# HG changeset patch
# User fubar
# Date 1711611964 0
# Node ID ac00dcfb5d1d2ee25e9b8705a30a9386a5757bad
# Parent ab0d6782a95fbc897b93cd143d702741a3805a14
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
diff -r ab0d6782a95f -r ac00dcfb5d1d jbrowse2.py
--- a/jbrowse2.py Thu Mar 28 04:51:06 2024 +0000
+++ b/jbrowse2.py Thu Mar 28 07:46:04 2024 +0000
@@ -15,7 +15,7 @@
import xml.etree.ElementTree as ET
from collections import defaultdict
-logging.basicConfig(level=logging.DEBUG)
+logging.basicConfig(level=logging.INFO)
log = logging.getLogger("jbrowse")
JB2VER = "v2.10.3"
@@ -493,7 +493,7 @@
else:
try:
fl = urllib.request.urlopen(fapath + ".fai").readline()
- except:
+ except Exception:
fl = None
if fl: # is first row of the text fai so the first contig name
this_genome["genome_firstcontig"] = (
@@ -622,7 +622,6 @@
# can be served - if public.
# dsId = trackData["metadata"]["dataset_id"]
# url = "%s/api/datasets/%s/display?to_ext=hic " % (self.giURL, dsId)
- hic_path = trackData.get("hic_path", None)
useuri = trackData["useuri"].lower() == "yes"
if useuri:
uri = data
@@ -682,7 +681,7 @@
sampu = list(dict.fromkeys(samp))
samples = [x.split(".")[0] for x in sampu]
samples.sort()
- logging.warn(
+ logging.debug(
"$$$$ cmd=%s, mafss=%s samp=%s samples=%s"
% (" ".join(cmd), mafss, samp, samples)
)
@@ -737,7 +736,7 @@
]
subprocess.check_call(cmd, cwd=self.outdir, stdout=gff3_unrebased)
gff3_unrebased.close()
- logging.warn("### blastxml to gff3 cmd = %s" % " ".join(cmd))
+ logging.debug("### blastxml to gff3 cmd = %s" % " ".join(cmd))
return gff3_unrebased.name
def add_blastxml(self, data, trackData, blastOpts, **kwargs):
@@ -749,7 +748,7 @@
cmd.append("--protein2dna")
cmd.extend([os.path.realpath(blastOpts["parent"]), gff3])
subprocess.check_call(cmd, cwd=self.outdir, stdout=gff3_rebased)
- logging.warn("### gff3rebase cmd = %s" % " ".join(cmd))
+ logging.debug("### gff3rebase cmd = %s" % " ".join(cmd))
gff3_rebased.close()
# Replace original gff3 file
shutil.copy(gff3_rebased.name, gff3)
@@ -1307,7 +1306,7 @@
track_types[tId] = track_conf["type"]
style_data = default_data["style"].get(tId, None)
if not style_data:
- logging.warn(
+ logging.debug(
"### No style data in default data %s for %s"
% (default_data, tId)
)
@@ -1488,7 +1487,6 @@
}
for x in ass.findall("metadata/genomes/genome")
]
- logging.warn("#!!! genomes=%s" % genomes)
assref_name = jc.process_genomes(genomes)
for track in ass.find("tracks"):
diff -r ab0d6782a95f -r ac00dcfb5d1d jbrowse2.xml
--- a/jbrowse2.xml Thu Mar 28 04:51:06 2024 +0000
+++ b/jbrowse2.xml Thu Mar 28 07:46:04 2024 +0000
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