Mercurial > repos > rnateam > infer_rnaformer

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer commit a0639f646e953fe490559b10bb7271a67d07cac4
author iuc
date Fri, 07 Mar 2025 15:22:24 +0000
parents 02b0ecc34d9a
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6c310acd2f87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer commit a0639f646e953fe490559b10bb7271a67d07cac4
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1 <tool id="infer_rnaformer" name="@EXECUTABLE@" version="@TOOL_VERSION@+galaxy1" profile="22.05">
0
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2 <description>Predict the secondary structure of an RNA with RNAformer</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements">
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7 <requirement type="package" version="1.83">biopython</requirement>
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8 <requirement type="package" version="3.7.2">matplotlib</requirement>
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9 <requirement type="package" version="0.13.2">seaborn</requirement>
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10 <requirement type="package" version="2.32.3">requests</requirement>
0
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11 </expand>
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12 <command detect_errors="exit_code"><![CDATA[python '$script_file' > '$output']]></command>
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13 <configfiles>
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14 <configfile name="script_file"><![CDATA[import RNAformer
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15 import os
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16 import argparse
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17 import torch
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18 import urllib.request
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19 import logging
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20 from collections import defaultdict
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21 import torch.cuda
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22 import loralib as lora
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23 from RNAformer.model.RNAformer import RiboFormer
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24 from RNAformer.utils.configuration import Config
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25
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26 from Bio import SeqIO
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27
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28 import logging
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29 import sys
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1
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31 import matplotlib
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32 matplotlib.use("Agg")
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33 import matplotlib.pyplot as plt
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34 import seaborn as sns
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35 import shutil
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36 import datetime
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37 import requests
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38
0
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39 def is_valid_rna_sequence(sequence):
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40 """Check if the sequence contains only RNA bases."""
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41 valid_bases = {'A', 'C', 'G', 'U', 'N'} # Include 'N' if unknown bases are allowed
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42 return all(base in valid_bases for base in sequence.upper())
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43
1
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44 def download_file(url, destination):
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45 response = requests.get(url, stream=True)
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46 response.raise_for_status()
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47 with open(destination, 'wb') as file:
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48 for chunk in response.iter_content(chunk_size=8192):
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49 file.write(chunk)
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50
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51 model_url = "https://ml.informatik.uni-freiburg.de/research-artifacts/RNAformer/models/RNAformer_32M_state_dict_intra_family_finetuned.pth"
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52 config_url = "https://ml.informatik.uni-freiburg.de/research-artifacts/RNAformer/models/RNAformer_32M_config_intra_family_finetuned.yml"
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53
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54 model_file_path = "./model/RNAformer_32M_state_dict_intra_family_finetuned.pth"
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55 config_file_path = "./model/RNAformer_32M_config_intra_family_finetuned.yml"
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56
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57 os.makedirs("./model", exist_ok=True)
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58
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59 model = '$model'
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60 model_config = '$model_config'
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61
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62 if model and os.path.exists(model):
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63 model_file_path = model
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64 else:
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65 download_file(model_url, model_file_path)
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66
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67 if model_config and os.path.exists(model_config):
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68 config_file_path = model_config
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69 else:
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70 download_file(config_url, config_file_path)
0
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71
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72 config = Config(config_file=config_file_path)
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73 config.RNAformer.cycling = 6
