import?tensorflow?as?tf
import?numpy?as?np
import?os
from?tqdm?import?tqdm
import?argparse
from?utils?import?create_tfr_files?prob_to_secondary_structure
import?time
start?=?time.time（）
from?argparse?import?RawTextHelpFormatter

parser?=?argparse.ArgumentParser（）
parser.add_argument（‘--inputs‘?default=‘sample_inputs/2zzm-B.fasta‘?type=str?help=‘Path?to?input?file?in?fasta?format?accept?multiple?sequences?as?well?in?fasta?format;?default?=?‘‘sample_inputs/2zzm-1-B.fasta‘‘\n‘?metavar=‘‘）
parser.add_argument（‘--outputs‘default=‘outputs/‘?type=str?help=‘Path?to?output?files;?SPOT-RNA?outputs?at?least?three?files?.ct?.bpseq?and?.prob?files;?default?=?‘‘outputs/\n‘?metavar=‘‘）
parser.add_argument（‘--gpu‘?default=-1?type=int?help=‘To?run?on?GPU?specifiy?GPU?number.?If?only?one?GPU?in?computer?specifiy?0;?default?=?-1?（no?GPU）\n‘?metavar=‘‘）
parser.add_argument（‘--plots‘default=False?type=bool?help=‘Set?this?to?“True“?to?get?the?2D?plots?of?predicted?secondary?structure?by?SPOT-RNA;?default?=?False\n‘?metavar=‘‘）
parser.add_argument（‘--motifs‘default=False?type=bool?help=‘Set?this?to?“True“?to?get?the?motifs?of?predicted?secondary?structure?by?SPOT-RNA;?default?=?False\n‘?metavar=‘‘）
#parser.add_argument（‘--NC‘default=True?type=bool?help=‘Set?this?to?“False“?to?predict?only?canonical?pairs;?default?=?True\n‘?metavar=‘‘）
args?=?parser.parse_args（）

os.environ[‘TF_CPP_MIN_LOG_LEVEL‘]?=?‘3‘
tf.compat.v1.logging.set_verbosity（tf.compat.v1.logging.ERROR）

create_tfr_files（args.inputs）

with?open（args.inputs）?as?file:
????input_data?=?[line.strip（）?for?line?in?file.read（）.splitlines（）?if?line.strip（）]

count?=?int（len（input_data）/2）

ids?=?[input_data[2*i].replace（“>“?““）?for?i?in?range（count）]
sequences?=?{}
for?iI?in?enumerate（ids）:
????sequences[I]?=?input_data[2*i+1].replace（“?“?““）.replace（“T“?“U“）.upper（）

os.environ[“CUDA_VISIBLE_DEVICES“]=?str（args.gpu）
#os.environ[‘TF_CPP_MIN_LOG_LEVEL‘]?=?‘3‘?
NUM_MODELS?=?5

test_loc?=?[“input_tfr_files/test_data.tfrecords“]

outputs?=?{}
mask?=?{}
def?sigmoid（x）:
????return?1/（1+np.exp（-np.array（x?dtype=np.float128）））

for?MODEL?in?range（NUM_MODELS）:
????config?=?tf.compat.v1.ConfigProto（）
????#config.gpu_options.allow_growth?=?True
????config.allow_soft_placement=True
????config.log_device_placement=False
????#session_conf?=?tf.ConfigProto（intra_op_parallelism_threads=1?inter_op_parallelism_threads=1）
????#sess?=?tf.Session（config=session_conf）
????print（‘\nPredicting?for?SPOT-RNA?model?‘+str（MODEL））
????with?tf.compat.v1.Session（config=config）?as?sess:
????????saver?=?tf.compat.v1.train.import_meta_graph（‘SPOT-RNA-models‘+‘/model‘+str（MODEL）+‘.meta‘）
????????saver.restore（sess‘SPOT-RNA-models‘+‘/model‘+str（MODEL））
????????graph?=?tf.compat.v1.get_default_graph（）
????????init_test?=??graph.get_operation_by_name（‘make_initializer_2‘）
????????tmp_out?=?graph.get_tensor_by_name（‘output_FC/fully_connected/BiasAdd:0‘）
????????name_tensor?=?graph.get_tensor_by_name（‘tensors_2/componen

