Reg. align_codes error in profile_build.py in Mod9v2
Please help me to rectify the error in mod9v2
My script
from modeller import * log.verbose() env = environ() #-- Prepare the input files #-- Read in the sequence database sdb = sequence_db(env) #sdb.read(seq_database_file='C:\Program Files\Modeller9v2\modlib\pdball.pir', seq_database_format='PIR',chains_list='ALL', minmax_db_seq_len=(30, 4000), clean_sequences=True) #-- Write the sequence database in binary form #sdb.write(seq_database_file='C:\Program Files\Modeller9v2\modlib\pdball.bin', seq_database_format='BINARY', chains_list='ALL') #-- Now, read in the binary database sdb.read(seq_database_file='C:\Program Files\Modeller9v2\modlib\pdball.bin', seq_database_format='BINARY', chains_list='ALL') #-- Read in the target sequence/alignment aln = alignment(env) aln.append(file='p17787.fas', alignment_format='FASTA', align_codes='p17787') #-- Convert the input sequence/alignment into # profile format prf = aln.to_profile() #-- Scan sequence database to pick up homologous sequences prf.build(sdb, matrix_offset=-450, rr_file='${LIB}/blosum62.sim.mat', gap_penalties_1d=(-500, -50), n_prof_iterations=1, check_profile=False, max_aln_evalue=0.01) #-- Write out the profile in text format prf.write(file='build_profile.prf', profile_format='TEXT') #-- Convert the profile back to alignment format aln = prf.to_alignment() #-- Write out the alignment file aln.write(file='build_profile.ali', alignment_format='PIR') aln.check()
error what i have got
'import site' failed; use -v for traceback Traceback (most recent call last): File "build_profile.py", line 21, in ? aln.append(file='p17787.fas', alignment_format='FASTA', align_codes='p17787' ) File "C:\Program Files\Modeller9v2\modlib\modeller\alignment.py", line 74, in append rewind_file, close_file) _modeller.error: read_al_373E> Protein specified in ALIGN_CODES(i) was not found in the alignment file; ALIGN_CODES( 1) = p17787
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saravanan wrote: > Traceback (most recent call last): > File "build_profile.py", line 21, in ? > aln.append(file='p17787.fas', alignment_format='FASTA', > align_codes='p17787' > ) > File "C:\Program Files\Modeller9v2\modlib\modeller\alignment.py", line > 74, in > append > rewind_file, close_file) > _modeller.error: read_al_373E> Protein specified in ALIGN_CODES(i) was > not found > in the alignment file; ALIGN_CODES( 1) = p17787
You have tried to read the sequence with code 'p17787' from the FASTA file 'p17787.fas', but Modeller couldn't find it. You should check the p17787.fas file to make sure it is in correct FASTA format, and does contain the p17787 sequence - i.e. it should contain the line '>p17787' followed by the sequence on the next line. Note that align codes are case-sensitive.
Ben Webb, Modeller Caretaker
participants (2)
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Modeller Caretaker
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saravanan