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74 model = RiboFormer(config.RNAformer)
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75 state_dict_file = model_file_path
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76
1
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77 matrix_color_type = '$matrix_color_type'
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78 matrix_out_type = '$matrix_out_type'
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79
0
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80 #if str($input_type.input_type) == 'True'
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81 fasta_path = '$input_type.fasta_input'
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82 sequences = [str(record.seq) for record in SeqIO.parse(fasta_path, 'fasta')]
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83 #else
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diff changeset
84 sequence_string = "$input_type.rna_input_string"
02b0ecc34d9a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer commit ee837e8d27a53baa3d4881412d4fbc566ae06499
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diff changeset
85 sequences = [seq.strip() for seq in sequence_string.split(',')]
02b0ecc34d9a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer commit ee837e8d27a53baa3d4881412d4fbc566ae06499
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diff changeset
86 #end if
02b0ecc34d9a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer commit ee837e8d27a53baa3d4881412d4fbc566ae06499
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diff changeset
87
02b0ecc34d9a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer commit ee837e8d27a53baa3d4881412d4fbc566ae06499
rnateam
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diff changeset
88 for seq in sequences:
02b0ecc34d9a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer commit ee837e8d27a53baa3d4881412d4fbc566ae06499
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diff changeset
89 if not is_valid_rna_sequence(seq):
02b0ecc34d9a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer commit ee837e8d27a53baa3d4881412d4fbc566ae06499
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diff changeset
90 print(f"Invalid RNA sequence detected: {seq}. Please ensure only RNA sequences are used as input.", file=sys.stderr)
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diff changeset
91 sys.exit(1)
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92
02b0ecc34d9a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer commit ee837e8d27a53baa3d4881412d4fbc566ae06499
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diff changeset
93 lora_config = {
02b0ecc34d9a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer commit ee837e8d27a53baa3d4881412d4fbc566ae06499
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94 "r": config.r,
02b0ecc34d9a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer commit ee837e8d27a53baa3d4881412d4fbc566ae06499
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95 "lora_alpha": config.lora_alpha,
02b0ecc34d9a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer commit ee837e8d27a53baa3d4881412d4fbc566ae06499
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96 "lora_dropout": config.lora_dropout,
02b0ecc34d9a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer commit ee837e8d27a53baa3d4881412d4fbc566ae06499
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97 }
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98
02b0ecc34d9a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer commit ee837e8d27a53baa3d4881412d4fbc566ae06499
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diff changeset
99 with torch.no_grad():
02b0ecc34d9a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer commit ee837e8d27a53baa3d4881412d4fbc566ae06499
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diff changeset
100 for name, module in model.named_modules():
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101 if any(replace_key in name for replace_key in config.replace_layer):
02b0ecc34d9a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer commit ee837e8d27a53baa3d4881412d4fbc566ae06499
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102 parent = model.get_submodule(".".join(name.split(".")[:-1]))
02b0ecc34d9a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer commit ee837e8d27a53baa3d4881412d4fbc566ae06499
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103 target_name = name.split(".")[-1]
02b0ecc34d9a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer commit ee837e8d27a53baa3d4881412d4fbc566ae06499
rnateam
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104 target = model.get_submodule(name)
02b0ecc34d9a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer commit ee837e8d27a53baa3d4881412d4fbc566ae06499
rnateam
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105 if isinstance(target, torch.nn.Linear) and "qkv" in name:
02b0ecc34d9a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer commit ee837e8d27a53baa3d4881412d4fbc566ae06499
rnateam
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diff changeset
106 new_module = lora.MergedLinear(target.in_features, target.out_features,
02b0ecc34d9a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer commit ee837e8d27a53baa3d4881412d4fbc566ae06499
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diff changeset
107 bias=target.bias is not None,
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rnateam
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diff changeset
108 enable_lora=[True, True, True], **lora_config)
02b0ecc34d9a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer commit ee837e8d27a53baa3d4881412d4fbc566ae06499
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diff changeset
109 new_module.weight.copy_(target.weight)
02b0ecc34d9a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer commit ee837e8d27a53baa3d4881412d4fbc566ae06499
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110 if target.bias is not None:
02b0ecc34d9a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer commit ee837e8d27a53baa3d4881412d4fbc566ae06499
rnateam
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diff changeset
111 new_module.bias.copy_(target.bias)
02b0ecc34d9a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer commit ee837e8d27a53baa3d4881412d4fbc566ae06499
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diff changeset
112 elif isinstance(target, torch.nn.Linear):