?屬性????????????大小?????日期????時間???名稱
-----------?---------??----------?-----??----
?????目錄???????????0??2020-03-05?00:34??SPOT-RNA-master\
?????文件???????16725??2020-03-05?00:34??SPOT-RNA-master\LICENSE
?????文件????????8845??2020-03-05?00:34??SPOT-RNA-master\README.md
?????文件?????1217434??2020-03-05?00:34??SPOT-RNA-master\SPOT-RNA-architecture.png
?????文件????????4188??2020-03-05?00:34??SPOT-RNA-master\SPOT-RNA.py
?????文件??????695802??2020-03-05?00:34??SPOT-RNA-master\VARNAv3-93.jar
?????目錄???????????0??2020-03-05?00:34??SPOT-RNA-master\__pycache__\
?????文件???????13869??2020-03-05?00:34??SPOT-RNA-master\__pycache__\utils.cpython-35.pyc
?????文件???????12314??2020-03-05?00:34??SPOT-RNA-master\__pycache__\utils.cpython-36.pyc
?????目錄???????????0??2020-03-05?00:34??SPOT-RNA-master\bpRNA-master\
?????文件????????3229??2020-03-05?00:34??SPOT-RNA-master\bpRNA-master\README
?????目錄???????????0??2020-03-05?00:34??SPOT-RNA-master\bpRNA-master\Segment?Graphs\
?????文件?????????787??2020-03-05?00:34??SPOT-RNA-master\bpRNA-master\Segment?Graphs\SegmentGraph_README
?????文件?????????553??2020-03-05?00:34??SPOT-RNA-master\bpRNA-master\Segment?Graphs\bpRNA_PDB_650.bpseq
?????文件????????8361??2020-03-05?00:34??SPOT-RNA-master\bpRNA-master\Segment?Graphs\bpRNA_PDB_650_PKGraph.svg
?????文件???????10976??2020-03-05?00:34??SPOT-RNA-master\bpRNA-master\Segment?Graphs\bpRNA_PDB_650_all_SegGraph.svg
?????文件????????3916??2020-03-05?00:34??SPOT-RNA-master\bpRNA-master\Segment?Graphs\bpRNA_PDB_650_pkf_SegGraph.svg
?????文件????????1603??2020-03-05?00:34??SPOT-RNA-master\bpRNA-master\Segment?Graphs\bpRNA_RFAM_34891.bpseq
?????文件????????2596??2020-03-05?00:34??SPOT-RNA-master\bpRNA-master\Segment?Graphs\bpRNA_RFAM_34891_PKGraph.svg
?????文件????????7495??2020-03-05?00:34??SPOT-RNA-master\bpRNA-master\Segment?Graphs\bpRNA_RFAM_34891_all_SegGraph.svg
?????文件????????5785??2020-03-05?00:34??SPOT-RNA-master\bpRNA-master\Segment?Graphs\bpRNA_RFAM_34891_pkf_SegGraph.svg
?????文件???????36467??2020-03-05?00:34??SPOT-RNA-master\bpRNA-master\Segment?Graphs\drawSegmentGraphs.pl
?????文件???????46704??2020-03-05?00:34??SPOT-RNA-master\bpRNA-master\bpRNA.pl
?????目錄???????????0??2020-03-05?00:34??SPOT-RNA-master\bpRNA-master\bpRNA_1m\
?????文件????????5131??2020-03-05?00:34??SPOT-RNA-master\bpRNA-master\bpRNA_1m\Create_bpRNA_1m.zip
?????文件??????161020??2020-03-05?00:34??SPOT-RNA-master\bpRNA-master\bpRNA_1m\bpRNA_1m_DatabaseDiagram.pdf
?????文件?????????851??2020-03-05?00:34??SPOT-RNA-master\bpRNA-master\bpRNA_1m\bpRNA_1m_README
?????文件????????1826??2020-03-05?00:34??SPOT-RNA-master\bpRNA-master\bpRNA_PDB_650.st
?????目錄???????????0??2020-03-05?00:34??SPOT-RNA-master\input_tfr_files\
?????文件??????623256??2020-03-05?00:34??SPOT-RNA-master\input_tfr_files\test_data.tfrecords
?????目錄???????????0??2020-03-05?00:34??SPOT-RNA-master\outputs\
............此處省略6個文件信息