gene's ID extraction
Dear people, I have 2 txt files, file1.txt with long ID's names (e.g TRINITY_DN14306_c0_g3_i4) and file2.txt with the ID's of my interest, however the isoform information is missing (e.g. TRINITY_DN14306_c0_g3). File1 has 40000 records while file2 has 5000. I would like to extract these 5000 from file1 along with the isoform information. I used the following command but the output I get is empty.
while read line; do grep -e "${line}_" file1.txt; done < file2.txt > out.txt
Any suggestions will be helpful. Thanks a lot in advance! Sofia
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paraskevopou •
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please, provide a sample of each files.
Thanks a lot for the comments. Here are mi files. I want to extract only the names that are present on file2.txt from file1.txt. But in file1.txt there is the isoform information (_i*) which I also need in my output file.
file1.txt
file2.txt
-eis for multiple pattern matching, while you have one per iteration. But I am not sure if this could matter.It is helpful if you have extended regular expressions, such as capture groups or even character classes in certain instances. I've rarely ever gone wrong with using an
-ewhen it's not really needed. I've found that more often than not, expected behavior is seen with-e(or-P) than without. Plus, it's easier to build on.