def makeFE_table(inFile, constCov, constrain):
if (type(inFile) == str) and (str(type(inFile[0])) != "<class 'Bio.SeqRecord.SeqRecord'>"):
inFile = GBcode(openFasta(inFile))
table = []
for item in inFile:
table.append([item.description, getFree_energy(str(item.seq)), getFree_energy(str(item.seq), constCov), getFree_energy(str(item.seq), constrain)])
return table
def haploRNA3D(templateInput, fastaFile, cycles, path, chain='A'):
"""
Creates a tertiary structure for each unique sequence in a Fasta file
using the methods from the module moderna. This function returns three
files for each sequences: (1) a fasta file comparing the target sequence with
the sequence of the template pdb structure, (2) a pdb file of the homologous
structure with no refinement, and (3) a pdb file of the homologous structure
with refinement.
Results are showed in a folder named 'haploRNA3D_month_day_hour_min'.
This folder is located in Home.
Module required:
- argparse
- subprocess
- time
- expanduser (from os.path)
Usage: <template> <fasta file> <cycles refinement> <path> <chain (default='A')>
"""
print 'Loading template...'
template = load_template(templateInput, str(chain))
clean_structure(template)
seqTemplate = str(get_sequence(template))
print 'Loading Fasta file...'
records = openFasta(fastaFile)
nameLst, seqLst = getNameSeq(records)
for index in range(len(nameLst)):
seqLst[index] = replaceBase(seqLst[index], seqTemplate)
if str(path).endswith('/'):
nameDir = str(path)+'haploRNA3D_'+time.ctime().replace(' ','_').replace(':','_')[4:16]
else:
nameDir = str(path)+'/'+'haploRNA3D_'+time.ctime().replace(' ','_').replace(':','_')[4:16]
subprocess.check_call(['mkdir', nameDir])
muscle = locate('muscle')
print 'Refining the models...'
refinementScript = locate('refine_model_mmtk.py')
secondStruct = open(nameDir+'/Secondary_Structure.fasta', 'w')
for elm in range(len(seqLst)):
print 'Refining', elm+1, 'of', len(seqLst)
seqTargTempl(seqLst[elm], seqTemplate, nameLst[elm], nameDir)
model(muscle, nameDir, nameLst[elm], templateInput, chain)
currentTemplate = load_template(nameDir+'/'+nameLst[elm][:10])
try:
subprocess.check_call(['python', refinementScript, '-m',
nameDir+'/'+nameLst[elm][:10], '-y',
str(cycles), '-o', nameDir+'/'+nameLst[elm][:11]+'_refined.pdb', '-t'])
except:
subprocess.check_call(['python', refinementScript, '-m',
nameDir+'/'+nameLst[elm][:10], '-y',
str(cycles), '-r', '2-'+str(len(currentTemplate)),
'-o', nameDir+'/'+nameLst[elm][:11]+'_refined.pdb', '-t'])
newmodel = load_model(nameDir+'/'+nameLst[elm][:11]+'_refined.pdb')
newmodelStruc = get_secstruc(newmodel)
newmodelSeqen = str(get_sequence(newmodel))
secondStruct.write('>'+nameLst[elm][:11]+'\n'+newmodelSeqen+'\n'+newmodelStruc+'\n')
secondStruct.close()
print 'Done!'
def adjusted_structure_entropy(inFile, outFile, title, structure):
"""
This function returns a figure of structural entropy when several sequences (from a fasta file)
are adjusted to a defined secondary RNA structure.
Usage: <inFile> <outFile> <title> <structure>
"""
if (type(inFile) == str) and (str(type(inFile[0])) != "<class 'Bio.SeqRecord.SeqRecord'>"):
inFile = openFasta(inFile)
for elem in inFile:
fit_result = fit_to_secondStruct(structure, str(elem.seq))
elem.seq = fit_result
info_content_file(inFile, title, outFile)
def tableByGB(inFile):
"""
WARNING: before to use this function identify yourself to NCBI using Entrez.email.
This function build a table based on a list. Each element is the info for each sequence.
Module required:
- Entrez (from Bio)
- SeqIO (from Bio)
"""
if (type(inFile) == str) and (str(type(inFile[0])) != "<class 'Bio.SeqRecord.SeqRecord'>"):
inFile = openFasta(inFile)
inFile = GBcode(inFile)
GB_table = []
for elem in inFile:
GB_table.append(get_info_byGB(elem.description))
return GB_table
