Mercurial > repos > ebi-gxa > decoupler_pathway_inference

annotate decoupler_pseudobulk.py @ 12:4523224b53ce draft default tip

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author ebi-gxa
date Fri, 13 Jun 2025 09:08:13 +0000
parents db14ac3f6b43
children
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1 import argparse
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3 import anndata
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4 import decoupler
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5 import numpy as np
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6 import pandas as pd
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9 def get_pseudobulk(
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10 adata,
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11 sample_col,
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12 groups_col,
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13 layer=None,
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14 mode="sum",
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15 min_cells=10,
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16 min_counts=1000,
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17 use_raw=False,
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18 ):
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19 """
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20 >>> import scanpy as sc
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21 >>> adata = sc.datasets.pbmc68k_reduced()
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22 >>> adata.X = abs(adata.X).astype(int)
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23 >>> pseudobulk = get_pseudobulk(adata, "bulk_labels", "louvain")
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24 """
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26 return decoupler.get_pseudobulk(
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27 adata,
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28 sample_col=sample_col,
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29 groups_col=groups_col,
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30 layer=layer,
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31 mode=mode,
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32 use_raw=use_raw,
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33 min_cells=min_cells,
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34 min_counts=min_counts,
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35 )
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37
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38 def create_pseudo_replicates(adata, sample_key, num_replicates, seed=None):
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39 """
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40 Create pseudo replicates for each sample in the sample_key groups.
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42 Parameters
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43 ----------
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44 adata : anndata.AnnData
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45 The AnnData object.
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46 sample_key : str
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47 The column in adata.obs that defines the samples.
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48 num_replicates : int
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49 Number of pseudo replicates to create per sample.
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50
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51 Returns
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52 -------
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53 anndata.AnnData
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54 The AnnData object with pseudo replicates.
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55
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56 Examples
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57 --------
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58 >>> import anndata
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59 >>> import pandas as pd
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60 >>> import numpy as np
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61 >>> data = {
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62 ... 'obs': pd.DataFrame({'sample': ['A', 'A', 'B', 'B']}),
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63 ... 'X': np.array([[1, 0], [0, 1], [1, 1], [0, 0]])
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64 ... }
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65 >>> adata = anndata.AnnData(X=data['X'], obs=data['obs'])
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66 >>> adata = create_pseudo_replicates(adata, 'sample', 2)
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67 >>> adata.obs['sample_pseudo'].tolist()
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68 ['A_rep1', 'A_rep2', 'B_rep1', 'B_rep2']
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69 """
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70 if seed is not None:
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71 np.random.seed(seed)
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72
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73 new_sample_key = f"{sample_key}_pseudo"
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74 adata.obs[new_sample_key] = adata.obs[sample_key].astype(str)
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75
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76 for sample in adata.obs[sample_key].unique():
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77 sample_indices = adata.obs[
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78 adata.obs[sample_key] == sample].index.to_numpy()
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79 np.random.shuffle(sample_indices) # Shuffle the indices to randomize
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80 replicate_size = int(len(sample_indices) / num_replicates)
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81 for i in range(num_replicates):
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82 start_idx = i * replicate_size
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83 end_idx = start_idx + replicate_size
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84 replicate_indices = sample_indices[start_idx:end_idx]
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85 adata.obs.loc[replicate_indices, new_sample_key] = (
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86 adata.obs.loc[replicate_indices, new_sample_key] + f"_rep{i+1}"
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87 )
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88
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89 return adata
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90
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91
0
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92 def prepend_c_to_index(index_value):
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93 if index_value and index_value[0].isdigit():
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94 return "C" + index_value
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95 return index_value
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96
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97
3
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98 def genes_to_ignore_per_contrast_field(
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99 count_matrix_df,
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100 samples_metadata,
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101 sample_metadata_col_contrasts,
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102 min_counts_per_sample=5,
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103 use_cpms=False,
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104 ):
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105 """
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106 # This function calculates the genes to ignore per contrast field
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107 # (e.g., bulk_labels, louvain).
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108 # It does this by first getting the count matrix for each group,
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109 # then identifying genes with a count below a specified threshold.
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110 # The genes to ignore are those that are present in more than a specified
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111 # number of groups.
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112
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113 >>> import pandas as pd
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114 >>> samples_metadata = pd.DataFrame({'sample':
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115 ... ['S1', 'S2', 'S3',
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116 ... 'S4', 'S5', 'S6'],
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117 ... 'contrast_field':
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118 ... ['A', 'A', 'A', 'B', 'B', 'B']})
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119 >>> count_matrix_df = pd.DataFrame(
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120 ... {'S1':
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121 ... [30, 1, 40, 50, 30],
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122 ... 'S2':
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123 ... [40, 2, 60, 50, 80],
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124 ... 'S3':
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125 ... [80, 1, 60, 50, 50],
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126 ... 'S4': [1, 50, 50, 50, 2],
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127 ... 'S5': [3, 40, 40, 40, 2],
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128 ... 'S6': [0, 50, 50, 50, 1]})
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129 >>> count_matrix_df.index = ['Gene1', 'Gene2', 'Gene3', 'Gene4', 'Gene5']
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130 >>> df = genes_to_ignore_per_contrast_field(count_matrix_df,
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131 ... samples_metadata, min_counts_per_sample=5,
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132 ... sample_metadata_col_contrasts='contrast_field')
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133 >>> df[df['contrast_field'] == 'A'].genes_to_ignore.tolist()[0]
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134 'Gene2'
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135 >>> df[df['contrast_field'] == 'B'].genes_to_ignore.tolist()[0]
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136 'Gene1'
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137 >>> df[df['contrast_field'] == 'B'].genes_to_ignore.tolist()[1]
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138 'Gene5'
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139 """
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140
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141 # Initialize a dictionary to store the genes to ignore per contrast field
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142 contrast_fields = []
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143 genes_to_ignore = []
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144
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145 # Iterate over the contrast fields
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146 for contrast_field in samples_metadata[
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147 sample_metadata_col_contrasts
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148 ].unique():
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149 # Get the count matrix for the current contrast field
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150 count_matrix_field = count_matrix_df.loc[
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151 :,
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152 (
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153 samples_metadata[sample_metadata_col_contrasts]
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154 == contrast_field
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155 ).tolist(),
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156 ]
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157
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158 # We derive min_counts from the number of samples with that
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159 # contrast_field value
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160 min_counts = count_matrix_field.shape[1] * min_counts_per_sample
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161
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162 if use_cpms:
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163 # Convert counts to counts per million (CPM)
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164 count_matrix_field = (
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165 count_matrix_field.div(count_matrix_field.sum(axis=1), axis=0)
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166 * 1e6
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167 )
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168 min_counts = 1 # use 1 CPM
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169
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170 # Calculate the total number of cells in the current contrast field
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171 # (this produces a vector of counts per gene)
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172 total_counts_per_gene = count_matrix_field.sum(axis=1)
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173
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174 # Identify genes with a count below the specified threshold
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175 genes = total_counts_per_gene[
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176 total_counts_per_gene < min_counts
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177 ].index.tolist()
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178 if len(genes) > 0:
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179 # genes_to_ignore[contrast_field] = " ".join(genes)
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180 for gene in genes:
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181 genes_to_ignore.append(gene)
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182 contrast_fields.append(contrast_field)
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183 # transform gene_to_ignore to a DataFrame
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184 # genes_to_ignore_df = pd.DataFrame(genes_to_ignore.items(),
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185 # columns=["contrast_field", "genes_to_ignore"])
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186 genes_to_ignore_df = pd.DataFrame(
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187 {"contrast_field": contrast_fields, "genes_to_ignore": genes_to_ignore}
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188 )
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189 return genes_to_ignore_df
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190
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191
0
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192 # write results for loading into DESeq2
3
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193 def write_DESeq2_inputs(
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194 pdata,
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195 layer=None,
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196 output_dir="",
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197 factor_fields=None,
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198 min_counts_per_sample_marking=20,
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199 ):
0
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200 """
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201 >>> import scanpy as sc
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202 >>> adata = sc.datasets.pbmc68k_reduced()
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203 >>> adata.X = abs(adata.X).astype(int)
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204 >>> pseudobulk = get_pseudobulk(adata, "bulk_labels", "louvain")
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205 >>> write_DESeq2_inputs(pseudobulk)
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206 """
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207 # add / to output_dir if is not empty or if it doesn't end with /
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208 if output_dir != "" and not output_dir.endswith("/"):
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209 output_dir = output_dir + "/"
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210 obs_for_deseq = pdata.obs.copy()
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211 # replace any index starting with digits to start with C instead.
