Mercurial > repos > rnateam > graphclust_postprocessing

annotate addCdhitseqs.py @ 3:79b9117aef01 draft

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planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit c03cf64554289eb098267c0923cf0cf7b245cc0c
author rnateam
date Wed, 04 Jan 2017 18:15:07 -0500
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children 869a6e807d76
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79b9117aef01 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit c03cf64554289eb098267c0923cf0cf7b245cc0c
rnateam
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diff changeset
1 import re
79b9117aef01 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit c03cf64554289eb098267c0923cf0cf7b245cc0c
rnateam
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2 import glob
79b9117aef01 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit c03cf64554289eb098267c0923cf0cf7b245cc0c
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3 import sys
79b9117aef01 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit c03cf64554289eb098267c0923cf0cf7b245cc0c
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79b9117aef01 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit c03cf64554289eb098267c0923cf0cf7b245cc0c
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5 cdhitcluster = sys.argv[1]
79b9117aef01 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit c03cf64554289eb098267c0923cf0cf7b245cc0c
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6 #clusters = sys.argv[2]
79b9117aef01 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit c03cf64554289eb098267c0923cf0cf7b245cc0c
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79b9117aef01 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit c03cf64554289eb098267c0923cf0cf7b245cc0c
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8 cluster_seqs_stats_path = "RESULTS/*.cluster.all"
79b9117aef01 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit c03cf64554289eb098267c0923cf0cf7b245cc0c
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9 cluster_seqs_stats_files = glob.glob(cluster_seqs_stats_path)
79b9117aef01 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit c03cf64554289eb098267c0923cf0cf7b245cc0c
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79b9117aef01 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit c03cf64554289eb098267c0923cf0cf7b245cc0c
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11 #clusterFiles = clusters.split(',')
79b9117aef01 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit c03cf64554289eb098267c0923cf0cf7b245cc0c
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12 repSeqRedSeqdict = {}
79b9117aef01 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit c03cf64554289eb098267c0923cf0cf7b245cc0c
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13 repLine = ""
79b9117aef01 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit c03cf64554289eb098267c0923cf0cf7b245cc0c
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14 count = 0
79b9117aef01 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit c03cf64554289eb098267c0923cf0cf7b245cc0c
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15 first = False
79b9117aef01 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit c03cf64554289eb098267c0923cf0cf7b245cc0c
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79b9117aef01 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit c03cf64554289eb098267c0923cf0cf7b245cc0c
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17 with open(cdhitcluster, 'r+') as f:
79b9117aef01 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit c03cf64554289eb098267c0923cf0cf7b245cc0c
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18 lines = f.readlines()
79b9117aef01 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit c03cf64554289eb098267c0923cf0cf7b245cc0c
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19 for i in range(0, len(lines)):
79b9117aef01 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit c03cf64554289eb098267c0923cf0cf7b245cc0c
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20 line = lines[i]
79b9117aef01 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit c03cf64554289eb098267c0923cf0cf7b245cc0c
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21 if ">Cluster" in line:
79b9117aef01 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit c03cf64554289eb098267c0923cf0cf7b245cc0c
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22 first = True
79b9117aef01 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit c03cf64554289eb098267c0923cf0cf7b245cc0c
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23 count = 0
79b9117aef01 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit c03cf64554289eb098267c0923cf0cf7b245cc0c
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24 if i+1 < len(lines):
79b9117aef01 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit c03cf64554289eb098267c0923cf0cf7b245cc0c
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25 repLine = lines[i+1]
79b9117aef01 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit c03cf64554289eb098267c0923cf0cf7b245cc0c
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26 continue
79b9117aef01 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit c03cf64554289eb098267c0923cf0cf7b245cc0c
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27 elif not first:
79b9117aef01 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit c03cf64554289eb098267c0923cf0cf7b245cc0c
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28 count += 1
79b9117aef01 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit c03cf64554289eb098267c0923cf0cf7b245cc0c
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29 first = False
79b9117aef01 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit c03cf64554289eb098267c0923cf0cf7b245cc0c
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30 else:
