Mercurial > repos > fubar > jbrowse2

comparison jbrowse2.py @ 53:bdfa6a7c4543 draft

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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 44df75b3714aa9e02983e0b67ef43fc0eee4a8d4-dirty
author fubar
date Thu, 07 Mar 2024 09:23:06 +0000
parents f350467f9433
children d6b0feb22584
comparison
equal deleted inserted replaced
52:ae12977c0e5e 53:bdfa6a7c4543
8 import os 8 import os
9 import re 9 import re
10 import shutil 10 import shutil
11 import struct 11 import struct
12 import subprocess 12 import subprocess
13 import sys
13 import tempfile 14 import tempfile
14 import urllib.request 15 import urllib.request
15 import xml.etree.ElementTree as ET 16 import xml.etree.ElementTree as ET
16 from collections import defaultdict 17 from collections import defaultdict
17 18
465 self.genome_names.append(genome_name) 466 self.genome_names.append(genome_name)
466 if self.genome_name is None: 467 if self.genome_name is None:
467 self.genome_name = ( 468 self.genome_name = (
468 genome_name # first one for all tracks - other than paf 469 genome_name # first one for all tracks - other than paf
469 ) 470 )
471 self.genome_sequence_adapter = assem["sequence"]["adapter"]
470 self.genome_firstcontig = None 472 self.genome_firstcontig = None
471 if not useuri: 473 if not useuri:
472 # https://lazarus.name/jbrowse/fish/bigwig_0_coverage_bedgraph_cov_count_count_bw.bigwig 474 # https://lazarus.name/jbrowse/fish/bigwig_0_coverage_bedgraph_cov_count_count_bw.bigwig
473 # https://lazarus.name/jbrowse/fish/klBraLanc5.haps_combined.decontam.20230620.fasta.fa.gz 475 # https://lazarus.name/jbrowse/fish/klBraLanc5.haps_combined.decontam.20230620.fasta.fa.gz
474 fl = open(fapath, "r").readline() 476 fl = open(fapath, "r").readline()
527 }, 529 },
528 "gziLocation": { 530 "gziLocation": {
529 "uri": faname + ".gzi", 531 "uri": faname + ".gzi",
530 }, 532 },
531 } 533 }
532 self.genome_sequence_adapter = adapter 534
533 trackDict = { 535 trackDict = {
534 "name": gname, 536 "name": gname,
535 "sequence": { 537 "sequence": {
536 "type": "ReferenceSequenceTrack", 538 "type": "ReferenceSequenceTrack",
537 "trackId": gname, 539 "trackId": gname,
872 if useuri: 874 if useuri:
873 url = data 875 url = data
874 else: 876 else:
875 fname = "%s.cram" % trackData["label"] 877 fname = "%s.cram" % trackData["label"]
876 dest = "%s/%s" % (self.outdir, fname) 878 dest = "%s/%s" % (self.outdir, fname)
877 bindex = fname + '.bai' 879 bindex = fname + '.crai'
878 url = fname 880 url = fname
879 self.subprocess_check_call(["cp", data, dest]) 881 self.subprocess_check_call(["cp", data, dest])
880
881 if bindex is not None and os.path.exists(bindex): 882 if bindex is not None and os.path.exists(bindex):
882 if not os.path.exists(dest+'.crai'): 883 if not os.path.exists(dest+'.crai'):
883 # most probably made by galaxy and stored in galaxy dirs, need to copy it to dest 884 # most probably made by galaxy and stored in galaxy dirs, need to copy it to dest
884 self.subprocess_check_call( 885 self.subprocess_check_call(
885 ["cp", os.path.realpath(cram_index), dest + ".crai"] 886 ["cp", os.path.realpath(cram_index), dest + ".crai"]
886 ) 887 )
887 else: 888 else:
888 # Can happen in exotic condition 889 cpath = os.path.realpath(dest) + '.crai'
889 # e.g. if bam imported as symlink with datatype=unsorted.bam, then datatype changed to bam 890 cmd = ["samtools", "index", "-c", "-o", cpath, os.path.realpath(dest)]
890 # => no index generated by galaxy, but there might be one next to the symlink target 891 logging.debug('executing cmd %s' % ' '.join(cmd))
891 # this trick allows to skip the bam sorting made by galaxy if already done outside 892 self.subprocess_check_call(cmd)
892 if os.path.exists(os.path.realpath(data) + ".crai"):
893 self.symlink_or_copy(
894 os.path.realpath(data) + ".crai", dest + ".crai"
895 )
896 else:
897 log.warn("Could not find a cram index (.crai file) for %s", data)
898 trackDict = { 893 trackDict = {
899 "type": "AlignmentsTrack", 894 "type": "AlignmentsTrack",
900 "trackId": tId, 895 "trackId": tId,
901 "name": trackData["name"], 896 "name": trackData["name"],
902 "assemblyNames": [self.genome_name], 897 "assemblyNames": [self.genome_name],
1278 1273
1279 refName = None 1274 refName = None
1280 drdict = { 1275 drdict = {
1281 "reversed": False, 1276 "reversed": False,
1282 "assemblyName": self.genome_name, 1277 "assemblyName": self.genome_name,
1283 "start": 0, 1278 "start": 2000,
1284 "end": 100000, 1279 "end": 0,
1285 "refName": "x", 1280 "refName": "x",
1286 } 1281 }
1287 1282
1288 if data.get("defaultLocation", ""): 1283 if data.get("defaultLocation", ""):
1289 ddl = data["defaultLocation"] 1284 ddl = data["defaultLocation"]