02b0ecc34d9a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer commit ee837e8d27a53baa3d4881412d4fbc566ae06499
rnateam
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diff changeset
113 new_module = lora.Linear(target.in_features, target.out_features,
02b0ecc34d9a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer commit ee837e8d27a53baa3d4881412d4fbc566ae06499
rnateam
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diff changeset
114 bias=target.bias is not None, **lora_config)
02b0ecc34d9a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer commit ee837e8d27a53baa3d4881412d4fbc566ae06499
rnateam
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diff changeset
115 new_module.weight.copy_(target.weight)
02b0ecc34d9a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer commit ee837e8d27a53baa3d4881412d4fbc566ae06499
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diff changeset
116 if target.bias is not None:
02b0ecc34d9a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer commit ee837e8d27a53baa3d4881412d4fbc566ae06499
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diff changeset
117 new_module.bias.copy_(target.bias)
02b0ecc34d9a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer commit ee837e8d27a53baa3d4881412d4fbc566ae06499
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118
02b0ecc34d9a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer commit ee837e8d27a53baa3d4881412d4fbc566ae06499
rnateam
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diff changeset
119 elif isinstance(target, torch.nn.Conv2d):
02b0ecc34d9a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer commit ee837e8d27a53baa3d4881412d4fbc566ae06499
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diff changeset
120 kernel_size = target.kernel_size[0]
02b0ecc34d9a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer commit ee837e8d27a53baa3d4881412d4fbc566ae06499
rnateam
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diff changeset
121 new_module = lora.Conv2d(target.in_channels, target.out_channels, kernel_size,
02b0ecc34d9a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer commit ee837e8d27a53baa3d4881412d4fbc566ae06499
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diff changeset
122 padding=(kernel_size - 1) // 2, bias=target.bias is not None,
02b0ecc34d9a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer commit ee837e8d27a53baa3d4881412d4fbc566ae06499
rnateam
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diff changeset
123 **lora_config)
02b0ecc34d9a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer commit ee837e8d27a53baa3d4881412d4fbc566ae06499
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124
02b0ecc34d9a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer commit ee837e8d27a53baa3d4881412d4fbc566ae06499
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diff changeset
125 new_module.conv.weight.copy_(target.weight)
02b0ecc34d9a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer commit ee837e8d27a53baa3d4881412d4fbc566ae06499
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diff changeset
126 if target.bias is not None:
02b0ecc34d9a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer commit ee837e8d27a53baa3d4881412d4fbc566ae06499
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diff changeset
127 new_module.conv.bias.copy_(target.bias)
02b0ecc34d9a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer commit ee837e8d27a53baa3d4881412d4fbc566ae06499
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128 setattr(parent, target_name, new_module)
02b0ecc34d9a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer commit ee837e8d27a53baa3d4881412d4fbc566ae06499
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129
02b0ecc34d9a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer commit ee837e8d27a53baa3d4881412d4fbc566ae06499
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diff changeset
130 state_dict = torch.load(state_dict_file, map_location=torch.device('cpu'))
02b0ecc34d9a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer commit ee837e8d27a53baa3d4881412d4fbc566ae06499
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131
02b0ecc34d9a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer commit ee837e8d27a53baa3d4881412d4fbc566ae06499
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diff changeset
132 model.load_state_dict(state_dict, strict=True)
02b0ecc34d9a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer commit ee837e8d27a53baa3d4881412d4fbc566ae06499
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diff changeset
133 model_name = state_dict_file.split(".pth")[0]
02b0ecc34d9a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer commit ee837e8d27a53baa3d4881412d4fbc566ae06499
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134
02b0ecc34d9a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer commit ee837e8d27a53baa3d4881412d4fbc566ae06499
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diff changeset
135 if torch.cuda.is_available():
02b0ecc34d9a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer commit ee837e8d27a53baa3d4881412d4fbc566ae06499
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diff changeset
136 model = model.cuda()
02b0ecc34d9a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer commit ee837e8d27a53baa3d4881412d4fbc566ae06499
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diff changeset
137
02b0ecc34d9a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer commit ee837e8d27a53baa3d4881412d4fbc566ae06499
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diff changeset
138 # check GPU can do bf16
02b0ecc34d9a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer commit ee837e8d27a53baa3d4881412d4fbc566ae06499
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diff changeset
139 if torch.cuda.is_bf16_supported():
02b0ecc34d9a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer commit ee837e8d27a53baa3d4881412d4fbc566ae06499
rnateam
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diff changeset
140 model = model.bfloat16()
02b0ecc34d9a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer commit ee837e8d27a53baa3d4881412d4fbc566ae06499
rnateam
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diff changeset
141 else:
02b0ecc34d9a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer commit ee837e8d27a53baa3d4881412d4fbc566ae06499
rnateam
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diff changeset
142 model = model.half()
02b0ecc34d9a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer commit ee837e8d27a53baa3d4881412d4fbc566ae06499