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212 obs_for_deseq.rename(index=prepend_c_to_index, inplace=True)
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213 # avoid dash that is read as point on R colnames.
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214 obs_for_deseq.index = obs_for_deseq.index.str.replace("-", "_")
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215 obs_for_deseq.index = obs_for_deseq.index.str.replace(" ", "_")
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216 col_metadata_file = f"{output_dir}col_metadata.tsv"
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217 # write obs to a col_metadata file
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218 if factor_fields:
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219 # only output the index plus the columns in factor_fields in that order
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220 obs_for_deseq[factor_fields].to_csv(
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221 col_metadata_file, sep="\t", index=True
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222 )
0
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223 else:
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224 obs_for_deseq.to_csv(col_metadata_file, sep="\t", index=True)
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225 # write var to a gene_metadata file
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226 pdata.var.to_csv(f"{output_dir}gene_metadata.tsv", sep="\t", index=True)
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227 # write the counts matrix of a specified layer to file
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228 if layer is None:
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229 # write the X numpy matrix transposed to file
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230 df = pd.DataFrame(
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231 pdata.X.T, index=pdata.var.index, columns=obs_for_deseq.index
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232 )
0
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233 else:
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234 df = pd.DataFrame(
3
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235 pdata.layers[layer].T,
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236 index=pdata.var.index,
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237 columns=obs_for_deseq.index,
0
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238 )
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239 df.to_csv(f"{output_dir}counts_matrix.tsv", sep="\t", index_label="")
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240
3
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241 if factor_fields:
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242 df_genes_ignore = genes_to_ignore_per_contrast_field(
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243 count_matrix_df=df,
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244 samples_metadata=obs_for_deseq,
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245 sample_metadata_col_contrasts=factor_fields[0],
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246 min_counts_per_sample=min_counts_per_sample_marking,
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247 )
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248 df_genes_ignore.to_csv(
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249 f"{output_dir}genes_to_ignore_per_contrast_field.tsv", sep="\t"
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250 )
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251
0
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252
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253 def plot_pseudobulk_samples(
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254 pseudobulk_data,
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255 groupby,
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256 figsize=(10, 10),
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257 save_path=None,
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258 ):
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259 """
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260 >>> import scanpy as sc
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261 >>> adata = sc.datasets.pbmc68k_reduced()
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262 >>> adata.X = abs(adata.X).astype(int)
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263 >>> pseudobulk = get_pseudobulk(adata, "bulk_labels", "louvain")
3
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264 >>> plot_pseudobulk_samples(pseudobulk,
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265 ... groupby=["bulk_labels", "louvain"],
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266 ... figsize=(10, 10))
0
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267 """
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268 fig = decoupler.plot_psbulk_samples(
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269 pseudobulk_data, groupby=groupby, figsize=figsize, return_fig=True
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270 )
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271 if save_path:
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272 fig.savefig(f"{save_path}/pseudobulk_samples.png")
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273 else:
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274 fig.show()
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275
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276
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277 def plot_filter_by_expr(
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278 pseudobulk_data,
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279 group,
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280 min_count=None,
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281 min_total_count=None,
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282 save_path=None,
0
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283 ):
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284 """
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285 >>> import scanpy as sc
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286 >>> adata = sc.datasets.pbmc68k_reduced()
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287 >>> adata.X = abs(adata.X).astype(int)
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288 >>> pseudobulk = get_pseudobulk(adata, "bulk_labels", "louvain")
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289 >>> plot_filter_by_expr(pseudobulk, group="bulk_labels",
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290 ... min_count=10, min_total_count=200)
0
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291 """
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292 fig = decoupler.plot_filter_by_expr(
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293 pseudobulk_data,
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294 group=group,
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295 min_count=min_count,
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296 min_total_count=min_total_count,
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297 return_fig=True,
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298 )
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299 if save_path:
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300 fig.savefig(f"{save_path}/filter_by_expr.png")
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301 else:
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302 fig.show()
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303
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304
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305 def filter_by_expr(pdata, min_count=None, min_total_count=None):
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306 """
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307 >>> import scanpy as sc
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308 >>> adata = sc.datasets.pbmc68k_reduced()
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309 >>> adata.X = abs(adata.X).astype(int)
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310 >>> pseudobulk = get_pseudobulk(adata, "bulk_labels", "louvain")
3
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311 >>> pdata_filt = filter_by_expr(pseudobulk,
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312 ... min_count=10, min_total_count=200)
0
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313 """
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314 genes = decoupler.filter_by_expr(
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315 pdata, min_count=min_count, min_total_count=min_total_count
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316 )
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317 return pdata[:, genes].copy()
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318
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319
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320 def check_fields(fields, adata, obs=True, context=None):
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321 """
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322 >>> import scanpy as sc
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323 >>> adata = sc.datasets.pbmc68k_reduced()
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324 >>> check_fields(["bulk_labels", "louvain"], adata, obs=True)
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325 """
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326
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327 # Fields that will be created during the pseudobulking process
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328 pseudobulk_generated_fields = ['psbulk_n_cells', 'psbulk_counts']
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329
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330 # Filter out the pseudobulk-generated fields from checking
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331 fields_to_check = [field for field in fields
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332 if field not in pseudobulk_generated_fields]
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333
0
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334 legend = ""
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335 if context:
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336 legend = f", passed in {context},"
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337 if obs:
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338 if not set(fields_to_check).issubset(set(adata.obs.columns)):
0
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339 raise ValueError(
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340 f"Some of the following fields {legend} are not present \
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341 in adata.obs: {fields_to_check}. \
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342 Possible fields are: {list(set(adata.obs.columns))}"
0
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343 )
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
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diff changeset
344 else:
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diff changeset
345 if not set(fields_to_check).issubset(set(adata.var.columns)):
0
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
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346 raise ValueError(
3
c6787c2aee46 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit eea5c13f9e6e070a2359c59400773b01f9cd7567
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347 f"Some of the following fields {legend} are not present \
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diff changeset
348 in adata.var: {fields_to_check}. \
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diff changeset
349 Possible fields are: {list(set(adata.var.columns))}"
0
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350 )
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
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351
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
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352
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
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353 def main(args):
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
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354 # Load AnnData object from file
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
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355 adata = anndata.read_h5ad(args.adata_file)
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
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356
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
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357 # Merge adata.obs fields specified in args.adata_obs_fields_to_merge
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
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358 if args.adata_obs_fields_to_merge:
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
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359 # first split potential groups by ":" and iterate over them
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
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360 for group in args.adata_obs_fields_to_merge.split(":"):
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
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361 fields = group.split(",")
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
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diff changeset
362 check_fields(fields, adata)
5
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diff changeset
363 merge_adata_obs_fields(fields, adata)
0
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
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diff changeset
364
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
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365 check_fields([args.groupby, args.sample_key], adata)
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
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366
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
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367 factor_fields = None
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
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368 if args.factor_fields:
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
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369 factor_fields = args.factor_fields.split(",")
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
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370 check_fields(factor_fields, adata)
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
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diff changeset
371
11
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diff changeset
372 # Create pseudo replicates if specified
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373 if args.num_pseudo_replicates:
db14ac3f6b43 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 487508282bda9dbb68138d5c7091f46ef54fe52a
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diff changeset
374 adata = create_pseudo_replicates(
db14ac3f6b43 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 487508282bda9dbb68138d5c7091f46ef54fe52a
ebi-gxa
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diff changeset
375 adata, args.sample_key, args.num_pseudo_replicates, seed=args.seed
db14ac3f6b43 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 487508282bda9dbb68138d5c7091f46ef54fe52a
ebi-gxa
parents: 7
diff changeset
376 )
db14ac3f6b43 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 487508282bda9dbb68138d5c7091f46ef54fe52a
ebi-gxa
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diff changeset
377 args.sample_key = f"{args.sample_key}_pseudo"
db14ac3f6b43 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 487508282bda9dbb68138d5c7091f46ef54fe52a
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diff changeset
378
0
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diff changeset
379 print(f"Using mode: {args.mode}")
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
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380 # Perform pseudobulk analysis
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381 pseudobulk_data = get_pseudobulk(
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
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diff changeset
382 adata,
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diff changeset
383 sample_col=args.sample_key,
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diff changeset
384 groups_col=args.groupby,
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diff changeset
385 layer=args.layer,
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diff changeset
386 mode=args.mode,
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diff changeset
387 use_raw=args.use_raw,
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
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diff changeset
388 min_cells=args.min_cells,
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
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diff changeset
389 min_counts=args.min_counts,
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diff changeset
390 )
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
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diff changeset
391
4
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diff changeset
392 print("Created pseudo-bulk AnnData, checking if fields still make sense.")
