Another If-else-then statment in bash

Question

I am running to a "weird" "if then else" problem (or I am just a novice). Or, I do not fully understand the semantics of specified statement.

What I want to do is read through a table (csv) like the one below

/home/trotos/I16_1505_09.fastq.gz,34,hg19
/home/trotos/I16_1505_06.fastq.gz,34,hg19
/home/trotos/I16_1505_12.fastq.gz,40,hg19
/home/trotos/I15_1277_01.fastq.gz,42,gg5
/home/trotos/I15_1458_01.fastq.gz,42,gg5
/home/trotos/I15_1314_01.fastq.gz,36,gg5
/home/trotos/I15_1458_03.fastq.gz,36,gg5

and then use input from each column (sequentially) to perform several commands. the script I am using (not refined yet) where file is the statedcsv

#!/bin/bash

shopt -s nullglob


file="$3"
human="$1"
mouse="$2"

while IFS=, read col1 col2 col3 ; do  # the file need to be loaded at the end of the loop, check a done
    echo $col1
    echo $col2
    echo $col3

for i in $col1; do

if [$col3="hg19"]
    then
       ref_genome=$human
echo "1"
echo $ref_genome
    else
        ref_genome=$mouse
echo "2"
echo $ref_genome

fi
echo $ref_genome
echo "....."

done
done < $file

the command is the following

./test '/home/trotos/Downloads/chromosomes/hg19.fa' '/home/trotos/Downloads/chromosomes/gg5.fa.gz' 'csv_file'

What it does correctly is to read the columns of the file, and get the data I need from a column per line in a loop.

But when I am using the third column (hg19 or gg5) as a statement of TRUE or FALSE to get a different condition:

if hg19 is TRUE then 'hg19.fa' is the correct

if gg5 is TRUE then 'gg5.fa.gz' is the correct but script's output differs:

LOOP
/home/trotos/lane2_I15_1458_08.fastq.gz
42
**gg5**
/home/trotos/lane2_I15_1458_08.fastq.gz
/home/trotos/lane2_I15_1458_08.fastq
/home/trotos/lane2_I15_1458_08

....
1
**/home/trotos/Downloads/chromosomes/hg19.fa**
.....
END LOOP

The first problem is that when col3==hg19 it gives the correct output that would be "/home/trotos/Downloads/chromosomes_hg19/hg19.fa". But when col3==gg5 i still get the same "/home/trotos/Downloads/chromosomes_hg19/hg19.fa". So who will I get the correct answer? The second is how to use the "if then else" statement to get the specific file that corresponds to the 3rd column and to use that information inside the loop defined by:

 for i in $col1; do.

Thank you in advance. I hope my description will not confuse you.

It would be great if you could cut down your script to provide us with a [mcve], i.e. by removing all the "debug" echoes and comments. At first glance, `[$col3="hg19"]` is wrong, since you need spaces like `[ "$col3" = hg19 ]`, but that might not be the only problem. — Tom Fenech, Aug 29 '17 at 13:20
script is cleaner, I added the spaces and it appears to work. but also spaces are needed between the "=". — trotos, Aug 29 '17 at 14:49

Another If-else-then statment in bash

0 Answers0