Print lines in one file matching patterns in another file
awk, extract, grep, sed, unix
Solution
Try `grep -Fwf file2 file1 > out`
The `-F` option specifies plain string matching, so should be faster without having to engage the regex engine.
Problem
I have a file with more than 40.000 lines (file1) and I want to extract the lines matching patterns in file2 (about 6000 lines). I use grep like this, but it is very slow: ``` grep -f file2 file1 > out ``` Is there a faster way to do this using `awk` or `sed`? Here's some extracts from my files: `File1`: ``` scitn003869.2| scign003869 CGCATGTGTGCATGTATTATCGTATCCCTTG scitn007747.1| scign007747 CACGCAGACGCAGTGGAGCATTCCAGGTCACAA scitn003155.1| scign003155 TAAAAATCGTTAGCACTCGCTTGGTACACTAAC scitn018252.1| scign018252 CGTGTGTGTGCATATGTGTGCATGCGTG scitn004671.2| scign004671 TCCTCAGGTTTTGAAAGGCAGGGTAAGTGCT ``` `File2`: ``` scign000003 scign000004 scign000005 scign004671 scign000013 ```