6c30272fb587 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 54818daabaf1251642a267e5766f13741cb7faeb
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diff changeset
393 print(
5
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diff changeset
394 "If this fails this check, it might mean that you asked for factors \
87f1eaa410cc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit dea8a066ccf04e241457719bf5162f9d39fe6c48
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diff changeset
395 that are not compatible with you sample identifiers (ie. asked for \
87f1eaa410cc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit dea8a066ccf04e241457719bf5162f9d39fe6c48
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diff changeset
396 phase in the factors, but each sample contains more than one phase,\
87f1eaa410cc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit dea8a066ccf04e241457719bf5162f9d39fe6c48
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diff changeset
397 try joining fields)."
4
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diff changeset
398 )
6c30272fb587 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 54818daabaf1251642a267e5766f13741cb7faeb
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diff changeset
399 if factor_fields:
6c30272fb587 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 54818daabaf1251642a267e5766f13741cb7faeb
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parents: 3
diff changeset
400 check_fields(
6c30272fb587 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 54818daabaf1251642a267e5766f13741cb7faeb
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diff changeset
401 factor_fields,
6c30272fb587 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 54818daabaf1251642a267e5766f13741cb7faeb
ebi-gxa
parents: 3
diff changeset
402 pseudobulk_data,
6c30272fb587 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 54818daabaf1251642a267e5766f13741cb7faeb
ebi-gxa
parents: 3
diff changeset
403 context=" after creation of pseudo-bulk AnnData",
6c30272fb587 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 54818daabaf1251642a267e5766f13741cb7faeb
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parents: 3
diff changeset
404 )
6c30272fb587 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 54818daabaf1251642a267e5766f13741cb7faeb
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diff changeset
405 print("Factors requested are adequate for the pseudo-bulked AnnData!")
6c30272fb587 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 54818daabaf1251642a267e5766f13741cb7faeb
ebi-gxa
parents: 3
diff changeset
406
0
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
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diff changeset
407 # Plot pseudobulk samples
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
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diff changeset
408 plot_pseudobulk_samples(
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
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diff changeset
409 pseudobulk_data,
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
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diff changeset
410 args.groupby,
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
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diff changeset
411 save_path=args.save_path,
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
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diff changeset
412 figsize=args.plot_samples_figsize,
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
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diff changeset
413 )
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
parents:
diff changeset
414
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
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parents:
diff changeset
415 plot_filter_by_expr(
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
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diff changeset
416 pseudobulk_data,
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
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diff changeset
417 group=args.groupby,
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
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diff changeset
418 min_count=args.min_counts,
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
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diff changeset
419 min_total_count=args.min_total_counts,
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
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diff changeset
420 save_path=args.save_path,
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
parents:
diff changeset
421 )
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
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parents:
diff changeset
422
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
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diff changeset
423 # Filter by expression if enabled
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
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diff changeset
424 if args.filter_expr:
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
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diff changeset
425 filtered_adata = filter_by_expr(
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
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diff changeset
426 pseudobulk_data,
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
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diff changeset
427 min_count=args.min_counts,
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
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diff changeset
428 min_total_count=args.min_total_counts,
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
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diff changeset
429 )
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
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diff changeset
430
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ebi-gxa
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diff changeset
431 pseudobulk_data = filtered_adata
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
parents:
diff changeset
432
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
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diff changeset
433 # Save the pseudobulk data
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
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diff changeset
434 if args.anndata_output_path:
3
c6787c2aee46 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit eea5c13f9e6e070a2359c59400773b01f9cd7567
ebi-gxa
parents: 0
diff changeset
435 pseudobulk_data.write_h5ad(
c6787c2aee46 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit eea5c13f9e6e070a2359c59400773b01f9cd7567
ebi-gxa
parents: 0
diff changeset
436 args.anndata_output_path, compression="gzip"
c6787c2aee46 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit eea5c13f9e6e070a2359c59400773b01f9cd7567
ebi-gxa
parents: 0
diff changeset
437 )
0
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
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diff changeset
438
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
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diff changeset
439 write_DESeq2_inputs(
3
c6787c2aee46 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit eea5c13f9e6e070a2359c59400773b01f9cd7567
ebi-gxa
parents: 0
diff changeset
440 pseudobulk_data,
c6787c2aee46 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit eea5c13f9e6e070a2359c59400773b01f9cd7567
ebi-gxa
parents: 0
diff changeset
441 output_dir=args.deseq2_output_path,
c6787c2aee46 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit eea5c13f9e6e070a2359c59400773b01f9cd7567
ebi-gxa
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diff changeset
442 factor_fields=factor_fields,
c6787c2aee46 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit eea5c13f9e6e070a2359c59400773b01f9cd7567
ebi-gxa
parents: 0
diff changeset
443 min_counts_per_sample_marking=args.min_counts_per_sample_marking,
0
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
parents:
diff changeset
444 )
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
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diff changeset
445
5
87f1eaa410cc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit dea8a066ccf04e241457719bf5162f9d39fe6c48
ebi-gxa
parents: 4
diff changeset
446 # if contrasts file is provided, produce a file with genes that should be
87f1eaa410cc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit dea8a066ccf04e241457719bf5162f9d39fe6c48
ebi-gxa
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diff changeset
447 # filtered for each contrasts
87f1eaa410cc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit dea8a066ccf04e241457719bf5162f9d39fe6c48
ebi-gxa
parents: 4
diff changeset
448 if args.contrasts_file:
87f1eaa410cc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit dea8a066ccf04e241457719bf5162f9d39fe6c48
ebi-gxa
parents: 4
diff changeset
449 contrast_genes_df = identify_genes_to_filter_per_contrast(
87f1eaa410cc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit dea8a066ccf04e241457719bf5162f9d39fe6c48
ebi-gxa
parents: 4
diff changeset
450 contrast_file=args.contrasts_file,
87f1eaa410cc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit dea8a066ccf04e241457719bf5162f9d39fe6c48
ebi-gxa
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451 min_perc_cells_expression=args.min_gene_exp_perc_per_cell,
87f1eaa410cc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit dea8a066ccf04e241457719bf5162f9d39fe6c48
ebi-gxa
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diff changeset
452 adata=adata,
87f1eaa410cc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit dea8a066ccf04e241457719bf5162f9d39fe6c48
ebi-gxa
parents: 4
diff changeset
453 obs_field=args.groupby
87f1eaa410cc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit dea8a066ccf04e241457719bf5162f9d39fe6c48
ebi-gxa
parents: 4
diff changeset
454 )