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diff changeset
143
02b0ecc34d9a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer commit ee837e8d27a53baa3d4881412d4fbc566ae06499
rnateam
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diff changeset
144 model.eval()
02b0ecc34d9a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer commit ee837e8d27a53baa3d4881412d4fbc566ae06499
rnateam
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diff changeset
145 predicted_structures = []
02b0ecc34d9a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer commit ee837e8d27a53baa3d4881412d4fbc566ae06499
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diff changeset
146
1
6c310acd2f87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer commit a0639f646e953fe490559b10bb7271a67d07cac4
iuc
parents: 0
diff changeset
147 orig_seq = ""
6c310acd2f87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer commit a0639f646e953fe490559b10bb7271a67d07cac4
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diff changeset
148
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iuc
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diff changeset
149 job_name = '$job_name'
6c310acd2f87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer commit a0639f646e953fe490559b10bb7271a67d07cac4
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diff changeset
150
6c310acd2f87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer commit a0639f646e953fe490559b10bb7271a67d07cac4
iuc
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diff changeset
151 if job_name == "":
6c310acd2f87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer commit a0639f646e953fe490559b10bb7271a67d07cac4
iuc
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diff changeset
152 job_name = f"RNAformer_{datetime.datetime.now().strftime('%Y-%m-%d_%H-%M-%S')}"
6c310acd2f87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer commit a0639f646e953fe490559b10bb7271a67d07cac4
iuc
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diff changeset
153
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iuc
parents: 0
diff changeset
154 count = 0
6c310acd2f87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer commit a0639f646e953fe490559b10bb7271a67d07cac4
iuc
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diff changeset
155 os.makedirs(f'./{job_name}', exist_ok=True)
6c310acd2f87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer commit a0639f646e953fe490559b10bb7271a67d07cac4
iuc
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diff changeset
156
6c310acd2f87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer commit a0639f646e953fe490559b10bb7271a67d07cac4
iuc
parents: 0
diff changeset
157 total_output_buffer = []
6c310acd2f87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer commit a0639f646e953fe490559b10bb7271a67d07cac4
iuc
parents: 0
diff changeset
158
0
02b0ecc34d9a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer commit ee837e8d27a53baa3d4881412d4fbc566ae06499
rnateam
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diff changeset
159 for sequence in sequences:
1
6c310acd2f87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer commit a0639f646e953fe490559b10bb7271a67d07cac4
iuc
parents: 0
diff changeset
160 output_buffer = []
6c310acd2f87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer commit a0639f646e953fe490559b10bb7271a67d07cac4
iuc
parents: 0
diff changeset
161 seq_dir = f'./{job_name}/{job_name}_{count}'
6c310acd2f87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer commit a0639f646e953fe490559b10bb7271a67d07cac4
iuc
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diff changeset
162 os.makedirs(seq_dir, exist_ok=True)
0
02b0ecc34d9a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer commit ee837e8d27a53baa3d4881412d4fbc566ae06499
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diff changeset
163 with torch.no_grad():
02b0ecc34d9a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer commit ee837e8d27a53baa3d4881412d4fbc566ae06499
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diff changeset
164 device = "cpu"
02b0ecc34d9a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer commit ee837e8d27a53baa3d4881412d4fbc566ae06499
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165
02b0ecc34d9a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer commit ee837e8d27a53baa3d4881412d4fbc566ae06499
rnateam
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diff changeset
166 seq_vocab = ['A', 'C', 'G', 'U', 'N']
02b0ecc34d9a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer commit ee837e8d27a53baa3d4881412d4fbc566ae06499
rnateam
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diff changeset
167 seq_stoi = dict(zip(seq_vocab, range(len(seq_vocab))))
02b0ecc34d9a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer commit ee837e8d27a53baa3d4881412d4fbc566ae06499
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168
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169 pdb_sample = 1
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170
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171 length = len(sequence)
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172 src_seq = torch.LongTensor(list(map(seq_stoi.get, sequence)))
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173
1
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diff changeset
174 orig_seq = sequence
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175
0
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176 sample = {}
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177 sample['src_seq'] = src_seq.clone()
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178 sample['length'] = torch.LongTensor([length])[0]
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179 sample['pdb_sample'] = torch.LongTensor([pdb_sample])[0]
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180
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181 sequence = sample['src_seq'].unsqueeze(0).to(device)
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182 src_len = torch.LongTensor([sequence.shape[-1]]).to(device)
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183 pdb_sample = torch.FloatTensor([[1]]).to(device)
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184
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185 logits, pair_mask = model(sequence, src_len, pdb_sample)
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186
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187 pred_mat = torch.sigmoid(logits[0, :, :, -1]) > 0.5
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188
