Mercurial > repos > siwaa > carboseq_s

annotate csopraSplitInput.py @ 15:de71663fbce4 draft

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"planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/a1d5502ae76ad46070a072641c73b7a51d21c82f/toos/CarboSeqSimulator commit a1d5502ae76ad46070a072641c73b7a51d21c82f-dirty"
author siwaa
date Tue, 10 Dec 2024 09:14:52 +0000
parents e455667fe22f
children
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3e7978af2ba2 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/5f761ea7dab0a6f8c978cbbe4946e16edc6d032e/toos/CarboSeqSimulator commit 5f761ea7dab0a6f8c978cbbe4946e16edc6d032e-dirty"
siwaa
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1 import pandas as pd
3e7978af2ba2 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/5f761ea7dab0a6f8c978cbbe4946e16edc6d032e/toos/CarboSeqSimulator commit 5f761ea7dab0a6f8c978cbbe4946e16edc6d032e-dirty"
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2 import os
3e7978af2ba2 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/5f761ea7dab0a6f8c978cbbe4946e16edc6d032e/toos/CarboSeqSimulator commit 5f761ea7dab0a6f8c978cbbe4946e16edc6d032e-dirty"
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3 import shutil
3e7978af2ba2 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/5f761ea7dab0a6f8c978cbbe4946e16edc6d032e/toos/CarboSeqSimulator commit 5f761ea7dab0a6f8c978cbbe4946e16edc6d032e-dirty"
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4 import math
3e7978af2ba2 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/5f761ea7dab0a6f8c978cbbe4946e16edc6d032e/toos/CarboSeqSimulator commit 5f761ea7dab0a6f8c978cbbe4946e16edc6d032e-dirty"
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5 import sys
3e7978af2ba2 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/5f761ea7dab0a6f8c978cbbe4946e16edc6d032e/toos/CarboSeqSimulator commit 5f761ea7dab0a6f8c978cbbe4946e16edc6d032e-dirty"
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3e7978af2ba2 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/5f761ea7dab0a6f8c978cbbe4946e16edc6d032e/toos/CarboSeqSimulator commit 5f761ea7dab0a6f8c978cbbe4946e16edc6d032e-dirty"
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7 def split_csv(input_folder, output_folder, max_chunck_size):
3e7978af2ba2 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/5f761ea7dab0a6f8c978cbbe4946e16edc6d032e/toos/CarboSeqSimulator commit 5f761ea7dab0a6f8c978cbbe4946e16edc6d032e-dirty"
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8 unit_path = input_folder + "/units.csv"
3e7978af2ba2 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/5f761ea7dab0a6f8c978cbbe4946e16edc6d032e/toos/CarboSeqSimulator commit 5f761ea7dab0a6f8c978cbbe4946e16edc6d032e-dirty"
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9 soil_path = input_folder + "/soil.csv"
3e7978af2ba2 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/5f761ea7dab0a6f8c978cbbe4946e16edc6d032e/toos/CarboSeqSimulator commit 5f761ea7dab0a6f8c978cbbe4946e16edc6d032e-dirty"
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10 crop_path = input_folder + "/crop.csv"
3e7978af2ba2 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/5f761ea7dab0a6f8c978cbbe4946e16edc6d032e/toos/CarboSeqSimulator commit 5f761ea7dab0a6f8c978cbbe4946e16edc6d032e-dirty"
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12 os.mkdir(output_folder)
3e7978af2ba2 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/5f761ea7dab0a6f8c978cbbe4946e16edc6d032e/toos/CarboSeqSimulator commit 5f761ea7dab0a6f8c978cbbe4946e16edc6d032e-dirty"
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14 dfs = pd.read_csv(soil_path)
3e7978af2ba2 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/5f761ea7dab0a6f8c978cbbe4946e16edc6d032e/toos/CarboSeqSimulator commit 5f761ea7dab0a6f8c978cbbe4946e16edc6d032e-dirty"
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15 dfc = pd.read_csv(crop_path)
3e7978af2ba2 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/5f761ea7dab0a6f8c978cbbe4946e16edc6d032e/toos/CarboSeqSimulator commit 5f761ea7dab0a6f8c978cbbe4946e16edc6d032e-dirty"
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e455667fe22f "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/494bf06621d4e5799cab9ef8384d4411a2cd4b84/toos/CarboSeqSimulator commit 494bf06621d4e5799cab9ef8384d4411a2cd4b84-dirty"
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17 fileS = open(soil_path, 'r')
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18 fileC = open(crop_path, 'r')
e455667fe22f "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/494bf06621d4e5799cab9ef8384d4411a2cd4b84/toos/CarboSeqSimulator commit 494bf06621d4e5799cab9ef8384d4411a2cd4b84-dirty"
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e455667fe22f "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/494bf06621d4e5799cab9ef8384d4411a2cd4b84/toos/CarboSeqSimulator commit 494bf06621d4e5799cab9ef8384d4411a2cd4b84-dirty"
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20 LineS = fileS.readlines()
e455667fe22f "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/494bf06621d4e5799cab9ef8384d4411a2cd4b84/toos/CarboSeqSimulator commit 494bf06621d4e5799cab9ef8384d4411a2cd4b84-dirty"
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21 LineC = fileC.readlines()
e455667fe22f "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/494bf06621d4e5799cab9ef8384d4411a2cd4b84/toos/CarboSeqSimulator commit 494bf06621d4e5799cab9ef8384d4411a2cd4b84-dirty"
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23 headerS = LineS.pop(0)
e455667fe22f "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/494bf06621d4e5799cab9ef8384d4411a2cd4b84/toos/CarboSeqSimulator commit 494bf06621d4e5799cab9ef8384d4411a2cd4b84-dirty"
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24 headerC = LineC.pop(0)
e455667fe22f "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/494bf06621d4e5799cab9ef8384d4411a2cd4b84/toos/CarboSeqSimulator commit 494bf06621d4e5799cab9ef8384d4411a2cd4b84-dirty"
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26 dfs['ID'] = dfs['ID'].astype('int')
20886bc40659 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/b1cafd3eb61b631ee0b1f8f6c5ef2f9a0e2b4ccf/toos/CarboSeqSimulator commit b1cafd3eb61b631ee0b1f8f6c5ef2f9a0e2b4ccf-dirty"
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27 dfc['ID'] = dfc['ID'].astype('int')