87f1eaa410cc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit dea8a066ccf04e241457719bf5162f9d39fe6c48
ebi-gxa
parents: 4
diff changeset
455 contrast_genes_df.to_csv(
87f1eaa410cc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit dea8a066ccf04e241457719bf5162f9d39fe6c48
ebi-gxa
parents: 4
diff changeset
456 f"{args.save_path}/genes_to_filter_by_contrast.tsv",
87f1eaa410cc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit dea8a066ccf04e241457719bf5162f9d39fe6c48
ebi-gxa
parents: 4
diff changeset
457 sep="\t",
87f1eaa410cc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit dea8a066ccf04e241457719bf5162f9d39fe6c48
ebi-gxa
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diff changeset
458 index=False,
87f1eaa410cc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit dea8a066ccf04e241457719bf5162f9d39fe6c48
ebi-gxa
parents: 4
diff changeset
459 )
87f1eaa410cc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit dea8a066ccf04e241457719bf5162f9d39fe6c48
ebi-gxa
parents: 4
diff changeset
460
0
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
parents:
diff changeset
461
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
parents:
diff changeset
462 def merge_adata_obs_fields(obs_fields_to_merge, adata):
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
parents:
diff changeset
463 """
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
parents:
diff changeset
464 Merge adata.obs fields specified in args.adata_obs_fields_to_merge
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
parents:
diff changeset
465
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
parents:
diff changeset
466 Parameters
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
parents:
diff changeset
467 ----------
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
parents:
diff changeset
468 obs_fields_to_merge : str
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
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diff changeset
469 Fields in adata.obs to merge, comma separated
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
parents:
diff changeset
470 adata : anndata.AnnData
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
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diff changeset
471 The AnnData object
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
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diff changeset
472
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
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diff changeset
473 Returns
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
parents:
diff changeset
474 -------
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
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diff changeset
475 anndata.AnnData
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
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diff changeset
476 The merged AnnData object
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
parents:
diff changeset
477
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
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diff changeset
478 docstring tests:
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
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diff changeset
479 >>> import scanpy as sc
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
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diff changeset
480 >>> ad = sc.datasets.pbmc68k_reduced()
5
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481 >>> merge_adata_obs_fields(["bulk_labels","louvain"], ad)
0
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
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diff changeset
482 >>> ad.obs.columns
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
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diff changeset
483 Index(['bulk_labels', 'n_genes', 'percent_mito', 'n_counts', 'S_score',
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
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diff changeset
484 'G2M_score', 'phase', 'louvain', 'bulk_labels_louvain'],
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
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diff changeset
485 dtype='object')
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
parents:
diff changeset
486 """
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
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diff changeset
487 field_name = "_".join(obs_fields_to_merge)
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
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diff changeset
488 for field in obs_fields_to_merge:
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
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diff changeset
489 if field not in adata.obs.columns:
3
c6787c2aee46 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit eea5c13f9e6e070a2359c59400773b01f9cd7567
ebi-gxa
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diff changeset
490 raise ValueError(
c6787c2aee46 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit eea5c13f9e6e070a2359c59400773b01f9cd7567
ebi-gxa
parents: 0
diff changeset
491 f"The '{field}' column is not present in adata.obs."
c6787c2aee46 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit eea5c13f9e6e070a2359c59400773b01f9cd7567
ebi-gxa
parents: 0
diff changeset
492 )
0
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
parents:
diff changeset
493 if field_name not in adata.obs.columns:
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
parents:
diff changeset
494 adata.obs[field_name] = adata.obs[field].astype(str)
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
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diff changeset
495 else:
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
parents:
diff changeset
496 adata.obs[field_name] = (
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
parents:
diff changeset
497 adata.obs[field_name] + "_" + adata.obs[field].astype(str)
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
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diff changeset
498 )
5
87f1eaa410cc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit dea8a066ccf04e241457719bf5162f9d39fe6c48
ebi-gxa
parents: 4
diff changeset
499
87f1eaa410cc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit dea8a066ccf04e241457719bf5162f9d39fe6c48
ebi-gxa
parents: 4
diff changeset
500
87f1eaa410cc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit dea8a066ccf04e241457719bf5162f9d39fe6c48
ebi-gxa
parents: 4
diff changeset
501 def identify_genes_to_filter_per_contrast(
87f1eaa410cc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit dea8a066ccf04e241457719bf5162f9d39fe6c48
ebi-gxa
parents: 4
diff changeset
502 contrast_file, min_perc_cells_expression, adata, obs_field
87f1eaa410cc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit dea8a066ccf04e241457719bf5162f9d39fe6c48
ebi-gxa
parents: 4
diff changeset
503 ):
87f1eaa410cc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit dea8a066ccf04e241457719bf5162f9d39fe6c48
ebi-gxa
parents: 4
diff changeset
504 """
87f1eaa410cc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit dea8a066ccf04e241457719bf5162f9d39fe6c48
ebi-gxa
parents: 4
diff changeset
505 Identify genes to filter per contrast based on expression percentage.
87f1eaa410cc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit dea8a066ccf04e241457719bf5162f9d39fe6c48
ebi-gxa
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diff changeset
506 We need those genes to be under the threshold for all conditions
87f1eaa410cc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit dea8a066ccf04e241457719bf5162f9d39fe6c48
ebi-gxa
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diff changeset
507 in a contrast to be identified for further filtering. If
87f1eaa410cc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit dea8a066ccf04e241457719bf5162f9d39fe6c48
ebi-gxa
parents: 4
diff changeset
508 one condition has the gene expressed above the threshold, the gene
87f1eaa410cc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit dea8a066ccf04e241457719bf5162f9d39fe6c48
ebi-gxa
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diff changeset
509 becomes of interest (it can be highly up or down regulated).
87f1eaa410cc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit dea8a066ccf04e241457719bf5162f9d39fe6c48
ebi-gxa
parents: 4
diff changeset
510
87f1eaa410cc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit dea8a066ccf04e241457719bf5162f9d39fe6c48
ebi-gxa
parents: 4
diff changeset
511 Parameters
87f1eaa410cc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit dea8a066ccf04e241457719bf5162f9d39fe6c48
ebi-gxa
parents: 4
diff changeset
512 ----------
87f1eaa410cc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit dea8a066ccf04e241457719bf5162f9d39fe6c48
ebi-gxa
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diff changeset
513 contrast_file : str
87f1eaa410cc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit dea8a066ccf04e241457719bf5162f9d39fe6c48
ebi-gxa
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diff changeset
514 Path to the contrasts file.
87f1eaa410cc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit dea8a066ccf04e241457719bf5162f9d39fe6c48
ebi-gxa
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diff changeset
515 min_perc_cells_expression : float
87f1eaa410cc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit dea8a066ccf04e241457719bf5162f9d39fe6c48
ebi-gxa
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diff changeset
516 Minimum percentage of cells that should express a gene.
87f1eaa410cc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit dea8a066ccf04e241457719bf5162f9d39fe6c48
ebi-gxa
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diff changeset
517 adata: adata
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518 Original AnnData file
87f1eaa410cc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit dea8a066ccf04e241457719bf5162f9d39fe6c48
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diff changeset
519 obs_field: str
87f1eaa410cc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit dea8a066ccf04e241457719bf5162f9d39fe6c48
