why the syntax error comes when i use the same command in loop in bash linux

Question

[Priya]

hi, I am using awk to sort a tsv file with command:

awk -F "\t" '{ if(($3 => 95) && ($13 >= 95) && ($11 <= 1e-5)) { print } }' FILENAME| sort -k1,1 -k12,12gr -k11,11g -k3,3gr | sort -u -k1,1 --merge > SORTED_FILENAME

It is working fine when i used this command for sorting of my file,but when I tried to loop the same command it's giving my syntax error. the Looped command that I used is:

ls|while read i;do awk -F "\t" '{ if(($3 => 95) && ($13 >= 95) && ($11 <= 1e-5)) { print } }' $i| sort -k1,1 -k12,12gr -k11,11g -k3,3gr | sort -u -k1,1 --merge > SORTED_$i ;done

And I have tried every possible alteration I can make here like making a bash.sh script of it and then run using

bash bash.sh

or using quotes but nothing worked. kindly help me understand why this syntax error is coming then i use the same command in loop?

the error is:

awk: cmd. line:1: { if(($3 => 95) && ($13 >= 95) && ($11 <= 1e-5)) { print } }
awk: cmd. line:1:           ^ syntax error
awk: cmd. line:1: { if(($3 => 95) && ($13 >= 95) && ($11 <= 1e-5)) { print } }
awk: cmd. line:1:                 ^ syntax error
awk: cmd. line:1: { if(($3 => 95) && ($13 >= 95) && ($11 <= 1e-5)) { print } }
awk: cmd. line:1:                                                  ^ syntax error

the file I am working on looks like this:

GCF_000240185.1_ASM24018v2_genomic_04835        WP_004181470    71.605  162     46      0       1       486     1       162     1.69e-84        243     99
GCF_000240185.1_ASM24018v2_genomic_04835        WP_002912829    29.480  173     99      9       4       480     10      173     2.03e-10        54.3    98
GCF_000240185.1_ASM24018v2_genomic_04835        WP_002903719    30.000  80      56      0       238     477     84      163     7.13e-06        41.6    49
GCF_000240185.1_ASM24018v2_genomic_04835        WP_009309163    41.270  63      35      2       244     432     67      127     5.26e-05        38.9    39
GCF_000240185.1_ASM24018v2_genomic_04835        WP_002921333    27.381  84      61      0       235     486     88      171     1.13e-04        38.1    52
GCF_000240185.1_ASM24018v2_genomic_04835        WP_004180150    98.98  118     82      2       133     483     68      182     1.84e-04        99    99
GCF_000240185.1_ASM24018v2_genomic_04835        WP_074177527    99.99  101     71      1       184     486     91      188     0.007   33.1    62
GCF_000240185.1_ASM24018v2_genomic_04835        WP_049186326    27.941  68      37      2       271     456     83      144     0.050   30.4    38
GCF_000240185.1_ASM24018v2_genomic_04835        WP_032435057    21.769  147     111     3       10      441     3       148     0.089   29.6    88
GCF_000240185.1_ASM24018v2_genomic_04835        WP_223168825    29.167  48      33      1       271     414     36      82      0.10    28.9    29

Answer 1

[ATpoint]

It must be >=, never =>.

Answer 2

[Michael]

 ls|while read i;do awk -F "\t" '{ if(($3 **=>** 95) && ($13 >= 95) && ($11 <= 1e-5)) { print } }' $i| sort -k1,1 -k12,12gr -k11,11g -k3,3gr | sort -u -k1,1 --merge > SORTED_$i ;done

I think it is a simple typo: => should be >= ('greater-equal')