On Fri, Apr 15, 2011 at 8:41 AM, Spyros Charonis <s.charo...@gmail.com>wrote:
> Hello, > > I'm doing a biomedical degree and am taking a course on bioinformatics. We > were given a raw version of a public database in a file (the file is in > simple ASCII) and need to extract only certain lines containing important > information. I've made a script that does not work and I am having trouble > understanding why. > > when I run it on the python shell, it prompts for a protein name but then > reports that there is no such entry. The first while loop nested inside a > for loop is intended to pick up all lines beginning with "gc;", chop off the > "gc;" part and keep only the text after that (which is a protein name). > Then it scans the file and collects all lines, chops the "gc;" and stores > in them in a tuple. This tuple is not built correctly, because as I posted > when the program is run it reports that it cannot find my query in the tuple > I created and it is certainly in the database. Can you detect what the > mistake is? Thank you in advance! > > Spyros > > _______________________________________________ > Tutor maillist - Tutor@python.org > To unsubscribe or change subscription options: > http://mail.python.org/mailman/listinfo/tutor > > import os, string printsdb = open('/users/spyros/folder1/python/PRINTSmotifs/prints41_1.kdat', 'r') lines = printsdb.readlines() # find PRINTS name entries you need to have a list to collect your strings: protnames = [] for line in lines: # this gets you each line #while line.startswith('gc;'): this is wrong if line.startswith('gc;'); # do this instead protnames.append(line.lstrip('gc;')) # this adds your stripped string to the protnames list if not protnames: print('error in creating tuple') # check if tuple is true or false #print(protnames) break query = input("search a protein: ") query = query.upper() if query in protnames: print("\nDisplaying Motifs") else: print("\nentry not in database") # Parse motifs def extract_motifs(query): motif_id = () motif = () while query in lines: ####for query, get motif_ids and motifs while line.startswith('ft;'): motif_id = line.lstrip('ft;') motif_ids = (motif_id) #print(motif_id) while line.startswith('fd;'): motif = line.lstrip('fd;') motifs = (motif) #print(motif) return motif_id, motif if __name__ == '__main__': final_motifs = extract_motifs('query') -- Joel Goldstick
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