Mercurial > repos > iuc > transit_resampling

annotate gff_to_prot.py @ 8:32a5211380bc draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit bd061799ebd49ada1a666d0815720c18291728da"
author iuc
date Wed, 16 Oct 2019 04:29:26 -0400
parents 3fcb70c1ca78
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
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173bf0f6ca1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0-dirty
iuc
parents:
diff changeset
1 #!/usr/bin/env python
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3fcb70c1ca78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents: 2
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2 import csv
3fcb70c1ca78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents: 2
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3 import os
2
173bf0f6ca1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0-dirty
iuc
parents:
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4 import sys
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3fcb70c1ca78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents: 2
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5
2
173bf0f6ca1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0-dirty
iuc
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6
173bf0f6ca1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0-dirty
iuc
parents:
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7 def get_description(line, parent):
173bf0f6ca1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0-dirty
iuc
parents:
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8 cols = line.split('\t')
173bf0f6ca1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0-dirty
iuc
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9 labels = {}
173bf0f6ca1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0-dirty
iuc
parents:
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10 for pair in cols[8].split(";"):
173bf0f6ca1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0-dirty
iuc
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11 k, v = pair.split('=')
173bf0f6ca1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0-dirty
iuc
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12 labels[k] = v
173bf0f6ca1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0-dirty
iuc
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173bf0f6ca1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0-dirty
iuc
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14 if (cols[2]) == "CDS" and labels["Parent"] == parent:
173bf0f6ca1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0-dirty
iuc
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15 return labels.get("Note", '-')
173bf0f6ca1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0-dirty
iuc
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16 return '-'
173bf0f6ca1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0-dirty
iuc
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173bf0f6ca1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0-dirty
iuc
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173bf0f6ca1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0-dirty
iuc
parents:
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19 def convert_to_prot_table(fname, output_name):
173bf0f6ca1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0-dirty
iuc
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20 gff_file = open(fname)
173bf0f6ca1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0-dirty
iuc
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21 output_file = open(output_name, 'w')
173bf0f6ca1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0-dirty
iuc
parents:
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22 writer = csv.writer(output_file, delimiter='\t')
173bf0f6ca1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0-dirty
iuc
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23 lines = gff_file.readlines()
173bf0f6ca1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0-dirty
iuc
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24 gff_file.close()
173bf0f6ca1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0-dirty
iuc
parents:
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25 for i, line in enumerate(lines):
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3fcb70c1ca78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents: 2
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26 line = line.strip()
3fcb70c1ca78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents: 2
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27 if line.startswith('#'):
3fcb70c1ca78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents: 2
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28 continue
2
173bf0f6ca1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0-dirty
iuc
parents:
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29 cols = line.split('\t')
173bf0f6ca1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0-dirty
iuc
parents:
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30 if (len(cols) < 9):
173bf0f6ca1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0-dirty
iuc
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31 print("Ignoring invalid row with entries: {0}".format(cols))
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3fcb70c1ca78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents: 2
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32 elif (cols[2]) == "region":
3fcb70c1ca78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents: 2
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33 continue
3fcb70c1ca78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents: 2
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34 elif (cols[2]) == "CDS":
3fcb70c1ca78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents: 2
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35 continue
2
173bf0f6ca1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0-dirty
iuc
parents:
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36 elif (cols[2]) == "gene":
173bf0f6ca1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0-dirty
iuc
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37 start = int(cols[3])
173bf0f6ca1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0-dirty
iuc
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38 end = int(cols[4])
173bf0f6ca1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0-dirty
iuc
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39 strand = cols[6].strip()
173bf0f6ca1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0-dirty
iuc
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40 labels = {}
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3fcb70c1ca78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents: 2
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41 diff = int(abs(end - start) / 3) # What is this called?
2
173bf0f6ca1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0-dirty
iuc
parents:
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42 for pair in cols[8].split(";"):
173bf0f6ca1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0-dirty
iuc
parents:
diff changeset
43 k, v = pair.split('=')
173bf0f6ca1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0-dirty
iuc
parents:
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44 labels[k.strip()] = v.strip()
173bf0f6ca1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0-dirty
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45
5
3fcb70c1ca78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
iuc
parents: 2
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46 Rv = labels["locus_tag"].strip() # error out if not found
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173bf0f6ca1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0-dirty
iuc
parents:
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47 gene = labels.get('Name', '')
173bf0f6ca1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0-dirty
iuc
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48 desc = get_description(lines[i + 1], labels.get("ID", "")) if (i + 1) < len(lines) else '-'
173bf0f6ca1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0-dirty
iuc
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49 vals = [desc, start, end, strand, diff, '-', '-', gene, Rv, '-']
173bf0f6ca1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0-dirty
iuc
parents:
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50 writer.writerow(vals)
173bf0f6ca1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0-dirty
iuc
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51 output_file.close()
173bf0f6ca1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0-dirty
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52
5
3fcb70c1ca78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 73c6b2baf9dda26c6809a4f36582f7cbdb161ea1
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53
2
173bf0f6ca1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0-dirty
iuc
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54 if __name__ == "__main__":
173bf0f6ca1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0-dirty
iuc
parents:
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55 usage_string = "Usage: python gff-prot-converter.py <gff filename> <output filename>"
173bf0f6ca1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0-dirty
iuc
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56
173bf0f6ca1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0-dirty
iuc
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57 if len(sys.argv) < 3:
173bf0f6ca1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0-dirty
iuc
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58 print(usage_string)
173bf0f6ca1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0-dirty
iuc
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59 sys.exit(0)
173bf0f6ca1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0-dirty
iuc
parents:
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60 file_name = sys.argv[1]
173bf0f6ca1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0-dirty
iuc
parents:
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61 if not os.path.exists(file_name):
173bf0f6ca1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0-dirty
iuc
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62 print("File not found. Exiting...")
173bf0f6ca1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0-dirty
iuc
parents:
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63 print(usage_string)
173bf0f6ca1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0-dirty
iuc
parents:
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64 sys.exit(0)
173bf0f6ca1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit/ commit 9ffba16c072c7dafe4ef0b70cd2ef166fbe903d0-dirty
iuc
parents:
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65 convert_to_prot_table(file_name, sys.argv[2])