As others have suggested, do you have a process that generates SAM output that can be piped directly to samtools?

# sam output generated, yet sam file never exists
bowtie alignment_index -c GGATCC --sam | samtools view -b -o output.bam -

What language/method would you like to loop with? What have you tried? A bash example:

#!/bin/bash

sam_file="my_filename.sam"
alignment_index="path_to_your_index"

for f in $sam_file
do
  bowtie $alignment_index -c GGATCC --sam > $f
  samtools view $f -b -o output.bam
  rm $f
done