[Tutor] Substitution problem

[Kent Johnson]

Srinivas Iyyer wrote:
> Dear group, 
>  I am trying to automate a process in statistical
> language R. 
> 
> There for 1 operation 50 lines of code is written.
> This process query postgres database and does some
> processing on the resulting data and writes back a
> file. 
> 
> I want to replicate the 50 line code, 90 times, by
> substituting with postgres.table_id and file name at 2
> places. 

> I want to read File_A, loop through it and substitute
> $MOL_ID = 1 and $MOL_NAME = A
> 
> I want to reproduce 50 lines * 90 times substituting
> ID and NAME by looping through File_A.
> 
> 
> I tried using re module, I do not know if this correct
> or wrong. 
> 
> 
> for m in file_A:
>     cols = m.split('\t')
>     molid = cols[0].strip()
>     molname = cols[1].strip()
>     for k in file_B:
>          pat1 = '$MOL_ID'
>          pat2 = '$MOL_NAME'
>          if re.search(pat1,k):
>                s = Template(k)
>                s.substitute($MOL_ID,molid)
>                if re.search(pat2,k):
>                       t = Template(k)
>                       t.substitute($MOL_NAME,molname)
> 
> 
> However, this is not working, somehow.

You don't need regexes for this, string replace will do what you want.

  >>> s = 
'''write.table(mol_towrite,"$MOL_NAME_adj_pval",sep='t',quote=F,col.names=F)'''
  >>> s2 = s.replace('$MOL_NAME', 'my data')
  >>> s2
'write.table(mol_towrite,"my data_adj_pval",sep=\'t\',quote=F,col.names=F)'

Your program could
- read all of file B with open('file_B').read()
- for each line of file A
   - split the line
   - substitute for '$MOL_ID' and '$MOL_NAME'
   - write the modified string to your output file

BTW $ is a special character in a regex, you need to escape it as \$
> 
> Can any one help me please. If more simple methods are
> available please show a new way. 

You might take a look at RPy, it would probably let you do all the work 
in a Python program instead of writing an R code generator.

Kent