Mercurial > repos > fubar > jbrowse2

comparison jbrowse2.py @ 120:af482048ca1a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 59fe39774d791bc684811b6ce03e13ef093d074e
author fubar
date Tue, 24 Sep 2024 03:57:09 +0000
parents 794aecef8327
children 478ee3e780de
comparison
equal deleted inserted replaced
119:2fff478aca4b 120:af482048ca1a
8 import logging 8 import logging
9 import os 9 import os
10 import re 10 import re
11 import shutil 11 import shutil
12 import ssl 12 import ssl
13 import string
13 import struct 14 import struct
14 import subprocess 15 import subprocess
15 import tempfile 16 import tempfile
16 import urllib.request 17 import urllib.request
17 import xml.etree.ElementTree as ET 18 import xml.etree.ElementTree as ET
1598 parser.add_argument("--outdir", help="Output directory", default="out") 1599 parser.add_argument("--outdir", help="Output directory", default="out")
1599 parser.add_argument("--version", "-V", action="version", version=JB2VER) 1600 parser.add_argument("--version", "-V", action="version", version=JB2VER)
1600 args = parser.parse_args() 1601 args = parser.parse_args()
1601 tree = ET.parse(args.xml) 1602 tree = ET.parse(args.xml)
1602 root = tree.getroot() 1603 root = tree.getroot()
1603 1604 removeMe = string.punctuation.replace('.','').replace('/','').replace('-','')
1605 nopunct = str.maketrans(dict.fromkeys(removeMe))
1604 # This should be done ASAP 1606 # This should be done ASAP
1605 GALAXY_INFRASTRUCTURE_URL = root.find("metadata/galaxyUrl").text 1607 GALAXY_INFRASTRUCTURE_URL = root.find("metadata/galaxyUrl").text
1606 # Sometimes this comes as `localhost` without a protocol 1608 # Sometimes this comes as `localhost` without a protocol
1607 if not GALAXY_INFRASTRUCTURE_URL.startswith("http"): 1609 if not GALAXY_INFRASTRUCTURE_URL.startswith("http"):
1608 # so we'll prepend `http://` and hope for the best. Requests *should* 1610 # so we'll prepend `http://` and hope for the best. Requests *should*
1615 trackI = 0 1617 trackI = 0
1616 for ass in root.findall("assembly"): 1618 for ass in root.findall("assembly"):
1617 genomes = [ 1619 genomes = [
1618 { 1620 {
1619 "path": x.attrib["path"], 1621 "path": x.attrib["path"],
1620 "label": x.attrib["label"].split(" ")[0].replace(",", ""), 1622 "label": x.attrib["label"].split(" ")[0].translate(nopunct),
1621 "useuri": x.attrib["useuri"], 1623 "useuri": x.attrib["useuri"],
1622 "meta": metadata_from_node(x.find("metadata")), 1624 "meta": metadata_from_node(x.find("metadata")),
1623 } 1625 }
1624 for x in ass.findall("metadata/genomes/genome") 1626 for x in ass.findall("metadata/genomes/genome")
1625 ] 1627 ]
1653 for x in trackfiles: 1655 for x in trackfiles:
1654 isBed = False 1656 isBed = False
1655 if x.attrib['ext'] == "bed": 1657 if x.attrib['ext'] == "bed":
1656 isBed = True 1658 isBed = True
1657 track_conf["label"] = "%s_%d" % ( 1659 track_conf["label"] = "%s_%d" % (
1658 x.attrib["label"].replace(" ", "_").replace(",", "_").replace("/", "_"), 1660 x.attrib["label"].translate(nopunct),
1659 trackI, 1661 trackI,
1660 ) 1662 )
1661 trackI += 1 1663 trackI += 1
1662 track_conf["useuri"] = x.attrib["useuri"] 1664 track_conf["useuri"] = x.attrib["useuri"]
1663 if is_multi_bigwig: 1665 if is_multi_bigwig:
1664 multi_bigwig_paths.append( 1666 multi_bigwig_paths.append(
1665 ( 1667 (
1666 track_conf["label"], 1668 track_conf["label"].translate(nopunct),
1667 track_conf["useuri"], 1669 track_conf["useuri"],
1668 os.path.realpath(x.attrib["path"]), 1670 os.path.realpath(x.attrib["path"]),
1669 ) 1671 )
1670 ) 1672 )
1671 else: 1673 else: