shell --array in while loop
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5 weeks ago

first I have a file which have some gene_IDs: ZM011,ZD012,ZF033,..... Then I want to convert these gene id to different numbers. Like ZM011 -> 1, ZD012 -> 2,.... I try use shell script like this:

   i=1
   cat ids.txt | while read id; do arr[$id]=$i let i++; done
   echo ${#arr[@]}

but the output is 0

I don't know how to do this

shell • 306 views
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cat -n ids.txt should do it? See below for more options:

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Thank you very much!

But, actually, I need to form a correspondence between the gene ID and the number for subsequent interconversion.

For example, I would save the generated numbers in a file to reduce the size of the file, and then pull out one and convert it back to the corresponding ID when needed

That's why I want to save it as an array

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save the output of cat -n in a sorted file. At the end use join.

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5 weeks ago
Sam ★ 4.1k

Not sure why will this be helpful, as gziping the file might save you more space to start with anyway, but you can do

awk -v it=0 '{for(i = 0; i <=NF; ++i){print $i,it; it++}}' ids.txt > newFile

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