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189 pos_id = torch.where(pred_mat == True)
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190 pos1_id = pos_id[0].cpu().tolist()
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191 pos2_id = pos_id[1].cpu().tolist()
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192 predicted_structure = f"Pairing index 1: {pos1_id} \nPairing index 2: {pos2_id}"
1
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193 pairs = [[a, b] for a, b in zip(pos1_id, pos2_id)]
0
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194
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195 seqlen = len(sample['src_seq'])
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196 dot_bracket =['.'] * seqlen
1
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197 pk_count = 0
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198 pk_list = []
0
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199 for i in range(len(pos1_id)):
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200 open_index = pos1_id[i]
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201 close_index = pos2_id[i]
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202
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203 if 0 <= open_index < len(dot_bracket) and 0 <= close_index < len(dot_bracket):
02b0ecc34d9a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer commit ee837e8d27a53baa3d4881412d4fbc566ae06499
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204 if dot_bracket[open_index] == '.' and dot_bracket[close_index] == '.':
02b0ecc34d9a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer commit ee837e8d27a53baa3d4881412d4fbc566ae06499
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205 dot_bracket[open_index] = '('
02b0ecc34d9a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer commit ee837e8d27a53baa3d4881412d4fbc566ae06499
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206 dot_bracket[close_index] = ')'
1
6c310acd2f87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer commit a0639f646e953fe490559b10bb7271a67d07cac4
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207 else:
6c310acd2f87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer commit a0639f646e953fe490559b10bb7271a67d07cac4
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208 ## pseudoknots or multiplets present in structure- cannot represent with dot-bracket
6c310acd2f87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer commit a0639f646e953fe490559b10bb7271a67d07cac4
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diff changeset
209 pk_count += 1
6c310acd2f87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer commit a0639f646e953fe490559b10bb7271a67d07cac4
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210 pk_list.append(pairs[i])
0
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211 dot_bracket_str_pred = ''.join(dot_bracket)
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212
1
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213 output_buffer.append(f"Job name: {job_name}_{count}\n")
6c310acd2f87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer commit a0639f646e953fe490559b10bb7271a67d07cac4
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214 output_buffer.append(f"Sequence: {orig_seq}\n")
6c310acd2f87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer commit a0639f646e953fe490559b10bb7271a67d07cac4
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215 output_buffer.append(f"Length: {len(orig_seq)}\n")
6c310acd2f87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer commit a0639f646e953fe490559b10bb7271a67d07cac4
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diff changeset
216 output_buffer.append(f"Base pairs: {str(pairs)}\n")
6c310acd2f87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer commit a0639f646e953fe490559b10bb7271a67d07cac4
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217 output_buffer.append(f"Predicted Structure: {dot_bracket_str_pred}\n")
0
02b0ecc34d9a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer commit ee837e8d27a53baa3d4881412d4fbc566ae06499
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218
1
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219 if pk_count > 0:
6c310acd2f87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer commit a0639f646e953fe490559b10bb7271a67d07cac4
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220 output_buffer.append(f"NOTE: {pk_count} pseudoknots and/or multiplets present in predicted structure excluded from dot-bracket notation: {pk_list}\n")
6c310acd2f87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer commit a0639f646e953fe490559b10bb7271a67d07cac4
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221
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222 heatmaps_dir = './heatmaps'
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223 os.makedirs(heatmaps_dir, exist_ok=True)
6c310acd2f87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer commit a0639f646e953fe490559b10bb7271a67d07cac4
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224 plt.figure(figsize=(12, 10))
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225
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226 if matrix_color_type == 'color':
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227 raw_pred_mat = torch.sigmoid(logits[0, :, :, -1])
6c310acd2f87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer commit a0639f646e953fe490559b10bb7271a67d07cac4
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228 sns.heatmap(raw_pred_mat, cmap="inferno", vmin=0.0, vmax=1.0,
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229 xticklabels=list(orig_seq),
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230 yticklabels=list(orig_seq)
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diff changeset
231 )
6c310acd2f87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer commit a0639f646e953fe490559b10bb7271a67d07cac4
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diff changeset
232 plt.title(f"RNAformer Base-pair Probability Matrix")
6c310acd2f87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer commit a0639f646e953fe490559b10bb7271a67d07cac4
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233 plt.xticks(rotation=90)
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diff changeset
234 plt.tight_layout()
6c310acd2f87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer commit a0639f646e953fe490559b10bb7271a67d07cac4
