Recently, I did de novo RNA-seq experiment for a non-model fish species and assembled transcripts for functional annotations. Before GO annotation, I blasted my assembled transcripts (1e-10) to InterProScan 5 and got PFAM IDs (File 1). Then, I downloaded GO annotations for each PFAM entries (from there; http://www.geneontology.org/page/download-mappings) and got PFAM IDs with corresponding GO mappings (File 2). I want to compare these two files and save the PFAM IDs with GO annotations for my file 1 entries:
File 1: (my file for analyses, as you notice that PF00015 and PF00016 are not absent in my file)
File 2: (downloaded file from the database PFAM IDs with GO annotations)
My question is that is there any perl or phyton script for comparing these two files and generating an output including File 1 PFAM IDs with GO annotations.
Thank you all in advance