(ensembl) and i just want to know that my 1st file where intersect to 2nd file then i can know the gene name of my 1st transcript file.

thanks in advance

intersect transcript_id • 478 views
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thanks for you valuable suggestion.

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11 months ago

quick n' dirty: use grep -f file1 file2

right way: use sort to sort both files on the ensembl ID and the join to get the instersection.

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A simple modification of Pierre's suggestion, building the proper pattern before the query, would be more than enough:

perl -lne 'print "^$_\\s"' file1.txt | grep -f - file2.txt
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11 months ago
abedkurdi10 ▴ 30

Or You can use dplyr R package to do the intersection.

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11 months ago

Base R works as well:

joint = df2[df2$ens_id %in% df1$ens_id,]
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