Linux command for data filtering

In your combined command you are still specifying a source file for each item in the pipeline:

cat all_pin | awk '{$4=""; print $0}' all_pin | awk '{print "eval " $0}' all_pin | sed -e /^editPin/'{ s#phy_inst/## ; s/{/{ 0 [ expr / ; s/}/]}/ ; }' all_pin
#   ^source                           ^again                             ^and again                                                                    ^and still again

Instead, you should let each command read from its predecessor. Here, I've combined the two awk commands and discarded the unnecessary cat:

awk '{ $4=""; print "eval " $0}' all_pin |
    sed -e '/^editPin/ { s#phy_inst/## ; s/{/{ 0 [ expr / ; s/}/]}/ ; }'

Depending on the answer to my comment question the second part may be equally straightforward, and I'll update my answer accordingly

Why not use tcl for the addition? Here is an example that just changes the expression to a have a nested expr so you can adjust the second value in tcl.

$ echo editPin -pin phy_inst/blah args  -assign {1443.0305 184.62} -options | \
    sed  '/editPin.*phy_inst/s/assign {\([0-9.]*\) \([0-9.]*\)}/assign { 0 [ expr \1 [ expr \2 + 123.3]]}/'
# returns editPin -pin phy_inst/blah args -assign { 0 [ expr 1443.0305 [ expr 184.62 + 123.3]]} -options

That way the sed is just a simple string replacement, and you aren't attempting to do any floating point math in shell/awk/bc/etc.

I came up with this awk

 {  for(i=1; i<=NF ; i++ ) {
        if ( $i ~ /^phy_inst/ ) {
                $i=substr($i,10) ;
                $(i+1)="" ; }
        if ( $i == "-assign" ) {
                $(i+1)="{ 0 [ expr " $(i+1) ;
                $(i+2)=$(i+2) "+" X " ]}" ;
                }
 }
        $1 = "eval " $1 ;
         print ;
 }

to be called with (replace foo_bar with proper value)

awk -v X=foo_bar -f SE.awk all_pin

yielding

eval editPin -pin i_dfi_row_cmd_p1_d[0]  -assign { 0 [ expr {1443.0305 184.62}+foo_bar ]} -layer M10 -pinWidth 0.038 -pinDepth 0.395 -fixOverlap false -fixedPin -snap MGRID
eval editPin -pin i_dfi_row_cmd_p1_d[1]  -assign { 0 [ expr {1444.0305 185.62}+foo_bar ]} -layer M10 -pinWidth 0.038 -pinDepth 0.395 -fixOverlap false -fixedPin -snap MGRID

where awk basically parse line by line,

• parsing is done by looping on all "field", awk use NF variable (Number of Field, see man awk)
• add eval in first field
• strip phy_inst/ string, delete following field (implicit specification)
• edit values after -assign field
• insert value of X variable (this must be called on command line)(and a poor choice for a variable name)

Untested

    if ( $i == "-assign" ) {
            $(i+1)="{ 0 [ expr " ($(i+1)+X) ;
            $(i+2)=($(i+2) + X) " ]}" ;
            }

Just add X value to proper field.