Mercurial > repos > iuc > nanocompore_db

annotate NanocomporeDB_process.py @ 0:ace1c453a190 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 652a872061324ba1073bfa286777ffeefa352671"
author iuc
date Mon, 08 Jun 2020 18:33:20 +0000
parents
children 97a6b3f9a98d
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ace1c453a190 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 652a872061324ba1073bfa286777ffeefa352671"
iuc
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1 #!/usr/bin/env python
ace1c453a190 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 652a872061324ba1073bfa286777ffeefa352671"
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3 import argparse
ace1c453a190 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 652a872061324ba1073bfa286777ffeefa352671"
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4 import os
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6 from nanocompore.SampCompDB import SampCompDB
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9 def is_valid_file(file_name):
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10 if os.path.isfile(file_name):
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11 return os.path.abspath(file_name)
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12 else:
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13 raise FileNotFoundError(os.path.abspath(file_name))
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16 def is_valid_directory(dir_name):
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17 if os.path.isdir(dir_name):
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18 return os.path.abspath(dir_name)
ace1c453a190 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 652a872061324ba1073bfa286777ffeefa352671"
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19 else:
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20 raise NotADirectoryError(os.path.abspath(dir_name))
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23 if __name__ == '__main__':
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25 parser = argparse.ArgumentParser(
ace1c453a190 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 652a872061324ba1073bfa286777ffeefa352671"
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26 description='save nanocompre sampcomp \
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27 results as interval outputs \
ace1c453a190 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 652a872061324ba1073bfa286777ffeefa352671"
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28 \nSample call: \"python Nannocompore-plot.py --db-path \
ace1c453a190 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 652a872061324ba1073bfa286777ffeefa352671"
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29 ./out_SampComp.db --ref-fasta ref.fa --annotation-bed annot.bed \
ace1c453a190 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 652a872061324ba1073bfa286777ffeefa352671"
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30 --out-dir ./plots/')
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31
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32 parser.add_argument('--ref-fasta', required=True, type=is_valid_file,
ace1c453a190 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 652a872061324ba1073bfa286777ffeefa352671"
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33 help='The reference genome used for read alignment.')
ace1c453a190 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 652a872061324ba1073bfa286777ffeefa352671"
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34 parser.add_argument('--db-path', default="./out_SampComp.db", type=str,
ace1c453a190 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 652a872061324ba1073bfa286777ffeefa352671"
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35 help='Path to the SampCompDB database path prefix.')
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36 parser.add_argument('--annotation-bed', required=False, type=is_valid_file,
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37 help='BED file containing the annotation of the transcriptome used as reference when mapping')
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38 parser.add_argument('--pvalue-types', type=str,
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39 default='GMM_logit_pvalue,KS_dwell_pvalue,KS_intensity_pvalue',
ace1c453a190 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 652a872061324ba1073bfa286777ffeefa352671"
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40 help='path to the annotations')
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41 parser.add_argument('--bedgraph', default=False,
ace1c453a190 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 652a872061324ba1073bfa286777ffeefa352671"
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42 help='write output in BEDGRAPH format instead of BED')
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43 parser.add_argument('--pvalue-threshold', default=1.0,
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44 help='Maximum reported p-value.')
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45 parser.add_argument('--out-dir', default="./", type=is_valid_directory,
ace1c453a190 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanocompore commit 652a872061324ba1073bfa286777ffeefa352671"
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46 help='path the plotting output directory.')
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47
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48 args = parser.parse_args()
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49
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50 db = SampCompDB(args.db_path, fasta_fn=args.ref_fasta,
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51 bed_fn=args.annotation_bed)
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52 print(db)
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53 print("DB read ids:", db.ref_id_list)
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54
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55 if args.annotation_bed:
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56 for pt in args.pvalue_types.split(','):
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57 print("bedgraph output for p-value type:", pt)
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58 db.save_to_bed(output_fn='{}/{}.bedgraph'.format(args.out_dir, pt),
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59 pvalue_field=pt, pvalue_thr=args.pvalue_threshold,
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60 bedgraph=args.bedgraph)