Hi all,
I have some code (attached) that is triggering a segfault in coot, and I can’t
figure out why. I’m trying to first grab raw sequences from a fasta file, and
assign each sequence to a dictionary - that part works fine.
Then I want to iterate through the dictionary, checking if each sequence
matches a chain in the PDB file, and if so, adding it to a new dictionary using
the same key as was used for the sequence dictionary (so I can then pass the
appropriate bits and pieces to align_and_mutate()). That part causes coot to
crash with the following error:
/usr/local/bin/coot: line 10: 20005 Segmentation fault: 11
/Library/Coot/bin/coot-real "$@“
When I restart coot after this, the GUI is unresponsive and whited-out - I have
to restart the terminal session before it behaves normally again.
Anyone have an idea what I’m doing wrong in the script?
It still fails if I omit the last two lines, so it’s not the last if statement…
I’m using r4867 on Mac OS X 10.9.
Oliver.
import re
def get_seqs_from_fasta(fasta_file):
with open(fasta_file) as fp:
i=0
raw_seqs_from_file={}
for result in re.findall('(>(.*?\n))(.*?)(>(.*?\n))', fp.read(), re.S):
raw_seqs_from_file[i]=str(result[2]).replace("\n","").upper()
i=i+1
return raw_seqs_from_file
raw_seqs_from_file=get_seqs_from_fasta("protein_seqs.txt")
chain_id_best={}
for key in sorted(raw_seqs_from_file):
seq=str(raw_seqs_from_file[key])
out=align_to_closest_chain(seq,0.95)
print out
if type(out) is list: #If matched, assign chain to dictionary
chain_id_best[key]=str(out[1]) #chain_id_best using same key as for raw_seqs_from_file
On Dec 31, 2013, at 11:45 AM, Paul Emsley <pems...@mrc-lmb.cam.ac.uk> wrote:
> On 31/12/13 16:31, Oliver Clarke wrote:
>
>>
>> Another note - what is active_atom_spec() supposed to do? I guessed it was
>> an equivalent of active_residue() but returning the specific atom rather
>> than the CA,
>
> That's right.
>
>> but it returns this when called:
>>
>> _90ac6c78c97f0000_p_std__pairT_bool_std__pairT_int_coot__atom_spec_t_t_t
>>
>> While pushing the following to the console:
>> BL INFO:: command input is: active_atom_spec()
>> BL INFO:: result is <Swig Object of type 'std::pair< bool,std::pair<
>> int,coot::atom_spec_t > > *' at 0x10c8cda50>
>> swig/python detected a memory leak of type 'std::pair< bool,std::pair<
>> int,coot::atom_spec_t > > *', no destructor found.
>>
>
> You understand that Python is not my preferred language, so I don't use it
> much. Now you are poking at the limits of my understanding. This does look
> bad though. I'll take a look - it might be a SWIG (version) problem.
>
> Paul.
>
