Mercurial > repos > artbio > repenrich
comparison RepEnrich_setup.py @ 11:6bba3e33c2e7 draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich commit 11df9f0b68d35d3a9424a17e4cefee6cfb9d4c19
author | artbio |
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date | Sat, 09 Mar 2024 22:32:46 +0000 |
parents | f6f0f1e5e940 |
children | 89e05f831259 |
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10:6f4143893463 | 11:6bba3e33c2e7 |
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5 import shlex | 5 import shlex |
6 import subprocess | 6 import subprocess |
7 import sys | 7 import sys |
8 | 8 |
9 from Bio import SeqIO | 9 from Bio import SeqIO |
10 from Bio.Alphabet import IUPAC | |
11 from Bio.Seq import Seq | 10 from Bio.Seq import Seq |
12 from Bio.SeqRecord import SeqRecord | 11 from Bio.SeqRecord import SeqRecord |
13 | 12 |
14 parser = argparse.ArgumentParser(description=''' | 13 parser = argparse.ArgumentParser(description=''' |
15 Part I: Prepartion of repetive element psuedogenomes and repetive\ | 14 Part I: Prepartion of repetive element psuedogenomes and repetive\ |
240 metagenome = metagenome + spacer + genome[chr][rstart:(rend+1)] | 239 metagenome = metagenome + spacer + genome[chr][rstart:(rend+1)] |
241 except KeyError: | 240 except KeyError: |
242 print("Unrecognised Chromosome: "+chr) | 241 print("Unrecognised Chromosome: "+chr) |
243 pass | 242 pass |
244 # Convert metagenome to SeqRecord object (required by SeqIO.write) | 243 # Convert metagenome to SeqRecord object (required by SeqIO.write) |
245 record = SeqRecord(Seq(metagenome, IUPAC.unambiguous_dna), id="repname", | 244 record = SeqRecord(Seq(metagenome), id="repname", |
246 name="", description="") | 245 name="", description="") |
247 print("saving repgenome " + newname + ".fa" + " (" + str(k) + " of " | 246 print("saving repgenome " + newname + ".fa" + " (" + str(k) + " of " |
248 + str(nrepgenomes) + ")") | 247 + str(nrepgenomes) + ")") |
249 fastafilename = os.path.realpath(setup_folder + os.path.sep | 248 fastafilename = os.path.realpath(setup_folder + os.path.sep |
250 + newname + ".fa") | 249 + newname + ".fa") |