Mercurial > repos > fubar > jbrowse2
changeset 29:f728cf0df71d draft
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit fe89199bded3f50aefb6958f0c4e85eede77ad81-dirty
| author | fubar |
|---|---|
| date | Fri, 16 Feb 2024 00:04:37 +0000 |
| parents | 9a5c409f33f4 |
| children | 8f02a84ee278 |
| files | jb2_webserver.py jbrowse2.py pafcount.py |
| diffstat | 3 files changed, 9 insertions(+), 62 deletions(-) [+] |
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--- a/jb2_webserver.py Wed Feb 07 22:51:54 2024 +0000 +++ b/jb2_webserver.py Fri Feb 16 00:04:37 2024 +0000 @@ -1,4 +1,5 @@ -#!/usr/bin/env python3# spec: simplest python web server with range support and multithreading that takes root path, +#!/usr/bin/env python3 +# spec: simplest python web server with range support and multithreading that takes root path, # port and bind address as command line arguments; by default uses the current dir as webroot, # port 8000 and bind address of 0.0.0.0 # borrowed from https://github.com/danvk/RangeHTTPServer
--- a/jbrowse2.py Wed Feb 07 22:51:54 2024 +0000 +++ b/jbrowse2.py Fri Feb 16 00:04:37 2024 +0000 @@ -564,11 +564,7 @@ # can be served - if public. # dsId = trackData["metadata"]["dataset_id"] # url = "%s/api/datasets/%s/display?to_ext=hic " % (self.giURL, dsId) - hname = trackData["name"] - dest = os.path.join(self.outdir, hname) - cmd = ["cp", data, dest] - # these can be very big. - self.subprocess_check_call(cmd) + hname = trackData["hic_url"] floc = { "uri": hname, } @@ -774,7 +770,6 @@ trackDict["style"] = style_json self.tracksToAdd.append(trackDict) self.trackIdlist.append(tId) - logging.info("#### wig trackData=%s" % str(trackData)) def add_bam(self, data, trackData, bamOpts, bam_index=None, **kwargs): tId = trackData["label"] @@ -1152,9 +1147,8 @@ outputTrackConfig, ) elif dataset_ext in ("cool", "mcool", "scool"): - hic_path = os.path.join( - self.outdir, "%s_%d_%s.hic" % (track_human_label, i, dataset_ext) - ) + hic_url = "%s_%d.hic" % (track_human_label, i) + hic_path = os.path.join(self.outdir, hic_url) self.subprocess_check_call( [ "hictk", @@ -1166,6 +1160,7 @@ hic_path, ] ) + outputTrackConfig["hic_url"] = hic_url self.add_hic( hic_path, outputTrackConfig, @@ -1227,7 +1222,7 @@ track["conf"]["options"]["paf"], ) else: - log.warn("Do not know how to handle %s", dataset_ext) + logging.warn("Do not know how to handle %s", dataset_ext) # Return non-human label for use in other fields yield outputTrackConfig["label"] @@ -1292,7 +1287,8 @@ "@@@ regexp could not match contig:start..end in the supplied location %s - please fix" % ddl ) - + else: + drdict["refName"] = self.genome_firstcontig if drdict.get("refName", None): # TODO displayedRegions is not just zooming to the region, it hides the rest of the chromosome view_json["displayedRegions"] = [
--- a/pafcount.py Wed Feb 07 22:51:54 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,50 +0,0 @@ -import sys - -""" - -Col Type Description -1 string Query sequence name -2 int Query sequence length -3 int Query start (0-based; BED-like; closed) -4 int Query end (0-based; BED-like; open) -5 char Relative strand: "+" or "-" -6 string Target sequence name -7 int Target sequence length -8 int Target start on original strand (0-based) -9 int Target end on original strand (0-based) -10 int Number of residue matches -11 int Alignment block length -12 int Mapping quality (0-255; 255 for missing) -""" - -qcis = {} -tcis = {} -qtrans = {} -ttrans = {} -pafname = sys.argv[1] -pf = open(pafname, "r").readlines() -for row in pf: - qn, ql, qs, qe, qrs, tn, tl, ts, te, nm, abl, mq = row.strip().split("\t")[:12] - - if qn == tn: # cis - print("cis", qn, tn) - tcis.setdefault(tn, 0) - tcis[tn] = tcis[tn] + 1 - qcis.setdefault(qn, 0) - qcis[qn] = qcis[qn] + 1 - else: # trans - print("trans", qn, tn) - k = "%s_%s" % (qn, tn) - ttrans.setdefault(k, 0) - ttrans[k] = ttrans[k] + 1 - qtrans.setdefault(k, 0) - qtrans[k] = qtrans[k] + 1 -# print('qcis', qcis,'\nqtrans', qtrans,'\ntcis', tcis,'\ntt', ttrans) -# print('\nqtrans', qtrans,'\nttrans', ttrans) -chroms = list(qtrans.keys()) -print("chroms=", chroms) -# print('chrom\tqcis\ttcis\tqtrans\tttrans') -print("chrom\tqtrans\tttrans") -for cr in chroms: - # print('%s\t%d\t%d\t%d\t%d' % (cr, qcis[cr], tcis[cr], qtrans[cr], ttrans[cr])) - print("%s\t%d\t%d" % (cr, qtrans[cr], ttrans[cr]))