RE: Peak list readingRE: Peak list reading|
The header line and atom name solved the problem. Thank you. Min-Kyu > Subject: Re: Peak list reading > From: min-kyu.cho@xxxxxxxx > Date: Sat, 21 Dec 2013 09:33:07 -0500 > To: edward@xxxxxxxxxxxxx > CC: tlinnet@xxxxxxxxxxxxx; relax-users@xxxxxxx > > Hi Ed and Troels, > > Thank you for the comment. I will try today when I get back to my laptop. > > Wish all you have merry Christmas and Happy new year! > > Min-Kyu > > Dec 21, 2013 7:14 AM "Edward d'Auvergne" <edward@xxxxxxxxxxxxx> 작성: > > > Hi Min-Kyu and Troels, > > > > From the messages, I can see 4 potential issues: > > > > 1) The assignment: > > > > 568?-? 123.445 8.765 3.45E06 > > > > is ambiguous, as it could be any spin pair. It is best to assign the > > atoms properly, otherwise relax cannot tell if it is a N-H pair, the > > Trp NE1-HE1 pair, or something more exotic. Note that you can analyse > > your Trp NE1 data at the same time as the backbone N data. Troels, on > > line 108 of the ./lib/spectrum/sparky.py file (as well as the other > > peak list files in that package), maybe it is worth searching for the > > "?-?" string in the assignment rather than matching "?-?" to skip the > > line of data? Actually it might be best if we just skip every single > > assignment containing "?", and just give a warning that the line is > > being skipped as the assignment has a question mark in it. > > > > > > 2) The Sparky assignment format is: > > > > [Group][atom1]-[Group][atom2]-[Group][atom3] > > > > The group is optional for the 2nd, 3rd, etc. dimensions. The format > > of the "Group" is not defined in Sparky, but in its manual it uses the > > convention of letters for the residue name followed by the residue > > number. However despite the warnings from relax about the missing > > residue name, I would assume that the data would be nevertheless read. > > The spectrum.read_intensities user function will print out a list of > > all the intensities read into the program at the end, so you will be > > able to tell what has been read or skipped. > > > > > > 3) For you Troels - could you have a look at line 172 of the > > ./lib/spectrum/sparky.py file? It has the confusing text "Improperly > > formatted NMRPipe SeriesTab file" which is probably a copy and paste > > error from the ./lib/spectrum/nmrpipe.py file. > > > > > > 4) The "IndexError: list index out of range" might be due to the > > badly formatted header line, as Troels mentioned. Min-Kyu, if you fix > > that, does the error go away? Alternatively, it could be that one > > line in the file is differently formatted, for some unknown reason. > > This can be tested by deleting lines out of the file one by one until > > the error goes away (except for the header which is needed to > > determine the "Data Height" column). If you do find that there is a > > problem with the file, could you submit a bug report at > > https://gna.org/bugs/?func=additem&group=relax and attach the > > truncated peak list which still causes the error? With this, I can > > construct a system test for relax and also make sure that an > > informative RelaxError or RelaxWarning is given so that the user knows > > exactly what the problem is and how it should be fixed. > > > > > > As for the FASTA format, this is not supported by relax yet. This is > > not a great format as you don't know the residue numbering and it will > > very likely not start at one. But as Troels mentioned, you can load > > the sequence from your peak lists. It might then be worth having the > > amino acid names in the group part of the Sparky assignment if you > > would like residue names to be present. > > > > Regards, > > > > Edward > > > > > > P. S. I may not be able to do much until after the new year so, if > > you don't hear from me until then, I wish you a merry Christmas and > > happy new year! > > > > > > > > > >> On 21 December 2013 02:41, Troels Emtekær Linnet <tlinnet@xxxxxxxxxxxxx> wrote: > >> Hi Min-Kyu. > >> > >> I believe you probably need to define the right header > >> for the file. > >> ex: > >> Assignment w1 w2 Data Height > >> > >> And see if you can fix the question marks. > >> 568N-HN > >> > >> Have a look in the test-suite for some typical definition of peaks files. > >> test_suite/shared_data/peak_lists > >> > >> If you have a peak list, the new 3.1.1 version allow you to define the spins > >> from > >> a typical peak list. > >> spectrum.read_spins(file='peak_file.list', dir='/path/to/file') > >> > >> Cheers > >> > >> > >> > >> 2013/12/20 Min-Kyu Cho <min-kyu.cho@xxxxxxxx> > >>> > >>> Hi , > >>> > >>> > >>> > >>> > >>> > >>> I got sparky peak list file written as > >>> > >>> > >>> > >>> 568?-? 123.445 8.765 3.45E06 > >>> > >>> . . . . . > >>> > >>> > >>> > >>> > >>> > >>> When I tried to read in this file through GUI, it complains > >>> > >>> ---------- > >>> > >>> Sparky formatted data file. > >>> > >>> > >>> > >>> Number of header lines found: 1 > >>> > >>> 2D peak list detected. > >>> > >>> RelaxWarning: Improperly formatted Sparky file, cannot process the residue > >>> name for dimension 1 in assignment: 546N-H. Setting residue name to None. > >>> > >>> RelaxWarning: Improperly formatted NMRPipe SeriesTab file, cannot process > >>> the residue name for dimension 2 in assignment: 546N-H. Setting residue name > >>> to None. > >>> > >>> Traceback (most recent call last): > >>> > >>> File "/home/mkc9/Programs/RELAX/relax-3.1.1/gui/wizards/wiz_objects.py", > >>> line 161, in _apply > >>> > >>> self.exec_status = self.on_execute() > >>> > >>> File "/home/mkc9/Programs/RELAX/relax-3.1.1/gui/uf_objects.py", line > >>> 883, in on_execute > >>> > >>> return_status = self.execute(self.name, **kargs) > >>> > >>> File "/home/mkc9/Programs/RELAX/relax-3.1.1/gui/uf_objects.py", line > >>> 805, in execute > >>> > >>> return_status = interpreter.apply(uf, *args, **kwds) > >>> > >>> File "/home/mkc9/Programs/RELAX/relax-3.1.1/gui/interpreter.py", line > >>> 109, in apply > >>> > >>> apply(fn, args, kwds) > >>> > >>> File "/home/mkc9/Programs/RELAX/relax-3.1.1/pipe_control/spectrum.py", > >>> line 530, in read > >>> > >>> peak_list = read_peak_list(file=file, dir=dir, int_col=int_col, > >>> spin_id_col=spin_id_col, mol_name_col=mol_name_col, res_num_col=res_num_col, > >>> res_name_col=res_name_col, spin_num_col=spin_num_col, > >>> spin_name_col=spin_name_col, sep=sep, spin_id=spin_id) > >>> > >>> File "/home/mkc9/Programs/RELAX/relax-3.1.1/lib/spectrum/peak_list.py", > >>> line 208, in read_peak_list > >>> > >>> sparky.read_list(peak_list=peak_list, file_data=file_data) > >>> > >>> File "/home/mkc9/Programs/RELAX/relax-3.1.1/lib/spectrum/sparky.py", > >>> line 203, in read_list > >>> > >>> intensity = float(line[int_col]) > >>> > >>> IndexError: list index out of range > >>> > >>> ----- > >>> > >>> > >>> > >>> Since I already made sequence & spin system with correct residue number, I > >>> expected the residue number in Sparky file should be enough. > >>> > >>> > >>> > >>> So,my questions are: > >>> > >>> > >>> > >>> 1. the sparky file format for relax should be made as written in the > >>> manual? > >>> > >>> > >>> > >>> 2. Can relax recognize FASTA sequence and automatically generate Spin > >>> system? > >>> > >>> > >>> > >>> Thanks and Happy Holiday! > >>> > >>> > >>> > >>> Min-Kyu > >>> > >>> > >>> > >>> > >>> _______________________________________________ > >>> relax (http://www.nmr-relax.com) > >>> > >>> This is the relax-users mailing list > >>> relax-users@xxxxxxx > >>> > >>> To unsubscribe from this list, get a password > >>> reminder, or change your subscription options, > >>> visit the list information page at > >>> https://mail.gna.org/listinfo/relax-users > >> > >> > >> _______________________________________________ > >> relax (http://www.nmr-relax.com) > >> > >> This is the relax-users mailing list > >> relax-users@xxxxxxx > >> > >> To unsubscribe from this list, get a password > >> reminder, or change your subscription options, > >> visit the list information page at > >> https://mail.gna.org/listinfo/relax-users > >> |