Mercurial > repos > iuc > anndata_export

annotate loompy_to_tsv.py @ 3:8623710d083c draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
author iuc
date Mon, 06 Jan 2020 13:44:46 -0500
parents
children 0cb889db0910
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3
8623710d083c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
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diff changeset
1 #!/usr/bin/env python
8623710d083c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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2
8623710d083c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
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3 """Converts a loompy file to tsv file(s). Each layer becomes a new file."""
8623710d083c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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4
8623710d083c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
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5 import argparse
8623710d083c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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6
8623710d083c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
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7 import loompy
8623710d083c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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8
8623710d083c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
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9 parser = argparse.ArgumentParser(description="Loompy file converter flags")
8623710d083c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
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10 parser.add_argument('--version', action='version', version='%(prog)s 0.1.0',
8623710d083c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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11 help="Displays tool version")
8623710d083c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
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12 parser.add_argument("-f", "--file", help="loom file to import")
8623710d083c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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13 args = parser.parse_args()
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14
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15 file = args.file
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16
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17 matrices = []
8623710d083c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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18 allcols = []
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19 colstrings = []
8623710d083c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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20 allrows = []
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21
8623710d083c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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22 # Build background info for all attributes and layers
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23 loompyfile = loompy.connect(file)
8623710d083c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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24 row_attributes = loompyfile.ra.keys() # List of row attributes
8623710d083c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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25 for row in row_attributes: # Each list represents rownames for row_attributes
8623710d083c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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26 c_row = loompyfile.ra[row]
8623710d083c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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27 c_row = [str(r) for r in c_row]
8623710d083c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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28 allrows.append(c_row)
8623710d083c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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29 col_attributes = loompyfile.ca.keys() # List of column attributes
8623710d083c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
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30 for col in col_attributes: # each list represents colnames for col_attributes
8623710d083c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
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31 c_col = loompyfile.ca[col]
8623710d083c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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32 c_col = [str(c) for c in c_col]
8623710d083c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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33 allcols.append(c_col)
8623710d083c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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34 layers = loompyfile.layers.keys() # List of layers
8623710d083c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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35 for layer in layers: # List with each element being a loompy layer
8623710d083c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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36 c_layer = loompyfile[layer]
8623710d083c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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37 c_layer = c_layer[:, :]
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38 c_layer = c_layer.astype(str)
8623710d083c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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39 matrices.append(c_layer)
8623710d083c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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40
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41 # Create column attribute output
8623710d083c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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42 with open("attributes/col_attr.tsv", "w") as colout:
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43 col_attributes = "\t".join(col_attributes) + "\n"
8623710d083c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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44 colout.write(col_attributes)
8623710d083c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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45 for length in range(0, len(c_col)):
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46 attributestring = ""
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47 for col in allcols:
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48 attributestring = attributestring + col[length] + "\t"
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49 while attributestring[-1] == "\t":
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50 attributestring = attributestring[:-1]
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51 colout.write(attributestring)
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52 colout.write("\n")
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53 # Create row attribute output
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54 with open("attributes/row_attr.tsv", "w") as rowout:
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55 row_attributes = "\t".join(row_attributes) + "\n"
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56 rowout.write(row_attributes)
8623710d083c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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57 for length in range(0, len(c_row)):
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58 attributestring = ""
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59 for row in allrows:
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60 attributestring = attributestring + row[length] + "\t"
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61 while attributestring[-1] == "\t":
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62 attributestring = attributestring[:-1]
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63 rowout.write(attributestring)
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64 rowout.write("\n")
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65
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66 # Build output files for each layer
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67 for x in range(0, len(layers)):
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68 # Output file name generation
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69 if layers[x] in layers[0: x]: # Different output names if layers have same names somehow
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70 repeats = layers[0, x].count(layer[x])
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71 outputname = "output/" + layers[x] + repeats + ".tsv"
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72 elif layers[x] == "": # Empty layer name
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73 outputname = "output/mainmatrix.tsv"
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74 else:
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75 outputname = "output/" + str(layers[x]) + ".tsv" # Usual case
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76 # Matrix output
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77 with open(outputname, "w") as outputmatrix:
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78 for line in matrices[x]:
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79 line = "\t".join(line)
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80 line += "\n"
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81 line = line
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82 outputmatrix.write(line)