It is imperative that there be public confidence that the laws of the United States are administered and enforced in an impartial manner. To that end, all components of the Department of Justice, including United States Attorneys' Offices, shall abide by the following procedures governing communication between the Department of Justice and the White House.
Pending Criminal Investigations and CasesThe Department shall provide the White House with information about pending criminal investigations or cases only when doing so is important for the performance of the President's duties and appropriate from a law enforcement perspective. Except with respect to national security matters, all initial communications that concern or may concern a pending criminal investigation or a criminal case pending at the trial level should take place only between the Office of the Deputy Attorney General and the Office of the Counsel to the President, and all initial communications that concern or may concern a criminal case pending at the appellate level should take place only between the Office of the Counsel to the President and either the Office of the Deputy Attorney General or the Office of the Solicitor General. If appropriate with regard to a particular case or investigation, the Office of the Counsel to the President and the senior Justice Department official with whom the White House is dealing will design and monitor a process for ongoing contact between the White House and Justice Department concerning that particular matter.
http://www.usdoj.gov/usao/eousa/foia_reading_room/usam/title1/doj00032.htm(In other words, it's up to the Justice Department, not the president, to decide if an investigation or prosecution should or should not be initiated.)