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235 plt.savefig(f'{seq_dir}/RNAformer_structure_adjacency_matrix_color_{count}.{matrix_out_type}', dpi=150)
6c310acd2f87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer commit a0639f646e953fe490559b10bb7271a67d07cac4
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diff changeset
236 plt.close()
6c310acd2f87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer commit a0639f646e953fe490559b10bb7271a67d07cac4
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diff changeset
237 else:
6c310acd2f87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer commit a0639f646e953fe490559b10bb7271a67d07cac4
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diff changeset
238 sns.heatmap(pred_mat, cmap="gray", vmin=0.0, vmax=1.0,
6c310acd2f87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer commit a0639f646e953fe490559b10bb7271a67d07cac4
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diff changeset
239 xticklabels=list(orig_seq),
6c310acd2f87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer commit a0639f646e953fe490559b10bb7271a67d07cac4
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diff changeset
240 yticklabels=list(orig_seq)
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diff changeset
241 )
6c310acd2f87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer commit a0639f646e953fe490559b10bb7271a67d07cac4
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diff changeset
242 plt.title(f"RNAformer Base-pair Binary Probability Matrix")
6c310acd2f87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer commit a0639f646e953fe490559b10bb7271a67d07cac4
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diff changeset
243 plt.xticks(rotation=90)
6c310acd2f87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer commit a0639f646e953fe490559b10bb7271a67d07cac4
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diff changeset
244 plt.tight_layout()
6c310acd2f87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer commit a0639f646e953fe490559b10bb7271a67d07cac4
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diff changeset
245 plt.savefig(f'{seq_dir}/RNAformer_structure_adjacency_matrix_binary_{count}.{matrix_out_type}', dpi=150)
6c310acd2f87 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rnaformer commit a0639f646e953fe490559b10bb7271a67d07cac4
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diff changeset
246 plt.close()
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diff changeset
247
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diff changeset
248 full_text = "".join(output_buffer)
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249 with open(f"{seq_dir}/RNAformer_output.txt", "w", encoding="utf-8") as txt_file:
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250 txt_file.write(full_text)
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251 txt_file.write("\n")
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252
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253 total_output_buffer.append(full_text)
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254 total_output_buffer.append("\n")
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255
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256 full_job_output = "".join(total_output_buffer)
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257 with open(f"./RNAformer_job_output.txt", "w", encoding="utf-8") as txt_file:
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258 txt_file.write(full_job_output)
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259
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260 count += 1
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261
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262 shutil.make_archive('output', "zip", job_name)
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263
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264 ]]></configfile>
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265 </configfiles>
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266 <inputs>
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267 <conditional name="input_type">
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268 <param name="input_type" type="select" label="Input from FASTA file">
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269 <option value="False">Provide a single RNA sequence string as text</option>
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270 <option value="True">Provide a FASTA file</option>
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271 </param>
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272 <when value="False">
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273 <param name="rna_input_string" label="Sequence(s) to fold" type="text" value="GCCCGCAUGGUGAAAUCGGUAAACACAUCGCACUAAUGCGCCGCCUCUGGCUUGCCGGUUCAAGUCCGGCUGCGGGCACCA" help="Enter RNA sequences. Separate multiple RNA sequences by commas.">
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274 <sanitizer>
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275 <valid>
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276 <add value="ACGUacgu,"/>
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277 </valid>
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278 </sanitizer>
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279 </param>
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280 </when>
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281 <when value="True">
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282 <param format="fasta" name="fasta_input" type="data" label="Sequence to fold (FASTA file)"/>
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283 </when>
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284 </conditional>
1
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285 <param name="job_name" type="text" label="Job name" value="" help="Please edit job name for output files. Default will be RNAformer_{date}_{time}."/>
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286 <param name="model" type="data" format="binary" value="None" optional="true" label="Model" help="Manually download saved RNAformer model file to save time: https://ml.informatik.uni-freiburg.de/research-artifacts/RNAformer/models/RNAformer_32M_state_dict_intra_family_finetuned.pth"/>
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287 <param name="model_config" type="data" format="yml" value="None" optional="true" label="Model configuration" help="Manually download saved RNAformer model configuration file to save time: https://ml.informatik.uni-freiburg.de/research-artifacts/RNAformer/models/RNAformer_32M_config_intra_family_finetuned.yml"/>