ebi-gxa
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diff changeset
520 Field in the AnnData observations where the contrasts are defined.
87f1eaa410cc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit dea8a066ccf04e241457719bf5162f9d39fe6c48
ebi-gxa
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diff changeset
521
87f1eaa410cc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit dea8a066ccf04e241457719bf5162f9d39fe6c48
ebi-gxa
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diff changeset
522 Returns
87f1eaa410cc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit dea8a066ccf04e241457719bf5162f9d39fe6c48
ebi-gxa
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diff changeset
523 -------
87f1eaa410cc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit dea8a066ccf04e241457719bf5162f9d39fe6c48
ebi-gxa
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diff changeset
524 None
87f1eaa410cc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit dea8a066ccf04e241457719bf5162f9d39fe6c48
ebi-gxa
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diff changeset
525
87f1eaa410cc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit dea8a066ccf04e241457719bf5162f9d39fe6c48
ebi-gxa
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diff changeset
526 Examples
87f1eaa410cc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit dea8a066ccf04e241457719bf5162f9d39fe6c48
ebi-gxa
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diff changeset
527 --------
87f1eaa410cc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit dea8a066ccf04e241457719bf5162f9d39fe6c48
ebi-gxa
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diff changeset
528 >>> import anndata
87f1eaa410cc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit dea8a066ccf04e241457719bf5162f9d39fe6c48
ebi-gxa
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529 >>> import pandas as pd
87f1eaa410cc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit dea8a066ccf04e241457719bf5162f9d39fe6c48
ebi-gxa
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diff changeset
530 >>> import numpy as np
87f1eaa410cc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit dea8a066ccf04e241457719bf5162f9d39fe6c48
ebi-gxa
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diff changeset
531 >>> import os
87f1eaa410cc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit dea8a066ccf04e241457719bf5162f9d39fe6c48
ebi-gxa
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diff changeset
532 >>> from io import StringIO
87f1eaa410cc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit dea8a066ccf04e241457719bf5162f9d39fe6c48
ebi-gxa
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533 >>> contrast_file = StringIO(f"contrast{os.linesep}condition1-\
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2c5686d627c0 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1efa285536ea940b459fd07f452a6eeb0cf0ffb9
ebi-gxa
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diff changeset
534 condition2{os.linesep}\
2c5686d627c0 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1efa285536ea940b459fd07f452a6eeb0cf0ffb9
ebi-gxa
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diff changeset
535 2*(condition1)-condition2{os.linesep}")
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87f1eaa410cc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit dea8a066ccf04e241457719bf5162f9d39fe6c48
ebi-gxa
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diff changeset
536 >>> min_perc_cells_expression = 30.0
87f1eaa410cc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit dea8a066ccf04e241457719bf5162f9d39fe6c48
ebi-gxa
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537 >>> data = {
87f1eaa410cc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit dea8a066ccf04e241457719bf5162f9d39fe6c48
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538 ... 'obs': pd.DataFrame({'condition': ['condition1', 'condition1',
87f1eaa410cc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit dea8a066ccf04e241457719bf5162f9d39fe6c48
ebi-gxa
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539 ... 'condition2', 'condition2']}),
87f1eaa410cc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit dea8a066ccf04e241457719bf5162f9d39fe6c48
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540 ... 'X': np.array([[1, 0, 0, 0, 0], [0, 0, 2, 2, 0],
87f1eaa410cc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit dea8a066ccf04e241457719bf5162f9d39fe6c48
ebi-gxa
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diff changeset
541 ... [0, 0, 1, 1, 0], [0, 0, 0, 2, 0]]),
87f1eaa410cc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit dea8a066ccf04e241457719bf5162f9d39fe6c48
ebi-gxa
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542 ... }
87f1eaa410cc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit dea8a066ccf04e241457719bf5162f9d39fe6c48
ebi-gxa
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543 >>> adata = anndata.AnnData(X=data['X'], obs=data['obs'])
87f1eaa410cc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit dea8a066ccf04e241457719bf5162f9d39fe6c48
ebi-gxa
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544 >>> df = identify_genes_to_filter_per_contrast(
87f1eaa410cc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit dea8a066ccf04e241457719bf5162f9d39fe6c48
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545 ... contrast_file, min_perc_cells_expression, adata, 'condition'
87f1eaa410cc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit dea8a066ccf04e241457719bf5162f9d39fe6c48
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546 ... ) # doctest:+ELLIPSIS
87f1eaa410cc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit dea8a066ccf04e241457719bf5162f9d39fe6c48
ebi-gxa
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547 Identifying genes to filter using ...
87f1eaa410cc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit dea8a066ccf04e241457719bf5162f9d39fe6c48
ebi-gxa
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diff changeset
548 >>> df.head() # doctest:+ELLIPSIS
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ebi-gxa
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549 contrast gene
2c5686d627c0 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1efa285536ea940b459fd07f452a6eeb0cf0ffb9
ebi-gxa
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diff changeset
550 0 condition1-condition2...
2c5686d627c0 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1efa285536ea940b459fd07f452a6eeb0cf0ffb9
ebi-gxa
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diff changeset
551 1 condition1-condition2...
2c5686d627c0 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1efa285536ea940b459fd07f452a6eeb0cf0ffb9
ebi-gxa
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diff changeset
552 2 2*(condition1)-condition2...
2c5686d627c0 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1efa285536ea940b459fd07f452a6eeb0cf0ffb9
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553 3 2*(condition1)-condition2...
