comparison jbrowse2.py @ 53:bdfa6a7c4543 draft

planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 44df75b3714aa9e02983e0b67ef43fc0eee4a8d4-dirty

52:ae12977c0e5e

import os
import re
import shutil
import struct
import subprocess
import tempfile
import urllib.request
import xml.etree.ElementTree as ET
from collections import defaultdict

                self.genome_names.append(genome_name)
                if self.genome_name is None:
                    self.genome_name = (
                        genome_name  # first one for all tracks - other than paf
                    )
                    self.genome_firstcontig = None
                    if not useuri:
                        # https://lazarus.name/jbrowse/fish/bigwig_0_coverage_bedgraph_cov_count_count_bw.bigwig
                        # https://lazarus.name/jbrowse/fish/klBraLanc5.haps_combined.decontam.20230620.fasta.fa.gz
                        fl = open(fapath, "r").readline()

                },
                "gziLocation": {
                    "uri": faname + ".gzi",
                },
            }
        self.genome_sequence_adapter = adapter
        trackDict = {
            "name": gname,
            "sequence": {
                "type": "ReferenceSequenceTrack",
                "trackId": gname,

        if useuri:
            url = data
        else:
            fname = "%s.cram" % trackData["label"]
            dest = "%s/%s" % (self.outdir, fname)
            bindex = fname + '.bai'
            url = fname
            self.subprocess_check_call(["cp", data, dest])

            if bindex is not None and os.path.exists(bindex):
                if not os.path.exists(dest+'.crai'):
                    # most probably made by galaxy and stored in galaxy dirs, need to copy it to dest
                    self.subprocess_check_call(
                        ["cp", os.path.realpath(cram_index), dest + ".crai"]
                    )
                else:
                    # Can happen in exotic condition
                    # e.g. if bam imported as symlink with datatype=unsorted.bam, then datatype changed to bam
                    #      => no index generated by galaxy, but there might be one next to the symlink target
                    #      this trick allows to skip the bam sorting made by galaxy if already done outside
                    if os.path.exists(os.path.realpath(data) + ".crai"):
                        self.symlink_or_copy(
                            os.path.realpath(data) + ".crai", dest + ".crai"
                        )
                    else:
                        log.warn("Could not find a cram index (.crai file) for %s", data)
        trackDict = {
            "type": "AlignmentsTrack",
            "trackId": tId,
            "name": trackData["name"],
            "assemblyNames": [self.genome_name],

        refName = None
        drdict = {
            "reversed": False,
            "assemblyName": self.genome_name,
            "start": 0,
            "end": 100000,
            "refName": "x",
        }

        if data.get("defaultLocation", ""):
            ddl = data["defaultLocation"]

53:bdfa6a7c4543

import os
import re
import shutil
import struct
import subprocess
import sys
import tempfile
import urllib.request
import xml.etree.ElementTree as ET
from collections import defaultdict

                self.genome_names.append(genome_name)
                if self.genome_name is None:
                    self.genome_name = (
                        genome_name  # first one for all tracks - other than paf
                    )
                    self.genome_sequence_adapter = assem["sequence"]["adapter"]
                    self.genome_firstcontig = None
                    if not useuri:
                        # https://lazarus.name/jbrowse/fish/bigwig_0_coverage_bedgraph_cov_count_count_bw.bigwig
                        # https://lazarus.name/jbrowse/fish/klBraLanc5.haps_combined.decontam.20230620.fasta.fa.gz
                        fl = open(fapath, "r").readline()

                },
                "gziLocation": {
                    "uri": faname + ".gzi",
                },
            }

        trackDict = {
            "name": gname,
            "sequence": {
                "type": "ReferenceSequenceTrack",
                "trackId": gname,

        if useuri:
            url = data
        else:
            fname = "%s.cram" % trackData["label"]
            dest = "%s/%s" % (self.outdir, fname)
            bindex = fname + '.crai'
            url = fname
            self.subprocess_check_call(["cp", data, dest])
            if bindex is not None and os.path.exists(bindex):
                if not os.path.exists(dest+'.crai'):
                    # most probably made by galaxy and stored in galaxy dirs, need to copy it to dest
                    self.subprocess_check_call(
                        ["cp", os.path.realpath(cram_index), dest + ".crai"]
                    )
            else:
                cpath = os.path.realpath(dest) + '.crai'
                cmd = ["samtools", "index", "-c", "-o", cpath, os.path.realpath(dest)]
                logging.debug('executing cmd %s' % ' '.join(cmd))
                self.subprocess_check_call(cmd)
        trackDict = {
            "type": "AlignmentsTrack",
            "trackId": tId,
            "name": trackData["name"],
            "assemblyNames": [self.genome_name],

        refName = None
        drdict = {
            "reversed": False,
            "assemblyName": self.genome_name,
            "start": 2000,
            "end": 0,
            "refName": "x",
        }

        if data.get("defaultLocation", ""):
            ddl = data["defaultLocation"]