def Extract(infa, results, outfa):
'''Extract lncRNA sequence'''
SeqID, SeqList = GetFasta(infa)
try:
fr = open(results, 'rU') # results file
except (IOError,ValueError) as e:
print >>sys.stderr, str(e)
sys.exit(1)
idlist = set()
for line in fr.readlines()[1:]:
line = line.strip()
if line.split("\t")[2] == "Noncoding":
idlist.add( line.split("\t")[0] )
fr.close()
try:
fo = open(outfa, 'w') # output file
except (IOError,ValueError) as e:
print >>sys.stderr, str(e)
sys.exit(1)
for seqid, seq in zip(SeqID, SeqList):
if seqid in idlist:
fo.write(">" + seqid + "\n")
fo.write(seq + "\n")
fo.close()
def Protein_StructureScore(protein_file, out_prefix=None):
'''to compute structure features of rnas and proteins'''
protein_out = os.path.join(out_prefix, "protein_score")
#####################
# protein structure
protein_file_part = os.path.join(out_prefix, "tmp.protein.file.")
protein_file_list = os.path.join(out_prefix, "tmp.filelist")
exedir = os.path.dirname(os.path.abspath(__file__))
stride_dat = os.path.join(exedir, "../src/stride.dat")
stride_cmd = "cp " + stride_dat + " " + os.path.abspath('.')
tmp_stride_dat = os.path.join(os.path.abspath('.'), "stride.dat")
subprocess.call(stride_cmd, shell=True)
proID, proSeq = GetFasta(protein_file)
i = 0
for proid, proseq in zip(proID, proSeq):
f_tmp = open(protein_file_part + str(i), "w")
i += 1
f_tmp.write(">" + proid + "\n")
f_tmp.write(proseq + "\n")
f_tmp.close()
file_list_cmd = "ls " + out_prefix + \
" |grep tmp.protein.file > " + protein_file_list
#print file_list_cmd
subprocess.call(file_list_cmd, shell=True)
exedir = os.path.dirname(os.path.abspath(__file__))
RNAScore2 = os.path.join(exedir, "../src/RNAScore2")
with open(protein_file_list, "rU") as fp:
for tmp in fp.readlines():
tmp = tmp.strip()
tmpfile = os.path.join(out_prefix, tmp)
tmpout = os.path.join(out_prefix, tmp + ".pro_score")
protein_cmd = RNAScore2 + " -i " + tmpfile + " -o " + tmpout + " -p"
#print protein_cmd
subprocess.call(protein_cmd, shell=True)
combine_cmd = "cat " + tmpout + " >> " + protein_out
#print combine_cmd
subprocess.call(combine_cmd, shell=True)
os.remove(tmpfile)
os.remove(tmpout)
fp.close()
#####################
os.remove(protein_file_list)
os.remove(tmp_stride_dat)
return protein_out
def GeneratePairs(rna_file, pro_file, out_prefix):
'''generate all rna_protein pairs'''
rnaID = GetFasta(rna_file)[0]
proID = GetFasta(pro_file)[0]
# generate can
pair_file_list = []
rna_id_list = []
for rnaid in rnaID:
tmp_pair = out_prefix + "." + rnaid.split("|")[0]
with open(tmp_pair, "w") as fo:
for proid in proID:
fo.write(rnaid + " " + proid + "\n")
pair_file_list.append(tmp_pair)
rna_id_list.append(rnaid)
fo.close()
return [rna_id_list, pair_file_list]
def GenEDPfeature(rna_file, pro_file, logscore_dict=None):
'''generate rna, protein features'''
rna_fea_1 = {}
rna_fea_2 = {}
pro_fea = {}
rna_ID, rna_Seq = GetFasta(rna_file)
pro_ID, pro_Seq = GetFasta(pro_file)
for rna_id, rna_seq in zip(rna_ID, rna_Seq):
nn_edp_fea, rna_lncfea = GetRNAfea(rna_seq, logscore_dict)
rna_fea_1[rna_id] = nn_edp_fea
rna_fea_2[rna_id] = rna_lncfea
for pro_id, pro_seq in zip(pro_ID, pro_Seq):
aa_edp_fea = GetPROfea(pro_seq)
pro_fea[pro_id] = aa_edp_fea
return [rna_fea_1, rna_fea_2, pro_fea]
def ReadProtein(pro_fa):
'''Read proteins fasta'''
SeqID, SeqList = GetFasta(pro_fa)
# lncRNA sequence
protein_dict = {}
for seqid, seq in zip(SeqID, SeqList):
protein_dict[seqid] = seq
return protein_dict
def ReadLncRNA(lncRNA_fa):
'''Read lncRNAs fasta'''
SeqID, SeqList = GetFasta(lncRNA_fa)
# lncRNA sequence
lncRNA_dict = {}
intap = "U"
outap = "T"
transtap = maketrans(intap, outap)
for seqid, seq in zip(SeqID, SeqList):
lncRNA_dict[seqid] = seq.translate(transtap)
return lncRNA_dict
def RNA_StructureScore(rna_file, out_prefix=None):
'''to compute structure features of rnas and proteins'''
rna_out = os.path.join(out_prefix, "rna_score")
#####################
# lncRNA structure
rna_file_part = os.path.join(out_prefix, "tmp.rna.file.")