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87f1eaa410cc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit dea8a066ccf04e241457719bf5162f9d39fe6c48
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554 """
87f1eaa410cc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit dea8a066ccf04e241457719bf5162f9d39fe6c48
ebi-gxa
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diff changeset
555 import re
87f1eaa410cc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit dea8a066ccf04e241457719bf5162f9d39fe6c48
ebi-gxa
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diff changeset
556
87f1eaa410cc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit dea8a066ccf04e241457719bf5162f9d39fe6c48
ebi-gxa
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diff changeset
557 # Implement the logic to identify genes to filter per contrast
87f1eaa410cc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit dea8a066ccf04e241457719bf5162f9d39fe6c48
ebi-gxa
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diff changeset
558 # This is a placeholder implementation
87f1eaa410cc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit dea8a066ccf04e241457719bf5162f9d39fe6c48
ebi-gxa
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diff changeset
559 print(
87f1eaa410cc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit dea8a066ccf04e241457719bf5162f9d39fe6c48
ebi-gxa
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diff changeset
560 f"Identifying genes to filter using {contrast_file} "
87f1eaa410cc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit dea8a066ccf04e241457719bf5162f9d39fe6c48
ebi-gxa
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diff changeset
561 f"with min expression {min_perc_cells_expression}%"
87f1eaa410cc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit dea8a066ccf04e241457719bf5162f9d39fe6c48
ebi-gxa
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diff changeset
562 )
87f1eaa410cc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit dea8a066ccf04e241457719bf5162f9d39fe6c48
ebi-gxa
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diff changeset
563 sides_regex = re.compile(r"[\+\-\*\/\(\)\^]+")
87f1eaa410cc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit dea8a066ccf04e241457719bf5162f9d39fe6c48
ebi-gxa
parents: 4
diff changeset
564
87f1eaa410cc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit dea8a066ccf04e241457719bf5162f9d39fe6c48
ebi-gxa
parents: 4
diff changeset
565 contrasts = pd.read_csv(contrast_file, sep="\t")
87f1eaa410cc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit dea8a066ccf04e241457719bf5162f9d39fe6c48
ebi-gxa
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diff changeset
566 # Iterate over each line in the contrast file
87f1eaa410cc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit dea8a066ccf04e241457719bf5162f9d39fe6c48
ebi-gxa
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diff changeset
567 genes_filter_for_contrast = dict()
87f1eaa410cc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit dea8a066ccf04e241457719bf5162f9d39fe6c48
ebi-gxa
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diff changeset
568 for contrast in contrasts.iloc[:, 0]:
87f1eaa410cc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit dea8a066ccf04e241457719bf5162f9d39fe6c48
ebi-gxa
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diff changeset
569 conditions = set(sides_regex.split(contrast))
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2c5686d627c0 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1efa285536ea940b459fd07f452a6eeb0cf0ffb9
ebi-gxa
parents: 6
diff changeset
570
2c5686d627c0 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1efa285536ea940b459fd07f452a6eeb0cf0ffb9
ebi-gxa
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diff changeset
571 selected_conditions = []
2c5686d627c0 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1efa285536ea940b459fd07f452a6eeb0cf0ffb9
ebi-gxa
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diff changeset
572 failed_conditions = []
2c5686d627c0 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1efa285536ea940b459fd07f452a6eeb0cf0ffb9
ebi-gxa
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diff changeset
573 for condition in conditions:
2c5686d627c0 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1efa285536ea940b459fd07f452a6eeb0cf0ffb9
ebi-gxa
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diff changeset
574 # remove any starting or trailing whitespaces from condition
2c5686d627c0 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1efa285536ea940b459fd07f452a6eeb0cf0ffb9
ebi-gxa
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diff changeset
575 condition = condition.strip()
2c5686d627c0 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1efa285536ea940b459fd07f452a6eeb0cf0ffb9
ebi-gxa
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diff changeset
576 if len(condition) == 0:
2c5686d627c0 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1efa285536ea940b459fd07f452a6eeb0cf0ffb9
ebi-gxa
parents: 6
diff changeset
577 continue
2c5686d627c0 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1efa285536ea940b459fd07f452a6eeb0cf0ffb9
ebi-gxa
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diff changeset
578 # check if the condition is simply a number, then skip it
2c5686d627c0 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1efa285536ea940b459fd07f452a6eeb0cf0ffb9
ebi-gxa
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diff changeset
579 if condition.isnumeric():
2c5686d627c0 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1efa285536ea940b459fd07f452a6eeb0cf0ffb9
ebi-gxa
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diff changeset
580 continue
2c5686d627c0 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1efa285536ea940b459fd07f452a6eeb0cf0ffb9
ebi-gxa
parents: 6
diff changeset
581 if condition not in adata.obs[obs_field].unique():
2c5686d627c0 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1efa285536ea940b459fd07f452a6eeb0cf0ffb9
ebi-gxa
parents: 6
diff changeset
582 # add condition to failed_conditions
2c5686d627c0 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1efa285536ea940b459fd07f452a6eeb0cf0ffb9
ebi-gxa
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diff changeset
583 failed_conditions.append(condition)
2c5686d627c0 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1efa285536ea940b459fd07f452a6eeb0cf0ffb9
ebi-gxa
parents: 6
diff changeset
584 continue
2c5686d627c0 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1efa285536ea940b459fd07f452a6eeb0cf0ffb9
ebi-gxa
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diff changeset
585 # append to selected_conditions
2c5686d627c0 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1efa285536ea940b459fd07f452a6eeb0cf0ffb9
ebi-gxa
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diff changeset
586 selected_conditions.append(condition)
2c5686d627c0 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1efa285536ea940b459fd07f452a6eeb0cf0ffb9
ebi-gxa
parents: 6
diff changeset
587
2c5686d627c0 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1efa285536ea940b459fd07f452a6eeb0cf0ffb9
ebi-gxa
parents: 6
diff changeset
588 if len(failed_conditions) > 0:
2c5686d627c0 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1efa285536ea940b459fd07f452a6eeb0cf0ffb9
ebi-gxa
parents: 6
diff changeset
589 raise ValueError(
2c5686d627c0 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1efa285536ea940b459fd07f452a6eeb0cf0ffb9
ebi-gxa
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diff changeset
590 f"Condition(s) '{failed_conditions}' "
2c5686d627c0 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1efa285536ea940b459fd07f452a6eeb0cf0ffb9
ebi-gxa
parents: 6
diff changeset
591 f"from contrast {contrast} "
2c5686d627c0 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1efa285536ea940b459fd07f452a6eeb0cf0ffb9
ebi-gxa
parents: 6
diff changeset
592 f"is/are not present in the "
2c5686d627c0 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1efa285536ea940b459fd07f452a6eeb0cf0ffb9
ebi-gxa
parents: 6
diff changeset
593 f"obs_field '{obs_field}' from the AnnData object."
2c5686d627c0 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1efa285536ea940b459fd07f452a6eeb0cf0ffb9
ebi-gxa
parents: 6
diff changeset
594 f"Possible values are: "
2c5686d627c0 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1efa285536ea940b459fd07f452a6eeb0cf0ffb9
ebi-gxa
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diff changeset
595 f"{', '.join(adata.obs[obs_field].unique())}.")
5
87f1eaa410cc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit dea8a066ccf04e241457719bf5162f9d39fe6c48
ebi-gxa
parents: 4
diff changeset
596 # we want to find the genes that are below the threshold
87f1eaa410cc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit dea8a066ccf04e241457719bf5162f9d39fe6c48
ebi-gxa
parents: 4
diff changeset
597 # of % of cells expressed for ALL the conditions in the
87f1eaa410cc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit dea8a066ccf04e241457719bf5162f9d39fe6c48
ebi-gxa
parents: 4
diff changeset
598 # contrast. It is enough for one of the conditions
87f1eaa410cc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit dea8a066ccf04e241457719bf5162f9d39fe6c48
ebi-gxa
parents: 4
diff changeset
599 # of the contrast to have the genes expressed above
87f1eaa410cc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit dea8a066ccf04e241457719bf5162f9d39fe6c48
ebi-gxa
parents: 4
diff changeset
600 # the threshold of % of cells to be of interest.
