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
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.
A simple modification of Pierre's suggestion, building the proper pattern before the query, would be more than enough:
perl -lne 'print "^$_\\s"' file1.txt | grep -f - file2.txt
Or You can use dplyr R package to do the intersection.
Base R works as well:
joint = df2[df2$ens_id %in% df1$ens_id,]
Since the transcript ids do not overlap, you can use:
cat file1 | while read line ; do grep "${line}" file2 >> file3; done
If you're interested in a few columns of the output, say col1 and col2:
cat file1 | while read line ; do grep "${line}" file2 | awk '{print $1,$2}' >> file3; done
That's a very slow solution compared to grep -f . Furthermore I said above that it was a quick 'n dirty general solution for example if you're searching for ENST00005678 in lines like:
ENST00001234 MT-RNR2 mitochondrially encoded 16S rRNA similar to ENST00005678
No he didn't. Pierre's suggestion is to include all possible patterns into a single grep query, which is much faster than to perform one grep per pattern, which implies reading the second file entirely on each query.
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thanks for you valuable suggestion.