79b9117aef01 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit c03cf64554289eb098267c0923cf0cf7b245cc0c
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31 first = False
79b9117aef01 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit c03cf64554289eb098267c0923cf0cf7b245cc0c
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32 lineArr = []
79b9117aef01 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit c03cf64554289eb098267c0923cf0cf7b245cc0c
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33 if count > 0:
79b9117aef01 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit c03cf64554289eb098267c0923cf0cf7b245cc0c
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34 repLine = repLine.strip()
79b9117aef01 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit c03cf64554289eb098267c0923cf0cf7b245cc0c
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35 rep_FullId = repLine.split()[2]
79b9117aef01 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit c03cf64554289eb098267c0923cf0cf7b245cc0c
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36 rep_FullId = rep_FullId.replace(">", "")
79b9117aef01 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit c03cf64554289eb098267c0923cf0cf7b245cc0c
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37 #rep_short_id = re.findall("_".join(["[^_]+"] * 2), rep_FullId)[0]
79b9117aef01 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit c03cf64554289eb098267c0923cf0cf7b245cc0c
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38 rep_FullId = rep_FullId.replace("...", "")
79b9117aef01 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit c03cf64554289eb098267c0923cf0cf7b245cc0c
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39 line = line.strip()
79b9117aef01 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit c03cf64554289eb098267c0923cf0cf7b245cc0c
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40 add_FullId = line.split()[2]
79b9117aef01 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit c03cf64554289eb098267c0923cf0cf7b245cc0c
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41 add_FullId = add_FullId.replace(">", "")
79b9117aef01 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit c03cf64554289eb098267c0923cf0cf7b245cc0c
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42 add_FullId = add_FullId.replace("...", "")
79b9117aef01 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit c03cf64554289eb098267c0923cf0cf7b245cc0c
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43 #add_short_id = re.findall("_".join(["[^_]+"] * 2), add_FullId)[0]
79b9117aef01 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit c03cf64554289eb098267c0923cf0cf7b245cc0c
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44 lineArr.append(add_FullId)
79b9117aef01 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit c03cf64554289eb098267c0923cf0cf7b245cc0c
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45 repSeqRedSeqdict[rep_FullId] = lineArr
79b9117aef01 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit c03cf64554289eb098267c0923cf0cf7b245cc0c
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46 #lineArr.append(add_short_id)
79b9117aef01 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit c03cf64554289eb098267c0923cf0cf7b245cc0c
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47 #repSeqRedSeqdict[rep_short_id] = lineArr
79b9117aef01 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit c03cf64554289eb098267c0923cf0cf7b245cc0c
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48
79b9117aef01 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit c03cf64554289eb098267c0923cf0cf7b245cc0c
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49 toWrite = ""
79b9117aef01 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit c03cf64554289eb098267c0923cf0cf7b245cc0c
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50
79b9117aef01 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit c03cf64554289eb098267c0923cf0cf7b245cc0c
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51 for singleFile in sorted(cluster_seqs_stats_files):
79b9117aef01 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit c03cf64554289eb098267c0923cf0cf7b245cc0c
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52 with open(singleFile, "a+") as clFile:
79b9117aef01 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit c03cf64554289eb098267c0923cf0cf7b245cc0c
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53 file_content = clFile.read()
79b9117aef01 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit c03cf64554289eb098267c0923cf0cf7b245cc0c
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54 first_line = file_content.split('\n')[0]
79b9117aef01 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit c03cf64554289eb098267c0923cf0cf7b245cc0c
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55 for key, val in repSeqRedSeqdict.items():
79b9117aef01 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit c03cf64554289eb098267c0923cf0cf7b245cc0c
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56 if key in file_content:
79b9117aef01 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit c03cf64554289eb098267c0923cf0cf7b245cc0c
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57 for i in val:
79b9117aef01 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit c03cf64554289eb098267c0923cf0cf7b245cc0c
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58 toWrite += first_line.split()[0] + " " + first_line.split()[1] + " " + first_line.split()[2] + " " + " - " + " " + "CD-Hit" + " " + first_line.split()[5] + " " + "ORIGID" + " " + str(i) + "\n"
79b9117aef01 planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/branchForIterations/tools/GraphClust/CollectResults commit c03cf64554289eb098267c0923cf0cf7b245cc0c
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59 clFile.write(toWrite)