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288 <param name="matrix_color_type" type="select" label="Coloring of base probability matrix">
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289 <option value="color">Color: base pair probabilities are shown and colored</option>
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290 <option value="binary">Binary: probabilities are binarized to show only final predicted structure without probabilities</option>
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291 </param>
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292 <param name="matrix_out_type" type="select" label="Base probability adjacency matrix heatmap format">
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293 <option value="pdf">PDF</option>
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294 <option value="eps">EPS</option>
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295 <option value="png">PNG</option>
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296 <option value="svg">SVG</option>
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297 </param>
0
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298 </inputs>
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299 <outputs>
1
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300 <data name="output" format="txt" label="RNAformer Base Pair Predictions" from_work_dir="RNAformer_job_output.txt"/>
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301 <data name="output_files" format="zip" label="RNAformer Predicted Structures Output" from_work_dir="output.zip"/>
0
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302 </outputs>
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303 <tests>
1
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304 <!-- Test 1: Single sequence as text input, color matrix PDF -->
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305 <test>
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306 <param name="input_type" value="False"/>
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307 <param name="rna_input_string" value="GCCCGCAUGGUGAAAUCGGUAAACACAUCGCACUAAUGCGCCGCCUCUGGCUUGCCGGUUCAAGUCCGGCUGCGGGCACCA"/>
1
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308 <param name="job_name" value="RNAformer_Prediction_Test_1"/>
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309 <param name="matrix_out_type" value="pdf"/>
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310 <param name="matrix_color_type" value="color"/>
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311 <output name="output" file="RNAformer_job_output.txt"/>
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312 <output name="output_files">
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313 <assert_contents>
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314 <has_size min="1" />
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315 </assert_contents>
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316 </output>
0
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317 </test>
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318 </tests>
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319 <help><![CDATA[
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320 **RNAformer**
1
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321 The tool reads RNA sequences and predicts their secondary structure using RNAformer. Note that unlike conventional methods, RNAformer is capable of predicting all possible secondary structure motifs, including pseudoknots and multiplets. These currently will not be represented in dot-bracket notation and thus the output will be partial in these cases, excluding these which will be noted in the output file below the (partial) dot-bracket structure. However, the full structure will be represented in the adjacency matrix heatmap. Tip: To speed up inference time, you can manually download the model and model configuration files from the following URLs (select "Upload Data" -> "Paste/Fetch Data" and copy the following URLs): `https://ml.informatik.uni-freiburg.de/research-artifacts/RNAformer/models/RNAformer_32M_state_dict_intra_family_finetuned.pth https://ml.informatik.uni-freiburg.de/research-artifacts/RNAformer/models/RNAformer_32M_config_intra_family_finetuned.yml`
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322
0
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323 **Input format**
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324
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325 RNAformer requires one or more RNA sequences either as a single FASTA file or as plain text.
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326
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327 **Outputs**
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328
1
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329 - Predicted secondary structures as a text file for all sequences provided containing the following:
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330 - Job name (with index based on order of input sequences in either plain text or FASTA file)
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331 - RNA input sequence
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332 - Length of input sequence
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333 - Base pairs of predicted secondary structure
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334 - Predicted secondary structure in dot-bracket notation (excluding pseudoknots and multiplets)
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335 - Optional: pseudoknots and/or multiplets present in predicted structure excluded from dot-bracket notation
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336 - A zip file containing:
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337 - Sub-directory for each input sequence with the name <job_name>_<index> containing:
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338 - Predicted secondary structure text file (same as above)
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339 - Heatmap of base pair probability matrix
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340
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341
0
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342 ]]></help>
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343 <expand macro="citations" />
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344 </tool>