What are the rulings on seeking permission to enter, and is it permissible for a father to enter upon his daughter to wake her for Fajr prayer?

Seeking permission (Istidhan) is prescribed and commanded so that one's gaze does not fall upon what is unlawful to look at. It is obligatory even for maharim (unmarriageable kin), such as a father, so that he does not see his daughter with her 'awrah (intimate parts) exposed.

This is supported by the Holy Quran, the purified Sunnah, the narrations of the Companions, and the principles of Sharia: - The Holy Quran: Allah Almighty's saying: {And when the children among you reach puberty, let them ask permission as those before them have asked permission.} - The purified Sunnah: What Imam Malik narrated from 'Ata bin Yasar that a man asked the Prophet (peace be upon him): "Should I ask permission to enter upon my mother?" He said: "Yes." And he said to him: "Do you like to see her naked?" He said: "No." He said: "Then ask permission to enter upon her." - Narrations of the Companions: Abdullah ibn Mas'ud's saying: "It is incumbent upon you to ask permission to enter upon your mothers and your sisters," and Ibn Abbas's saying to 'Ata: "Ask permission to enter upon your sister," and Hudhayfah ibn al-Yaman's saying to someone who asked him: "Should I ask permission to enter upon my sister?" He said: "If you do not ask permission, you will see what displeases you." - Principles of Sharia: If one enters without permission, the person might be exposed, and one's gaze might fall upon what is unlawful to look at. Therefore, seeking permission is obligatory as a way of blocking the means (sadd al-dhari'ah).

Based on this, your father must seek your permission when entering to wake you for Fajr prayer, such as by knocking on the door, so that you wake up and are covered.