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2c5686d627c0 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1efa285536ea940b459fd07f452a6eeb0cf0ffb9
ebi-gxa
parents: 6
diff changeset
601 for condition in selected_conditions:
5
87f1eaa410cc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit dea8a066ccf04e241457719bf5162f9d39fe6c48
ebi-gxa
parents: 4
diff changeset
602 # check the percentage of cells that express each gene
87f1eaa410cc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit dea8a066ccf04e241457719bf5162f9d39fe6c48
ebi-gxa
parents: 4
diff changeset
603 # Filter the AnnData object based on the obs_field value
87f1eaa410cc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit dea8a066ccf04e241457719bf5162f9d39fe6c48
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diff changeset
604 adata_filtered = adata[adata.obs[obs_field] == condition]
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diff changeset
605 # Calculate the percentage of cells expressing each gene
87f1eaa410cc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit dea8a066ccf04e241457719bf5162f9d39fe6c48
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606 gene_expression = (adata_filtered.X > 0).mean(axis=0) * 100
87f1eaa410cc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit dea8a066ccf04e241457719bf5162f9d39fe6c48
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diff changeset
607 genes_to_filter = set(adata_filtered.var[
87f1eaa410cc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit dea8a066ccf04e241457719bf5162f9d39fe6c48
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diff changeset
608 gene_expression.transpose() < min_perc_cells_expression
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609 ].index.tolist())
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diff changeset
610 # Update the genes_filter_for_contrast dictionary
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diff changeset
611 if contrast in genes_filter_for_contrast.keys():
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612 genes_filter_for_contrast[contrast].intersection_update(
87f1eaa410cc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit dea8a066ccf04e241457719bf5162f9d39fe6c48
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613 genes_to_filter
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614 )
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diff changeset
615 else:
87f1eaa410cc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit dea8a066ccf04e241457719bf5162f9d39fe6c48
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616 genes_filter_for_contrast[contrast] = genes_to_filter
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diff changeset
617
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618 # write the genes_filter_for_contrast to pandas dataframe of two columns:
87f1eaa410cc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit dea8a066ccf04e241457719bf5162f9d39fe6c48
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619 # contrast and gene
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620
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621 # Initialize an empty list to store the expanded pairs
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622 expanded_pairs = []
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623
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624 # Iterate over the dictionary
87f1eaa410cc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit dea8a066ccf04e241457719bf5162f9d39fe6c48
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625 for contrast, genes in genes_filter_for_contrast.items():
87f1eaa410cc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit dea8a066ccf04e241457719bf5162f9d39fe6c48
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626 for gene in genes:
87f1eaa410cc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit dea8a066ccf04e241457719bf5162f9d39fe6c48
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627 expanded_pairs.append((contrast, gene))
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diff changeset
628
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629 # Create the DataFrame
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630 contrast_genes_df = pd.DataFrame(
87f1eaa410cc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit dea8a066ccf04e241457719bf5162f9d39fe6c48
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631 expanded_pairs, columns=["contrast", "gene"]
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632 )
87f1eaa410cc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit dea8a066ccf04e241457719bf5162f9d39fe6c48
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diff changeset
633
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634 return contrast_genes_df
0
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diff changeset
635
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diff changeset
636
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diff changeset
637 if __name__ == "__main__":
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diff changeset
638 # Create argument parser
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diff changeset
639 parser = argparse.ArgumentParser(
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
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diff changeset
640 description="Perform pseudobulk analysis on an AnnData object"
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
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diff changeset
641 )
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
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diff changeset
642
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diff changeset
643 # Add arguments
3
c6787c2aee46 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit eea5c13f9e6e070a2359c59400773b01f9cd7567
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644 parser.add_argument(
c6787c2aee46 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit eea5c13f9e6e070a2359c59400773b01f9cd7567
ebi-gxa
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diff changeset
645 "adata_file", type=str, help="Path to the AnnData file"
c6787c2aee46 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit eea5c13f9e6e070a2359c59400773b01f9cd7567
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646 )
0
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
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diff changeset
647 parser.add_argument(
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
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diff changeset
648 "-m",
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
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diff changeset
649 "--adata_obs_fields_to_merge",
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
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diff changeset
650 type=str,
3
c6787c2aee46 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit eea5c13f9e6e070a2359c59400773b01f9cd7567
ebi-gxa
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diff changeset
651 help="Fields in adata.obs to merge, comma separated. \
c6787c2aee46 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit eea5c13f9e6e070a2359c59400773b01f9cd7567
ebi-gxa
parents: 0
diff changeset
652 You can have more than one set of fields, \
c6787c2aee46 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit eea5c13f9e6e070a2359c59400773b01f9cd7567
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parents: 0
diff changeset
653 separated by semi-colon ;",
0
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
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diff changeset
654 )
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
parents:
diff changeset
655 parser.add_argument(
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
parents:
diff changeset
656 "--groupby",
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
parents:
diff changeset
657 type=str,
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
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diff changeset
658 required=True,
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
parents:
diff changeset
659 help="The column in adata.obs that defines the groups",
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
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diff changeset
660 )
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
parents:
diff changeset
661 parser.add_argument(
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
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diff changeset
662 "--sample_key",
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
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diff changeset
663 required=True,
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
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diff changeset
664 type=str,
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
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diff changeset
665 help="The column in adata.obs that defines the samples",
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
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diff changeset
666 )
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
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diff changeset
667 # add argument for layer
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
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diff changeset
668 parser.add_argument(
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
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diff changeset
669 "--layer",
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
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diff changeset
670 type=str,
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
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diff changeset
671 default=None,
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
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diff changeset
672 help="The name of the layer of the AnnData object to use",
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
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diff changeset
673 )
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
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diff changeset
674 # add argument for mode
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
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diff changeset
675 parser.add_argument(
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
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diff changeset
676 "--mode",
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ebi-gxa
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diff changeset
677 type=str,
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
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diff changeset
678 default="sum",
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
parents:
diff changeset
679 help="The mode for Decoupler pseudobulk analysis",
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
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diff changeset
680 choices=["sum", "mean", "median"],
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
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diff changeset
681 )
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
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diff changeset
682 # add boolean argument for use_raw
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
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diff changeset
683 parser.add_argument(
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
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diff changeset
684 "--use_raw",
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
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diff changeset
685 action="store_true",
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diff changeset
686 default=False,
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diff changeset
687 help="Whether to use the raw part of the AnnData object",
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
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diff changeset
688 )
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689 # add argument for min_cells
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
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diff changeset
690 parser.add_argument(
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
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691 "--min_cells",
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diff changeset
