Mercurial > repos > iuc > anndata_export

annotate tsv_to_loompy.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
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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"
iuc
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2 """This module converts a tsv file into a binary loom file"""
8623710d083c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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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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4 import argparse
8623710d083c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
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5 import os
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"
iuc
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8 import numpy as np
8623710d083c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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9
8623710d083c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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10 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"
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11 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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12 help="Displays tool version")
8623710d083c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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13 parser.add_argument('--rowfile', '-r', help="File of row attributes & values")
8623710d083c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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14 parser.add_argument('--colfile', '-c',
8623710d083c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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15 help="File of column attributes and values")
8623710d083c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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16 parser.add_argument('--output', '-o', help="Output file name")
8623710d083c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
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17 parser.add_argument('--files', '-f', nargs='*',
8623710d083c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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18 help="Input tsv files. First file becomes main layer.")
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19 args = parser.parse_args()
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20
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21 colsfile = args.colfile
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22 rowsfile = args.rowfile
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23 if args.output:
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24 filename = args.output
8623710d083c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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25 else:
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26 filename = "converted.loom"
8623710d083c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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27 alldata = args.files
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28 alayers = []
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29 layernames = []
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30 rowdict = {}
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31 coldict = {}
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32
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33 # Creates dictionary based on row file
8623710d083c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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34 # For each attribute:
8623710d083c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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35 # Attribute: [attribute values]
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36 with open(rowsfile, "r") as rows:
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37 count = 0
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38 for line in rows:
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39 line = line.strip().split("\t")
8623710d083c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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40 if count == 0: # First time through
8623710d083c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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41 row_attributes = line
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42 for x in row_attributes:
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43 rowdict[x] = []
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44 count += 1
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45 else:
8623710d083c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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46 for x in range(0, len(line)):
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47 rowdict[row_attributes[x]].append(line[x])
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48 # Same as above, but for columns
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49 with open(colsfile, "r") as cols:
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50 count = 0
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51 for line in cols:
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52 line = line.replace('\"', "")
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53 line = line.replace(' ', "")
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54 line = line.strip().split("\t")
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55 if count == 0: # First time through
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56 col_attributes = line
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57 for x in col_attributes:
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58 coldict[x] = []
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59 count += 1
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60 else:
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61 for x in range(0, len(line)):
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62 coldict[col_attributes[x]].append(line[x])
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63 # Finding dimensions for the loom layers
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64 rowshape = len(rowdict[list(rowdict.keys())[0]])
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65 colshape = len(coldict[list(coldict.keys())[0]])
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66
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67 # Creates a list with each element being entire matrix of
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68 # each layer file as floats
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69 for file in range(0, len(alldata)):
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70 layer = alldata[file][:-4]
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71 layer = layer.split("/")[-1]
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72 if layer == "":
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73 raise Exception("Please only use named files")
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74 layernames.append(layer)
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75 cfile = alldata[file]
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76 with open(cfile, "r") as tsv:
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77 cmatrix = []
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78 for line in tsv:
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79 line = line.strip().split("\t")
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80 line = [float(i) for i in line]
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81 cmatrix += line
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82 alayers.append(cmatrix)
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83
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84 # Loompy cannot overwright existing files. If somehow it finds
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85 # a second file with the same name, it must be deleted
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86 if os.path.isfile(filename):
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87 os.remove(filename)
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88 # To create the file properly, the first row and column attributes must be
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89 # added separately in the form of individual dictionaries
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90 row_attrs = {row_attributes[0]: np.asarray(rowdict[row_attributes[0]])}
8623710d083c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents:
diff changeset
91 col_attrs = {col_attributes[0]: np.asarray(coldict[col_attributes[0]])}
8623710d083c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents:
diff changeset
92 matrix = np.asarray(alayers[0])
8623710d083c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents:
diff changeset
93 matrix = matrix.astype(float)
8623710d083c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents:
diff changeset
94 matrix = matrix.reshape(rowshape, colshape)
8623710d083c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents:
diff changeset
95 # Creation of initial loom file
8623710d083c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents:
diff changeset
96 if "loom" not in filename[-5:]:
8623710d083c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents:
diff changeset
97 filename = filename + ".loom"
8623710d083c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents:
diff changeset
98 loompy.create(filename, matrix, row_attrs, col_attrs)
8623710d083c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents:
diff changeset
99 # Adding all row and column attributes, then all layers
8623710d083c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents:
diff changeset
100 with loompy.connect(filename) as loomfile:
8623710d083c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents:
diff changeset
101 for x in row_attributes:
8623710d083c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents:
diff changeset
102 loomfile.ra[x] = rowdict[x]
8623710d083c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents:
diff changeset
103 for y in col_attributes:
8623710d083c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents:
diff changeset
104 loomfile.ca[y] = coldict[y]
8623710d083c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents:
diff changeset
105 for z in range(1, len(alayers)):
8623710d083c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents:
diff changeset
106 matrix = np.asarray(alayers[z])
8623710d083c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents:
diff changeset
107 matrix = matrix.astype(float)
8623710d083c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents:
diff changeset
108 matrix = matrix.reshape(rowshape, colshape)
8623710d083c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents:
diff changeset
109 loomfile[layernames[z]] = matrix