Does anyone know why 'grep' will not recognise a text file that I used this script to split into a series of truncated text file with just 1000 lines from a largerfile:
split -l 1000 -d file.txt file --additional-suffix=.txt, (#file00.txt, file01.txt, file02.txt...file26.txt)
However, when I use 'grep' on the same text file content of 1000 lines that I copy from a larger text file and save as another text file, then 'grep' recognises it and carries out the action that I want?
1 answer
I have the answer:
I opened in notepad and in the bottom right corner it told me the split text file created a windows cr/lf file, whereas the original was a unix lf file, both are UTF-8, so the below script fixed the file and now my grep command works:
awk '{ sub("\r$", ""); print }' windows.txt > unix.txt
Alternate methods to convert windows to unix and vice versa can be found here: https://www.maketecheasier.com/convert-files-from-linux-format-windows/
Log in to answer this question.
-
How to save the results of norm to txt
written by Serij´s •
-
Why is my code only printing the first position?
written by CourtneyGoRawr •
-
Linux bash: How to pipe several files?
written by Simon •
-
Snakemake/Google-Life-Sciences aggregate funtion issue
written by Stephan •
-
How do I count a number of ("-") in a reference string and remove it in a second string?
written by USER •
-
Awk, Sed, Grep to create a sequential numerical text replacement in my gtf file
written by sdbaney •
-
Split SAM file into smaller SAM files by line count
written by cacampbell •
-
Print all rows that are in specified value range based on specific column as pairs
written by 5heikki
-
Download UniProt page source using python
written by dovah •
-
Get Filenames Of All Files With 'Atg' In Fasta Files
written by Sam •
This is not reproducible. Please add data examples.
how is it related to bioinformatcs ?