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annotate cut_up_fasta.py @ 2:bd409bbd287f draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 77dea70f156d56c83b6851b61dc997d2b344bdc9
author iuc
date Fri, 01 Jul 2022 14:10:59 +0000
parents 1f4286d836a3
children
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1f4286d836a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
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1 #!/usr/bin/env python
1f4286d836a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
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1f4286d836a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
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3 import argparse
1f4286d836a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
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4 import gzip
1f4286d836a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
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5 from functools import partial
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7 from Bio import SeqIO
1f4286d836a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
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1f4286d836a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
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10 def cut_up_fasta(input_fasta, chunk_size, overlap, merge_last, output_fasta, output_bed, gzipped):
1f4286d836a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
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11 if gzipped:
1f4286d836a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
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12 _open = partial(gzip.open, mode='rt')
1f4286d836a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
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13 else:
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14 _open = open
1f4286d836a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
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16 fasta_fh = open(output_fasta, 'w')
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18 if output_bed is not None:
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19 bed_fh = open(output_bed, 'w')
1f4286d836a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
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21 with _open(input_fasta) as input_fh:
1f4286d836a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
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22 for record in SeqIO.parse(input_fh, "fasta"):
1f4286d836a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
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23 if (not merge_last and len(record.seq) > chunk_size) or (merge_last and len(record.seq) >= 2 * chunk_size):
1f4286d836a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
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24 for index, split_seq in enumerate(chunks(record.seq, chunk_size, overlap, merge_last)):
1f4286d836a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
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25 fasta_fh.write(f">{record.id}.concoct_part_{index}\n{split_seq}\n")
1f4286d836a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
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26 if output_bed is not None:
1f4286d836a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
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27 bed_fh.write(f"{record.id}\t{chunk_size * index}\t{chunk_size * index + len(split_seq)}\t{record.id}.concoct_part_{index}\n")
1f4286d836a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
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28 else:
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29 fasta_fh.write(f">{record.id}.concoct_part_0\n{record.seq}\n")
1f4286d836a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
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30 if output_bed is not None:
1f4286d836a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
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31 bed_fh.write(f"{record.id}\t0\t{len(record.seq)}\t{record.id}.concoct_part_0\n")
1f4286d836a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
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32 if output_bed is not None:
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33 bed_fh.close()
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36 def chunks(seq, chunk_size, overlap_size, merge_last):
1f4286d836a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
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37 # Yield successive chunk_size-sized chunks from seq
1f4286d836a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
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38 # with given overlap overlap_size between the chunks.
1f4286d836a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
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39 assert chunk_size > overlap_size
1f4286d836a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
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40 if merge_last:
1f4286d836a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
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41 for i in range(0, len(seq) - chunk_size + 1, chunk_size - overlap_size):
1f4286d836a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
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42 yield seq[i:i + chunk_size] if i + chunk_size + chunk_size - overlap_size <= len(seq) else seq[i:]
1f4286d836a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
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43 else:
1f4286d836a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
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44 for i in range(0, len(seq), chunk_size - overlap_size):
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45 yield seq[i:i + chunk_size]
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48 parser = argparse.ArgumentParser()
1f4286d836a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
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49 parser.add_argument("--input_fasta", action="store", dest="input_fasta", help="Fasta files with contigs")
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50 parser.add_argument("--gzipped", action="store_true", dest="gzipped", help="Input file is gzipped")
1f4286d836a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
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51 parser.add_argument("--chunk_size", action="store", dest="chunk_size", type=int, help="Chunk size\n")
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52 parser.add_argument("--overlap_size", action="store", dest="overlap_size", type=int, help="Overlap size\n")
1f4286d836a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
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53 parser.add_argument("--merge_last", default=False, action="store_true", dest="merge_last", help="Concatenate final part to last contig\n")
1f4286d836a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
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54 parser.add_argument("--output_bed", action="store", dest="output_bed", default=None, help="BED file to be created with exact regions of the original contigs corresponding to the newly created contigs")
1f4286d836a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
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55 parser.add_argument("--output_fasta", action="store", dest="output_fasta", help="Output fasta file with cut contigs")
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57 args = parser.parse_args()
1f4286d836a3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
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58 cut_up_fasta(args.input_fasta, args.chunk_size, args.overlap_size, args.merge_last, args.output_fasta, args.output_bed, args.gzipped)