In bash, I have created a function. In this function, I am constructing an URL that will be used to download a selected chromosome, unzip it and save it as a fasta file using curl. The following is my code.
#!/bin/bash
function getSequence {
#echo $1
URL="http://hgdownload.cse.ucsc.edu/goldenPath/hg38/chromosomes/chr"
UNZIP=".fa.gz | gunzip -c > chr"
FE=".fa"
SPACE=" "
FINAL="$SPACE$URL$1$UNZIP$1$FE"
curl "$FINAL"
}
echo "Enter a number between 1-22 or the letters X or Y"
read chromosome
regex='^[0-9]+$'
if [[ $chromosome =~ $regex ]]
then
if [ $chromosome -gt 0 -a $chromosome -lt 23 ]
then
#echo "$chromosome is numeric"
getSequence $chromosome
else
echo "Your input is invalid!"
fi
else
if [ $chromosome = "y" ] || [ $chromosome = "Y" ]
then
echo "You entered $chromosome"
elif [ $chromosome = "x" ] || [ $chromosome = "X" ]
then
echo "You entered $chromosome"
else
echo "Your input is invalid!"
fi
fi
echo "$FINAL", gives http://hgdownload.cse.ucsc.edu/goldenPath/hg38/chromosomes/chr20.fa.gz | gunzip -c > chr20.fa If I copy and paste on the terminal it works fine. However, the line curl "$FINAL" in the function causes this error: curl: (3) URL using bad/illegal format or missing URL
Thanks
•
written
by
nadarajan_v •
you are inserting a useless space in front of the url.
SPACE=" "
FINAL="$SPACE$URL$1$UNZIP$1$FE"
that said, Shell programs requiring such user input :
echo "Enter a number between 1-22 or the letters X or Y"
read chromosome
are evil. Please don't. Use a command line parser (getpopt).
Yes, I will be using getopt later. If I remove the $SPACE, I get the following warning and the .fa file is not created.
Warning: Binary output can mess up your terminal. Use "--output -" to tell
Warning: curl to output it to your terminal anyway, or consider "--output
Warning: <FILE>" to save to a file.
Thanks
curl --output - "${URL}" | gunzip -c > chr
This worked great. Thank you!
You can simplify your function as Pierre suggests:
getSequence() {
local nth=$1
local URL="http://hgdownload.cse.ucsc.edu/goldenPath/hg38/chromosomes/chr${nth}.fa.gz"
curl -sS -o - "${URL}" | gunzip -c > chr"${nth}".fa
}
Otherwise, you will get an error something like: curl: (6) Could not resolve host: "http because of split the URL.
The option -S when is used with -s, --silent, it makes curl show an error message if it fails.
Thank you so much. It worked perfectly!
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