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annotate list_spaln_tables.py @ 4:2e92e1929cb1 draft default tip

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planemo upload for repository https://github.com/ogotoh/spaln commit ab06c07b81a9a6883ec58d3da22bed6e2b63d4d5
author iuc
date Thu, 09 Jun 2022 22:57:17 +0000
parents 37b5e1f0b544
children
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37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
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1 #!/usr/bin/env python3
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3 import argparse
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4 import shlex
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5 import sys
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6 from subprocess import run
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7 from typing import TextIO
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10 def find_common_ancestor_distance(
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11 taxon: str, other_taxon: str, taxonomy_db_path: str, only_canonical: bool
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12 ):
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13 canonical = "--only_canonical" if only_canonical else ""
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14 cmd_str = f"taxonomy_util -d {taxonomy_db_path} common_ancestor_distance {canonical} '{other_taxon}' '{taxon}'"
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15 cmd = shlex.split(cmd_str)
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16 proc = run(cmd, encoding="utf8", capture_output=True)
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17 return proc
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20 def find_distances(gnm2tab_file: TextIO, taxon: str, taxonomy_db_path: str):
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21 cmd = ["taxonomy_util", "-d", taxonomy_db_path, "get_id", taxon]
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22 proc = run(cmd, capture_output=True, encoding="utf8")
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23 if "not found in" in proc.stderr:
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24 exit("Error: " + proc.stderr.strip())
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25 for line in gnm2tab_file:
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26 fields = line.split("\t")
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27 (species_code, settings, other_taxon) = map(lambda el: el.strip(), fields[:3])
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28 proc = find_common_ancestor_distance(taxon, other_taxon, taxonomy_db_path, True)
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29 ancestor_info = proc.stdout.rstrip()
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30 if proc.stderr != "":
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31 print("Warning:", other_taxon, proc.stderr.rstrip(), file=sys.stderr)
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32 else:
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33 proc = find_common_ancestor_distance(
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34 taxon, other_taxon, taxonomy_db_path, False
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35 )
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36 non_canonical_distance = proc.stdout.split("\t")[0]
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37 print(
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38 non_canonical_distance,
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39 ancestor_info,
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40 species_code,
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41 settings,
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42 other_taxon,
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43 sep="\t",
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44 )
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45
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46
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47 if __name__ == "__main__":
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48 parser = argparse.ArgumentParser(description="Find distance to common ancestor")
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49 parser.add_argument(
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50 "--taxonomy_db", required=True, help="NCBI Taxonomy database (SQLite format)"
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51 )
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52 parser.add_argument(
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53 "--gnm2tab_file",
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54 required=True,
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55 type=argparse.FileType(),
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56 help="gnm2tab file from spal",
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57 )
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58 parser.add_argument("taxon")
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59 args = parser.parse_args()
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60
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61 find_distances(args.gnm2tab_file, args.taxon, args.taxonomy_db)