692 type=int,
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
parents:
diff changeset
693 default=10,
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
parents:
diff changeset
694 help="Minimum number of cells for pseudobulk analysis",
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
parents:
diff changeset
695 )
5
87f1eaa410cc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit dea8a066ccf04e241457719bf5162f9d39fe6c48
ebi-gxa
parents: 4
diff changeset
696 # add argument for min percentage of cells that should express a gene
87f1eaa410cc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit dea8a066ccf04e241457719bf5162f9d39fe6c48
ebi-gxa
parents: 4
diff changeset
697 parser.add_argument(
87f1eaa410cc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit dea8a066ccf04e241457719bf5162f9d39fe6c48
ebi-gxa
parents: 4
diff changeset
698 "--min_gene_exp_perc_per_cell",
87f1eaa410cc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit dea8a066ccf04e241457719bf5162f9d39fe6c48
ebi-gxa
parents: 4
diff changeset
699 type=float,
87f1eaa410cc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit dea8a066ccf04e241457719bf5162f9d39fe6c48
ebi-gxa
parents: 4
diff changeset
700 default=50,
87f1eaa410cc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit dea8a066ccf04e241457719bf5162f9d39fe6c48
ebi-gxa
parents: 4
diff changeset
701 help="If all the conditions of one side of a contrast express a \
87f1eaa410cc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit dea8a066ccf04e241457719bf5162f9d39fe6c48
ebi-gxa
parents: 4
diff changeset
702 gene in less than this percentage of cells, then the genes \
87f1eaa410cc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit dea8a066ccf04e241457719bf5162f9d39fe6c48
ebi-gxa
parents: 4
diff changeset
703 will be added to a list of genes to ignore for that contrast.\
87f1eaa410cc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit dea8a066ccf04e241457719bf5162f9d39fe6c48
ebi-gxa
parents: 4
diff changeset
704 Requires the contrast file to be provided.",
87f1eaa410cc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit dea8a066ccf04e241457719bf5162f9d39fe6c48
ebi-gxa
parents: 4
diff changeset
705 )
87f1eaa410cc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit dea8a066ccf04e241457719bf5162f9d39fe6c48
ebi-gxa
parents: 4
diff changeset
706 parser.add_argument(
87f1eaa410cc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit dea8a066ccf04e241457719bf5162f9d39fe6c48
ebi-gxa
parents: 4
diff changeset
707 "--contrasts_file",
87f1eaa410cc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit dea8a066ccf04e241457719bf5162f9d39fe6c48
ebi-gxa
parents: 4
diff changeset
708 type=str,
87f1eaa410cc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit dea8a066ccf04e241457719bf5162f9d39fe6c48
ebi-gxa
parents: 4
diff changeset
709 required=False,
87f1eaa410cc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit dea8a066ccf04e241457719bf5162f9d39fe6c48
ebi-gxa
parents: 4
diff changeset
710 help="Contrasts file, a one column tsv with a header, each line \
87f1eaa410cc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit dea8a066ccf04e241457719bf5162f9d39fe6c48
ebi-gxa
parents: 4
diff changeset
711 represents a contrast as a combination of conditions at each \
87f1eaa410cc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit dea8a066ccf04e241457719bf5162f9d39fe6c48
ebi-gxa
parents: 4
diff changeset
712 side of a substraction.",
87f1eaa410cc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit dea8a066ccf04e241457719bf5162f9d39fe6c48
ebi-gxa
parents: 4
diff changeset
713 )
87f1eaa410cc planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit dea8a066ccf04e241457719bf5162f9d39fe6c48
ebi-gxa
parents: 4
diff changeset
714
0
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
parents:
diff changeset
715 parser.add_argument(
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
parents:
diff changeset
716 "--save_path", type=str, help="Path to save the plot (optional)"
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
parents:
diff changeset
717 )
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
parents:
diff changeset
718 parser.add_argument(
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
parents:
diff changeset
719 "--min_counts",
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
parents:
diff changeset
720 type=int,
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
parents:
diff changeset
721 help="Minimum count threshold for filtering by expression",
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
parents:
diff changeset
722 )
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
parents:
diff changeset
723 parser.add_argument(
3
c6787c2aee46 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit eea5c13f9e6e070a2359c59400773b01f9cd7567
ebi-gxa
parents: 0
diff changeset
724 "--min_counts_per_sample_marking",
c6787c2aee46 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit eea5c13f9e6e070a2359c59400773b01f9cd7567
ebi-gxa
parents: 0
diff changeset
725 type=int,
c6787c2aee46 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit eea5c13f9e6e070a2359c59400773b01f9cd7567
ebi-gxa
parents: 0
diff changeset
726 default=20,
c6787c2aee46 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit eea5c13f9e6e070a2359c59400773b01f9cd7567
ebi-gxa
parents: 0
diff changeset
727 help="Minimum count threshold per sample for \
c6787c2aee46 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit eea5c13f9e6e070a2359c59400773b01f9cd7567
ebi-gxa
parents: 0
diff changeset
728 marking genes to be ignored after DE",
c6787c2aee46 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit eea5c13f9e6e070a2359c59400773b01f9cd7567
ebi-gxa
parents: 0
diff changeset
729 )
c6787c2aee46 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit eea5c13f9e6e070a2359c59400773b01f9cd7567
ebi-gxa
parents: 0
diff changeset
730 parser.add_argument(
0
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
parents:
diff changeset
731 "--min_total_counts",
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
parents:
diff changeset
732 type=int,
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
parents:
diff changeset
733 help="Minimum total count threshold for filtering by expression",
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
parents:
diff changeset
734 )
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
parents:
diff changeset
735 parser.add_argument(
11
db14ac3f6b43 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 487508282bda9dbb68138d5c7091f46ef54fe52a
ebi-gxa
parents: 7
diff changeset
736 "--num_pseudo_replicates",
db14ac3f6b43 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 487508282bda9dbb68138d5c7091f46ef54fe52a
ebi-gxa
parents: 7
diff changeset
737 type=int,
db14ac3f6b43 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 487508282bda9dbb68138d5c7091f46ef54fe52a
ebi-gxa
parents: 7
diff changeset
738 choices=range(3, 1000),
db14ac3f6b43 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 487508282bda9dbb68138d5c7091f46ef54fe52a
ebi-gxa
parents: 7
diff changeset
739 help="Number of pseudo replicates to create per sample (at least 3)",
db14ac3f6b43 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 487508282bda9dbb68138d5c7091f46ef54fe52a
ebi-gxa
parents: 7
diff changeset
740 required=False
db14ac3f6b43 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 487508282bda9dbb68138d5c7091f46ef54fe52a
ebi-gxa
parents: 7
diff changeset
741 )
db14ac3f6b43 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 487508282bda9dbb68138d5c7091f46ef54fe52a
ebi-gxa
parents: 7
diff changeset
742 parser.add_argument(
db14ac3f6b43 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 487508282bda9dbb68138d5c7091f46ef54fe52a
ebi-gxa
parents: 7
diff changeset
743 "--seed",
db14ac3f6b43 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 487508282bda9dbb68138d5c7091f46ef54fe52a
ebi-gxa
parents: 7
diff changeset
744 type=int,
db14ac3f6b43 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 487508282bda9dbb68138d5c7091f46ef54fe52a
ebi-gxa
parents: 7
diff changeset
745 default=None,
db14ac3f6b43 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 487508282bda9dbb68138d5c7091f46ef54fe52a
ebi-gxa
parents: 7
diff changeset
746 help="Random seed for pseudo replicate sampling",
db14ac3f6b43 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 487508282bda9dbb68138d5c7091f46ef54fe52a
ebi-gxa
parents: 7
diff changeset
747 )
db14ac3f6b43 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 487508282bda9dbb68138d5c7091f46ef54fe52a
ebi-gxa
parents: 7
diff changeset
748 parser.add_argument(
0
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
parents:
diff changeset
749 "--anndata_output_path",
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
parents:
diff changeset
750 type=str,
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
parents:
diff changeset
751 help="Path to save the filtered AnnData object or pseudobulk data",
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
parents:
diff changeset
752 )
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
parents:
diff changeset
753 parser.add_argument(
3
c6787c2aee46 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit eea5c13f9e6e070a2359c59400773b01f9cd7567
ebi-gxa
parents: 0
diff changeset
754 "--filter_expr",
c6787c2aee46 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit eea5c13f9e6e070a2359c59400773b01f9cd7567
ebi-gxa
parents: 0
diff changeset
755 action="store_true",
c6787c2aee46 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit eea5c13f9e6e070a2359c59400773b01f9cd7567
ebi-gxa
parents: 0
diff changeset
756 help="Enable filtering by expression",
0
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
parents:
diff changeset
757 )
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
parents:
diff changeset
758 parser.add_argument(
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
parents:
diff changeset
759 "--factor_fields",
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
parents:
diff changeset
760 type=str,
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
parents:
diff changeset
761 help="Comma separated list of fields for the factors",
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
parents:
diff changeset
762 )
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
parents:
diff changeset
763 parser.add_argument(
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
parents:
diff changeset
764 "--deseq2_output_path",
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
parents:
diff changeset
765 type=str,
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
parents:
diff changeset
766 help="Path to save the DESeq2 inputs",
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
parents:
diff changeset
767 required=True,
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
parents:
diff changeset
768 )
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
parents:
diff changeset
769 parser.add_argument(
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
parents:
diff changeset
770 "--plot_samples_figsize",
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
parents:
diff changeset
771 type=int,
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
parents:
diff changeset
772 default=[10, 10],
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
parents:
diff changeset
773 nargs=2,
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
parents:
diff changeset
774 help="Size of the samples plot as a tuple (two arguments)",
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
parents:
diff changeset
775 )
3
c6787c2aee46 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit eea5c13f9e6e070a2359c59400773b01f9cd7567
ebi-gxa
parents: 0
diff changeset
776 parser.add_argument(
c6787c2aee46 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit eea5c13f9e6e070a2359c59400773b01f9cd7567
ebi-gxa
parents: 0
diff changeset
777 "--plot_filtering_figsize", type=int, default=[10, 10], nargs=2
c6787c2aee46 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit eea5c13f9e6e070a2359c59400773b01f9cd7567
ebi-gxa
parents: 0
diff changeset
778 )
0
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
parents:
diff changeset
779
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
parents:
diff changeset
780 # Parse the command line arguments
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
parents:
diff changeset
781 args = parser.parse_args()
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
parents:
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782
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
parents:
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783 # Call the main function
77d680b36e23 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 1034a450c97dcbb77871050cf0c6d3da90dac823
ebi-gxa
parents:
diff changeset
784 main(args)