20886bc40659 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/b1cafd3eb61b631ee0b1f8f6c5ef2f9a0e2b4ccf/toos/CarboSeqSimulator commit b1cafd3eb61b631ee0b1f8f6c5ef2f9a0e2b4ccf-dirty"
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29 IDs = dfs['ID'].unique()
20886bc40659 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/b1cafd3eb61b631ee0b1f8f6c5ef2f9a0e2b4ccf/toos/CarboSeqSimulator commit b1cafd3eb61b631ee0b1f8f6c5ef2f9a0e2b4ccf-dirty"
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20886bc40659 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/b1cafd3eb61b631ee0b1f8f6c5ef2f9a0e2b4ccf/toos/CarboSeqSimulator commit b1cafd3eb61b631ee0b1f8f6c5ef2f9a0e2b4ccf-dirty"
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31 max_ID = len(IDs)
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33 step = max_chunck_size
3e7978af2ba2 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/5f761ea7dab0a6f8c978cbbe4946e16edc6d032e/toos/CarboSeqSimulator commit 5f761ea7dab0a6f8c978cbbe4946e16edc6d032e-dirty"
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35 nb_split = math.ceil(max_ID / max_chunck_size)
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37 for i in range(1, nb_split + 1):
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39 firstID = IDs[(i-1) * step]
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40 lastID = IDs[min((i * step) - 1 , max_ID - 1)]
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42 splitIDs = IDs[(i-1) * step : min((i * step) , max_ID)]
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44 whereS = dfs['ID'].isin(splitIDs)
e455667fe22f "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/494bf06621d4e5799cab9ef8384d4411a2cd4b84/toos/CarboSeqSimulator commit 494bf06621d4e5799cab9ef8384d4411a2cd4b84-dirty"
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45 whereSid = whereS[whereS].index.values
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46 firstSid = min(whereSid)
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47 lastSid = max(whereSid)
e455667fe22f "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/494bf06621d4e5799cab9ef8384d4411a2cd4b84/toos/CarboSeqSimulator commit 494bf06621d4e5799cab9ef8384d4411a2cd4b84-dirty"
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49 lineSsplit = LineS[firstSid:lastSid+1]
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51 whereC = dfc['ID'].isin(splitIDs)
e455667fe22f "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/494bf06621d4e5799cab9ef8384d4411a2cd4b84/toos/CarboSeqSimulator commit 494bf06621d4e5799cab9ef8384d4411a2cd4b84-dirty"
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52 whereCid = whereC[whereC].index.values
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53 firstCid = min(whereCid)
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54 lastCid = max(whereCid)
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56 lineCsplit = LineC[firstCid:lastCid+1]
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3e7978af2ba2 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/5f761ea7dab0a6f8c978cbbe4946e16edc6d032e/toos/CarboSeqSimulator commit 5f761ea7dab0a6f8c978cbbe4946e16edc6d032e-dirty"
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58 os.mkdir(os.path.join(output_folder, f"{input_folder}_{i}"))
3e7978af2ba2 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/5f761ea7dab0a6f8c978cbbe4946e16edc6d032e/toos/CarboSeqSimulator commit 5f761ea7dab0a6f8c978cbbe4946e16edc6d032e-dirty"
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59 shutil.copy(unit_path, os.path.join(output_folder, f"{input_folder}_{i}"))
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60
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61 splitFileS = open(os.path.join(output_folder, f"{input_folder}_{i}", "soil.csv"), 'w')
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62 splitFileS.writelines(headerS)
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63 splitFileS.writelines(lineSsplit)
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64 splitFileS.close()
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65
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66 splitFileC = open(os.path.join(output_folder, f"{input_folder}_{i}", "crop.csv"), 'w')
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67 splitFileC.writelines(headerC)
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68 splitFileC.writelines(lineCsplit)
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69 splitFileC.close()
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70
5
3e7978af2ba2 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/5f761ea7dab0a6f8c978cbbe4946e16edc6d032e/toos/CarboSeqSimulator commit 5f761ea7dab0a6f8c978cbbe4946e16edc6d032e-dirty"
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71 shutil.make_archive( os.path.join(output_folder,f"{input_folder}_{i}"), 'zip', os.path.join(output_folder, f"{input_folder}_{i}"))
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72
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73
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74
5
3e7978af2ba2 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/5f761ea7dab0a6f8c978cbbe4946e16edc6d032e/toos/CarboSeqSimulator commit 5f761ea7dab0a6f8c978cbbe4946e16edc6d032e-dirty"
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75 # Example usage
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76 input_folder = "input"
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77 output_folder = "outputs"
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78
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79 input_file = sys.argv[1]
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80 max_chunck_size = int(sys.argv[2])
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81
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82 shutil.unpack_archive(input_file, input_folder, 'zip')
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83
3e7978af2ba2 "planemo upload for repository https://forgemia.inra.fr/carboseq/record-projet-carboseq/-/tree/5f761ea7dab0a6f8c978cbbe4946e16edc6d032e/toos/CarboSeqSimulator commit 5f761ea7dab0a6f8c978cbbe4946e16edc6d032e-dirty"
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84 split_csv(input_folder, output_folder, max_chunck_size)