Mercurial > repos > iuc > anndata_import
annotate tsv_to_loompy.py @ 11:fb9e030ffae4 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 7decaee045e15bd71deb3bc46b81aa39caf1ed31
author | iuc |
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date | Wed, 22 Jun 2022 07:21:48 +0000 |
parents | b5c7ba11401d |
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rev | line source |
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3
b5c7ba11401d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
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1 #!/usr/bin/env python |
b5c7ba11401d
"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""" |
b5c7ba11401d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
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3 |
b5c7ba11401d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
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4 import argparse |
b5c7ba11401d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
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5 import os |
b5c7ba11401d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
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6 |
b5c7ba11401d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
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7 import loompy |
b5c7ba11401d
"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 |
b5c7ba11401d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
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9 |
b5c7ba11401d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
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10 parser = argparse.ArgumentParser(description="Loompy file converter flags") |
b5c7ba11401d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
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11 parser.add_argument('--VERSION', action='version', version='%(prog)s 0.1.0', |
b5c7ba11401d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
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12 help="Displays tool version") |
b5c7ba11401d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
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13 parser.add_argument('--rowfile', '-r', help="File of row attributes & values") |
b5c7ba11401d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
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14 parser.add_argument('--colfile', '-c', |
b5c7ba11401d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
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15 help="File of column attributes and values") |
b5c7ba11401d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
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16 parser.add_argument('--output', '-o', help="Output file name") |
b5c7ba11401d
"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='*', |
b5c7ba11401d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
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18 help="Input tsv files. First file becomes main layer.") |
b5c7ba11401d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
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19 args = parser.parse_args() |
b5c7ba11401d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
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20 |
b5c7ba11401d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
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21 colsfile = args.colfile |
b5c7ba11401d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
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22 rowsfile = args.rowfile |
b5c7ba11401d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
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23 if args.output: |
b5c7ba11401d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
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24 filename = args.output |
b5c7ba11401d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
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25 else: |
b5c7ba11401d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
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26 filename = "converted.loom" |
b5c7ba11401d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
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27 alldata = args.files |
b5c7ba11401d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
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28 alayers = [] |
b5c7ba11401d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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29 layernames = [] |
b5c7ba11401d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
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30 rowdict = {} |
b5c7ba11401d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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31 coldict = {} |
b5c7ba11401d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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32 |
b5c7ba11401d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
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33 # Creates dictionary based on row file |
b5c7ba11401d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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34 # For each attribute: |
b5c7ba11401d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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35 # Attribute: [attribute values] |
b5c7ba11401d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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36 with open(rowsfile, "r") as rows: |
b5c7ba11401d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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37 count = 0 |
b5c7ba11401d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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38 for line in rows: |
b5c7ba11401d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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39 line = line.strip().split("\t") |
b5c7ba11401d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
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40 if count == 0: # First time through |
b5c7ba11401d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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41 row_attributes = line |
b5c7ba11401d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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42 for x in row_attributes: |
b5c7ba11401d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
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43 rowdict[x] = [] |
b5c7ba11401d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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44 count += 1 |
b5c7ba11401d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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45 else: |
b5c7ba11401d
"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)): |
b5c7ba11401d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
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47 rowdict[row_attributes[x]].append(line[x]) |
b5c7ba11401d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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48 # Same as above, but for columns |
b5c7ba11401d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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49 with open(colsfile, "r") as cols: |
b5c7ba11401d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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50 count = 0 |
b5c7ba11401d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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51 for line in cols: |
b5c7ba11401d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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52 line = line.replace('\"', "") |
b5c7ba11401d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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53 line = line.replace(' ', "") |
b5c7ba11401d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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54 line = line.strip().split("\t") |
b5c7ba11401d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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55 if count == 0: # First time through |
b5c7ba11401d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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56 col_attributes = line |
b5c7ba11401d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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57 for x in col_attributes: |
b5c7ba11401d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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58 coldict[x] = [] |
b5c7ba11401d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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59 count += 1 |
b5c7ba11401d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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60 else: |
b5c7ba11401d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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61 for x in range(0, len(line)): |
b5c7ba11401d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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62 coldict[col_attributes[x]].append(line[x]) |
b5c7ba11401d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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63 # Finding dimensions for the loom layers |
b5c7ba11401d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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64 rowshape = len(rowdict[list(rowdict.keys())[0]]) |
b5c7ba11401d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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65 colshape = len(coldict[list(coldict.keys())[0]]) |
b5c7ba11401d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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66 |
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67 # Creates a list with each element being entire matrix of |
b5c7ba11401d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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68 # each layer file as floats |
b5c7ba11401d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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69 for file in range(0, len(alldata)): |
b5c7ba11401d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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70 layer = alldata[file][:-4] |
b5c7ba11401d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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71 layer = layer.split("/")[-1] |
b5c7ba11401d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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72 if layer == "": |
b5c7ba11401d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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73 raise Exception("Please only use named files") |
b5c7ba11401d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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74 layernames.append(layer) |
b5c7ba11401d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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75 cfile = alldata[file] |
b5c7ba11401d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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76 with open(cfile, "r") as tsv: |
b5c7ba11401d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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77 cmatrix = [] |
b5c7ba11401d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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78 for line in tsv: |
b5c7ba11401d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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79 line = line.strip().split("\t") |
b5c7ba11401d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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80 line = [float(i) for i in line] |
b5c7ba11401d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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81 cmatrix += line |
b5c7ba11401d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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82 alayers.append(cmatrix) |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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83 |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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84 # Loompy cannot overwright existing files. If somehow it finds |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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85 # a second file with the same name, it must be deleted |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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86 if os.path.isfile(filename): |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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87 os.remove(filename) |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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88 # To create the file properly, the first row and column attributes must be |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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89 # added separately in the form of individual dictionaries |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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90 row_attrs = {row_attributes[0]: np.asarray(rowdict[row_attributes[0]])} |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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91 col_attrs = {col_attributes[0]: np.asarray(coldict[col_attributes[0]])} |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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92 matrix = np.asarray(alayers[0]) |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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93 matrix = matrix.astype(float) |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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94 matrix = matrix.reshape(rowshape, colshape) |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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95 # Creation of initial loom file |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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96 if "loom" not in filename[-5:]: |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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97 filename = filename + ".loom" |
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98 loompy.create(filename, matrix, row_attrs, col_attrs) |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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99 # Adding all row and column attributes, then all layers |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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100 with loompy.connect(filename) as loomfile: |
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101 for x in row_attributes: |
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102 loomfile.ra[x] = rowdict[x] |
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103 for y in col_attributes: |
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104 loomfile.ca[y] = coldict[y] |
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105 for z in range(1, len(alayers)): |
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106 matrix = np.asarray(alayers[z]) |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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107 matrix = matrix.astype(float) |
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108 matrix = matrix.reshape(rowshape, colshape) |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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109 loomfile[layernames[z]] = matrix |