Hello there!
Your suggestions returns ERZ914
Thank you
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blackadder •
Get middle part of a url
Hello there,
I have a file with ftp links that look like this:
> ftp.sra.ebi.ac.uk/vol1/sequence/ERZ914/ERZ914930/contig.fa.gz
> ftp.sra.ebi.ac.uk/vol1/sequence/ERZ928/ERZ928990/contig.fa.gz
> ....
I am reading them one by one with a while loop in bash and what I'm trying to do is to drop everything before and after ERZ914930. So, I only want to keep ERZ914930
I have tried the following:
basename=${line##*/} - This returns contig.fa.gz
base=${line%%/ERZ*} - This returns ftp.sra.ebi.ac.uk/vol1/sequence
with line being the iteration variable
Thanks!
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Joe
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blackadder •
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blackadder •
2 answers
base=`echo "${line}" | cut -d '/' -f 5`
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Pierre Lindenbaum
yeah --f5...
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Pierre Lindenbaum
Op yeah it works now!
Thank you!
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blackadder •
Another solution using regex:
$ [[ "ftp.sra.ebi.ac.uk/vol1/sequence/ERZ928/ERZ928990/contig.fa.gz" =~ ([[:alpha:]]{3}[[:digit:]]{6}) ]] && echo ${BASH_REMATCH[1]}
ERZ928990
You can use this approach to extract any pattern you wish should you want to capture more information or do more complex filtering.
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