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Top Forums UNIX for Beginners Questions & Answers Read line and save fields as variables Post 302979027 by Splinter479 on Monday 8th of August 2016 05:36:17 AM
Old 08-08-2016
thanks so far for your replies. I kind of have the feeling too that it is somehow related to the calls.txt
I thought the minimal example would do the job, but let's give you a more real copy of what I have done:

my.sh :
Code:
#!/bin/bash
echo " I AM OUTSIDE THE LOOP"

infile="calls.txt"

while IFS=',' read -r f1 f2 f3 f4 f5 f6 f7 f8 f9 f10 f11 f12 f13 f14 f15 f16 f17 f18 f19
do
        echo " I AM INSIDE THE LOOP"

        my_file1=$f1
        species1=$f2
        chrom1=$f3
        my_file2=$f4
        species2=$f5
        chrom2=$f6
        binSize=$f7
        foo1=$f8
        foo2=$f9
        foo3=$f10
        foo4=$f11
        variance=$f12
        bar1=$f13
        bar2=$f14
        java_jar=$f15
        bar3=$f16
        bar4=$f17
        unit=$f18
        bar5=$f19

        # program calls here

done < "$infile"

my calls.txt is just a one liner right now, but later many lines according to the same format shall follow:
Code:
/path/to/my/file.txt,string1,string2,/path/to/my/other/file.txt,string3,string4,int1,string5,string6,int2,int3,int4,/path/to/a/third/file.txt,path/to/a/fourth/file.txt,/path/to/a/java.jar,anotherString,anotherString,anotherString,aFloatNumber

so this is exactly a renamed representation of the calls.txt. Sorry for the censorship, but in fact I am currently developing a software tool I am ofc not allowed to share everything in detail :/

I came up with the thoughts of maybe the paths messing it up? I 'll retry with quoting the paths. Other ideas?

EDIT: quoting didn't help :/
 

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read(1) 						      General Commands Manual							   read(1)

NAME
read - read a line from standard input SYNOPSIS
var ... DESCRIPTION
reads a single line from standard input. The line is split into fields as when processed by the shell (refer to shells in the first field is assigned to the first variable var, the second field to the second variable var, and so forth. If there are more fields than there are specified var operands, the remaining fields and their intervening separators are assigned to the last var. If there are more vars than fields, the remaining vars are set to empty strings. The setting of variables specified by the var operands affect the current shell execution environment. Standard input to can be redirected from a text file. Since affects the current shell execution environment, it is usually provided as a normal shell special (built-in) command. Thus, if it is called in a subshell or separate utility execution environment similar to the following, it does not affect the shell variables in the caller's environment: Options recognizes the following options: Do not treat a backslash character in any special way. Consider each backslash to be part of the input line. Opperands recognizes the following operands: var The name of an existing or nonexisting shell variable. EXTERNAL INFLUENCES
Environment Variables determines the internal field separators used to delimit fields. RETURN VALUE
exits with one of the following values: 0 Successful completion. >0 End-of-file was detected or an error occurred. EXAMPLES
Print a file with the first field of each line moved to the end of the line. while read -r xx yy do printf "%s %s " "$yy" "$xx" done < input_file SEE ALSO
csh(1), ksh(1), sh(1), sh-posix(1). STANDARDS CONFORMANCE
read(1)
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