Mercurial > repos > bgruening > augustus_training

annotate extract_features.py @ 6:533b140a196a draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
author iuc
date Mon, 30 Aug 2021 21:43:32 +0000
parents da01a05d91c5
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
101933e63fa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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1 #!/usr/bin/env python
101933e63fa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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2
101933e63fa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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3 import argparse
101933e63fa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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4 import sys
101933e63fa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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5 import textwrap
101933e63fa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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6
101933e63fa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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7
4
da01a05d91c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
iuc
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8 def main(args):
0
101933e63fa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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9 """
4
da01a05d91c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
iuc
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10 Extract the protein and coding section from an augustus gff, gtf file
da01a05d91c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
iuc
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11 Example file:
da01a05d91c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
iuc
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12 HS04636 AUGUSTUS stop_codon 6901 6903 . + 0 Parent=g1.t1
da01a05d91c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
iuc
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13 HS04636 AUGUSTUS transcription_end_site 8857 8857 . + . Parent=g1.t1
da01a05d91c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
iuc
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14 # protein sequence = [MLARALLLCAVLALSHTANPCCSHPCQNRGVCMSVGFDQYKCDCTRTGFYGENCSTPEFLTRIKLFLKPTPNTVHYIL
da01a05d91c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
iuc
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15 # THFKGFWNVVNNIPFLRNAIMSYVLTSRSHLIDSPPTYNADYGYKSWEAFSNLSYYTRALPPVPDDCPTPLGVKGKKQLPDSNEIVEKLLLRRKFIPD
da01a05d91c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
iuc
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16 # PQGSNMMFAFFAQHFTHQFFKTDHKRGPAFTNGLGHGVDLNHIYGETLARQRKLRLFKDGKMKYQIIDGEMYPPTVKDTQAEMIYPPQVPEHLRFAVG
da01a05d91c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
iuc
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17 # QEVFGLVPGLMMYATIWLREHNRVCDVLKQEHPEWGDEQLFQTSRLILIGETIKIVIEDYVQHLSGYHFKLKFDPELLFNKQFQYQNRIAAEFNTLYH
da01a05d91c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
iuc
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18 # WHPLLPDTFQIHDQKYNYQQFIYNNSILLEHGITQFVESFTRQIAGRVAGGRNVPPAVQKVSQASIDQSRQMKYQSFNEYRKRFMLKPYESFEELTGE
da01a05d91c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
iuc
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19 # KEMSAELEALYGDIDAVELYPALLVEKPRPDAIFGETMVEVGAPFSLKGLMGNVICSPAYWKPSTFGGEVGFQIINTASIQSLICNNVKGCPFTSFSV
da01a05d91c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
iuc
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20 # PDPELIKTVTINASSSRSGLDDINPTVLLKERSTEL]
da01a05d91c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
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21 # end gene g1
da01a05d91c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
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22 ###
da01a05d91c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
iuc
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23 #
da01a05d91c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
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24 # ----- prediction on sequence number 2 (length = 2344, name = HS08198) -----
da01a05d91c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
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25 #
da01a05d91c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
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26 # Predicted genes for sequence number 2 on both strands
da01a05d91c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
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27 # start gene g2
da01a05d91c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
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28 HS08198 AUGUSTUS gene 86 2344 1 + . ID=g2
da01a05d91c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
iuc
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29 HS08198 AUGUSTUS transcript 86 2344 . + . ID=g2.t1;Parent=g2
da01a05d91c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
iuc
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30 HS08198 AUGUSTUS transcription_start_site 86 86 . + . Parent=g2.t1
da01a05d91c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
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31 HS08198 AUGUSTUS exon 86 582 . + . Parent=g2.t1
da01a05d91c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
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32 HS08198 AUGUSTUS start_codon 445 447 . + 0 Parent=g2.t1
0
101933e63fa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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33 """
4
da01a05d91c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
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34 protein_seq = ""
da01a05d91c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
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35 coding_seq = ""
0
101933e63fa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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36 if args.protein:
4
da01a05d91c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
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37 po = open(args.protein, "w+")
0
101933e63fa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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38 if args.codingseq:
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da01a05d91c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
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39 co = open(args.codingseq, "w+")
0
101933e63fa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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40
101933e63fa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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41 for line in sys.stdin:
101933e63fa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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42 # protein- and coding-sequence are stored as comments
4
da01a05d91c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
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43 if line.startswith("#"):
0
101933e63fa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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44 line = line[2:].strip()
4
da01a05d91c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
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45 if line.startswith("start gene"):
0
101933e63fa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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46 gene_name = line[11:].strip()
101933e63fa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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47
101933e63fa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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48 if protein_seq:
4
da01a05d91c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
iuc
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49 if line.endswith("]"):
0
101933e63fa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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50 protein_seq += line[:-1]
4
da01a05d91c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
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51 po.write(
da01a05d91c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
iuc
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52 ">%s\n%s\n"
da01a05d91c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
iuc
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53 % (gene_name, "\n".join(textwrap.wrap(protein_seq, 80)))
da01a05d91c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
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54 )
da01a05d91c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
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55 protein_seq = ""
0
101933e63fa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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56 else:
101933e63fa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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57 protein_seq += line
101933e63fa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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58
101933e63fa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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59 if coding_seq:
4
da01a05d91c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
iuc
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60 if line.endswith("]"):
0
101933e63fa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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61 coding_seq += line[:-1]
4
da01a05d91c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
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62 co.write(
da01a05d91c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
iuc
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63 ">%s\n%s\n"
da01a05d91c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
iuc
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64 % (gene_name, "\n".join(textwrap.wrap(coding_seq, 80)))
da01a05d91c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
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65 )
da01a05d91c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
iuc
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66 coding_seq = ""
0
101933e63fa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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67 else:
101933e63fa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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68 coding_seq += line
101933e63fa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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69
4
da01a05d91c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
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70 if args.protein and line.startswith("protein sequence = ["):
da01a05d91c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
iuc
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71 if line.endswith("]"):
0
101933e63fa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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72 protein_seq = line[20:-1]
4
da01a05d91c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
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73 po.write(
da01a05d91c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
iuc
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74 ">%s\n%s\n"
da01a05d91c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
iuc
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75 % (gene_name, "\n".join(textwrap.wrap(protein_seq, 80)))
da01a05d91c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
iuc
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76 )
da01a05d91c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
iuc
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77 protein_seq = ""
0
101933e63fa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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78 else:
101933e63fa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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79 line = line[20:]
101933e63fa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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80 protein_seq = line
101933e63fa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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81
4
da01a05d91c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
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82 if args.codingseq and line.startswith("coding sequence = ["):
da01a05d91c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit bba7f5df059fcbeb06e89cf689e9a04d4f22cb76"
iuc
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83 if line.endswith("]"):
0
101933e63fa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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84 coding_seq = line[19:-1]
4
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85 co.write(
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86 ">%s\n%s\n"
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87 % (gene_name, "\n".join(textwrap.wrap(coding_seq, 80)))
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88 )
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89 coding_seq = ""
0
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90 else:
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91 line = line[19:]
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92 coding_seq = line
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93
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94 if args.codingseq:
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95 co.close()
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96 if args.protein:
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97 po.close()
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98
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99
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100 if __name__ == "__main__":
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101 parser = argparse.ArgumentParser()
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102 parser.add_argument("-p", "--protein", help="Path to the protein file.")
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103 parser.add_argument("-c", "--codingseq", help="Path to the coding file.")
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104
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105 args = parser.parse_args()
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106 main(args)