rna_file_list = os.path.join(out_prefix, "tmp.filelist")
rnaID, rnaSeq = GetFasta(rna_file)
i = 0
for rnaid, rnaseq in zip(rnaID, rnaSeq):
f_tmp = open(rna_file_part + str(i), "w")
i += 1
f_tmp.write(">" + rnaid + "\n")
f_tmp.write(rnaseq + "\n")
f_tmp.close()
file_list_cmd = "ls " + out_prefix + " |grep tmp.rna.file > " + rna_file_list
#print file_list_cmd
subprocess.call(file_list_cmd, shell=True)
exedir = os.path.dirname(os.path.abspath(__file__))
RNAScore2 = os.path.join(exedir, "../src/RNAScore2")
with open(rna_file_list, "rU") as fr:
for tmp in fr.readlines():
tmp = tmp.strip()
tmpfile = os.path.join(out_prefix, tmp)
tmpout = os.path.join(out_prefix, tmp + ".r_score")
rna_cmd = RNAScore2 + " -i " + tmpfile + " -o " + tmpout + " -l 250 -r"
#print rna_cmd
subprocess.call(rna_cmd, shell=True)
combine_cmd = "cat " + tmpout + " >> " + rna_out
#print combine_cmd
subprocess.call(combine_cmd, shell=True)
os.remove(tmpfile)
os.remove(tmpout)
fr.close()
#####################
os.remove(rna_file_list)
return rna_out
def GenerateTrans(fasta, outfile):
'''generate translated fasta file'''
try:
f = open(outfile, "w")
except (IOError, ValueError) as e:
print >> sys.stderr, str(e)
sys.exit(1)
SeqID, SeqList = GetFasta(fasta)
#print "Translate to AA"
for seqid, seq in zip(SeqID, SeqList):
tmp_protein_list = SixFrame(seq, direction=1)
for tmp_protein in tmp_protein_list:
f.write("".join([">", seqid]) + "\n")
f.write(tmp_protein + "\n")
f.close()
def GenAnnoEDPfeature(rna_file, pro_file, logscore_dict=None):
'''generate rna, protein features'''
rna_fea_1 = {}
rna_fea_2 = {}
pro_fea = {}
rna_ID, rna_Seq = GetFasta(rna_file)
for rna_id, rna_seq in zip(rna_ID, rna_Seq):
nn_edp_fea, rna_lncfea = GetRNAfea(rna_seq, logscore_dict)
rna_fea_1[rna_id] = nn_edp_fea
rna_fea_2[rna_id] = rna_lncfea
exedir = os.path.dirname(os.path.abspath(__file__))
pro_fea_file = os.path.join(exedir,
"../src/Swiss-Uniprot.human.protein.seq_fea")
fp1 = open(pro_fea_file, "rU")
for line in fp1.readlines():
line = line.strip()
pro_fea[line.split()[0]] = "\t".join(line.split()[1:])
fp1.close()
return [rna_fea_1, rna_fea_2, pro_fea]
def HexamerFrequency(fasta):
'''count the hexamer usage as features'''
HexamerCount = {}
for k in _6mer_list:
HexamerCount[k] = 0.0
SeqID, SeqList = GetFasta(fasta)
totalcount = 0.0
for seq in SeqList:
ORF = GetORF(seq)
if (len(ORF) > 3):
num = len(ORF) / 3
for i in range(0, num - 1):
totalcount += 1.0
tmp = ORF[i * 3:(i + 2) * 3]
if HexamerCount.has_key(tmp):
HexamerCount[tmp] += 1.0
for k, v in HexamerCount.items():
HexamerCount[k] = v / totalcount
return HexamerCount