mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-19 02:21:32 +08:00
Nicola Soranzo
5fe5b53bf3
Also: - Add and fix type annotations - Fix call of `object_store_allows_id_selection()` method
85 lines
2.6 KiB
Python
85 lines
2.6 KiB
Python
#!/usr/bin/env python
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"""
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Connects to a UCSC table browser and scrapes chrominfo for every build
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specified by an input file (such as one output by parse_builds.py).
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If not input file specified, it will connect using parse_builds.py to
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retrieve a list of available builds.
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All chromInfo is placed in a path with the convention
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{dbpath}/buildname.len
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Usage:
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python build_chrom_db.py dbpath/ [builds_file]
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"""
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import fileinput
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import os
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import sys
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from urllib.parse import urlencode
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import parse_builds
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from galaxy.util import requests
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def getchrominfo(url, db):
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tableURL = "http://genome-test.gi.ucsc.edu/cgi-bin/hgTables?"
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URL = tableURL + urlencode(
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{
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"clade": "",
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"org": "",
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"db": db,
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"hgta_outputType": "primaryTable",
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"hgta_group": "allTables",
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"hgta_table": "chromInfo",
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"hgta_track": db,
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"hgta_regionType": "",
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"position": "",
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"hgta_doTopSubmit": "get info",
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}
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)
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page = requests.get(URL).text
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for i, line in enumerate(page.splitlines()):
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line = line.rstrip("\r\n")
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if line.startswith("#"):
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continue
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fields = line.split("\t")
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if len(fields) > 1 and len(fields[0]) > 0 and int(fields[1]) > 0:
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yield [fields[0], fields[1]]
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else:
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raise Exception(f"Problem parsing line {i} '{line}' in page '{page}'")
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if __name__ == "__main__":
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if len(sys.argv) == 1:
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sys.exit("Path to place chromInfo tables must be specified.")
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dbpath = sys.argv[1]
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builds = []
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if len(sys.argv) > 2:
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try:
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buildfile = fileinput.FileInput(sys.argv[2])
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for line in buildfile:
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if line.startswith("#"):
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continue
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builds.append(line.split("\t")[0])
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except Exception:
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sys.exit("Bad input file.")
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else:
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try:
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for build in parse_builds.getbuilds("http://genome.cse.ucsc.edu/cgi-bin/das/dsn"):
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builds.append(build[0])
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except Exception:
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sys.exit("Unable to retrieve builds.")
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for build in builds:
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if build == "?":
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continue # no lengths for unspecified chrom
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print("Retrieving " + build)
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outfile_name = dbpath + build + ".len"
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try:
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with open(outfile_name, "w") as outfile:
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for chrominfo in getchrominfo("http://genome-test.gi.ucsc.edu/cgi-bin/hgTables?", build):
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print("\t".join(chrominfo), file=outfile)
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except Exception as e:
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print(f"Failed to retrieve {build}: {e}")
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os.remove(outfile_name)
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