installation issue: AttributeError: '_Environ' object has no attribute 'has_key':

[hafizmtalha]

hi, I am trying to install CirComPara but facing this issue during installation: scons: Reading SConscript files ... AttributeError: '_Environ' object has no attribute 'has_key': File "/media/alphagenomics/Bay2/Softwares/CirComPara/src/ccp_install_tools.scons", line 18: if not env['ENV'].has_key('VIRTUAL_ENV'):

[egaffo]

Which Python version are you running? Mind that you must use Python2.7. Python 3 is not supported (several reasons prevented me from updating the Python version). As it is an old Python version, you may consider virtualenv to get a python2.7 sandbox.

[hafizmtalha]

Thanks.. that helped I was working on python 3.7 but now It's installed but new error.. TypeError: Tried to lookup Dir 'ccp_dbs/ccp_indexes' as a File: File "/media/alphagenomics/Bay2/Softwares/CirComPara/src/ccp_main.scons", line 356: exports = '''env_check_indexes''') File "/media/alphagenomics/Bay2/Softwares/CirComPara/tools/scons/scons-local-3.1.2/SCons/Script/SConscript.py", line 660: return method(*args, kw) File "/media/alphagenomics/Bay2/Softwares/CirComPara/tools/scons/scons-local-3.1.2/SCons/Script/SConscript.py", line 597: return _SConscript(self.fs, *files, *subst_kw) File "/media/alphagenomics/Bay2/Softwares/CirComPara/tools/scons/scons-local-3.1.2/SCons/Script/SConscript.py", line 286: exec(compile(scriptdata, scriptname, 'exec'), call_stack[-1].globals) File "/media/alphagenomics/Bay2/Softwares/CirComPara/src/ccp_check_indexes.scons", line 117: exports = '''env_build_indexes ''') File "/media/alphagenomics/Bay2/Softwares/CirComPara/tools/scons/scons-local-3.1.2/SCons/Script/SConscript.py", line 660: return method(args, kw) File "/media/alphagenomics/Bay2/Softwares/CirComPara/tools/scons/scons-local-3.1.2/SCons/Script/SConscript.py", line 597: return _SConscript(self.fs, *files, subst_kw) File "/media/alphagenomics/Bay2/Softwares/CirComPara/tools/scons/scons-local-3.1.2/SCons/Script/SConscript.py", line 286: exec(compile(scriptdata, scriptname, 'exec'), call_stack[-1].globals) File "/media/alphagenomics/Bay2/Softwares/CirComPara/src/ccp_build_indexes.scons", line 60: env_index_hisat2['GENOME'] = ','.join([File(f).abspath for f in env['GENOME'].split(',')]) File "/media/alphagenomics/Bay2/Softwares/CirComPara/tools/scons/scons-local-3.1.2/SCons/Script/SConscript.py", line 660: return method(*args, *kw) File "/media/alphagenomics/Bay2/Softwares/CirComPara/tools/scons/scons-local-3.1.2/SCons/Environment.py", line 2092: return self.fs.File(s, args, kw) File "/media/alphagenomics/Bay2/Softwares/CirComPara/tools/scons/scons-local-3.1.2/SCons/Node/FS.py", line 1382: return self._lookup(name, directory, File, create) File "/media/alphagenomics/Bay2/Softwares/CirComPara/tools/scons/scons-local-3.1.2/SCons/Node/FS.py", line 1361: return root._lookup_abs(p, fsclass, create) File "/media/alphagenomics/Bay2/Softwares/CirComPara/tools/scons/scons-local-3.1.2/SCons/Node/FS.py", line 2406: result.must_be_same(klass) File "/media/alphagenomics/Bay2/Softwares/CirComPara/tools/scons/scons-local-3.1.2/SCons/Node/FS.py", line 618: (self.class.name, self.get_internal_path(), klass.name))

[egaffo]

Could you paste your vars.py and meta.csv? It seems CirComPara2 cannot generate the genome index files. Perhaps there is an error in the genome sequence file path?

[hafizmtalha]

m using the test files for this.. I have posting these files bellow

meta.csv

file,sample,condition test_circompara/reads/readsA_1.fq,S1,WT test_circompara/reads/readsA_2.fq,S1,WT test_circompara/reads/readsB_1.fq,S2,MU test_circompara/reads/readsB_2.fq,S2,MU

vars.py

META = 'meta.csv' GENOME_FASTA = '../annotation/CFLAR_HIPK3.fa' ANNOTATION = '../annotation/CFLAR_HIPK3.gtf' CPUS = '4' PREPROCESSOR = 'trimmomatic' PREPROCESSOR_PARAMS = 'MAXINFO:40:0.5 LEADING:20 TRAILING:20 SLIDINGWINDOW:4:30 MINLEN:35 AVGQUAL:30' CIRCRNA_METHODS = 'dcc,ciri,findcirc,testrealign,'\ 'circexplorer2_star,circexplorer2_segemehl,'\ 'circexplorer2_bwa,circexplorer2_tophat,circrna_finder'

TOGGLE_TRANSCRIPTOME_RECONSTRUCTION = 'False' FIX_READ_HEADER = 'True'

MIN_READS = 2 #default

aligners' custom parameters

HISAT2_EXTRA_PARAMS = '--rna-strandness RF' # stranded libraries

parameters from CIRI

BWA_PARAMS = ['-T', '19', '-c', '1']

parameters from CIRCexplorer2

SEGEMEHL_PARAMS = ['-M','1'] #'-D', '0', '-Z', '20' TOPHAT_PARAMS = ['--max-multihits', '1']#'--zpacker','pigz'

parameters used in DCC manual example

STAR_PARAMS = ['--outFilterMultimapNmax', '1', '--outSJfilterOverhangMin', '15', '15', '15', '15', '--alignSJoverhangMin', '15', '--alignSJDBoverhangMin', '15', '--seedSearchStartLmax', '30', '--outFilterScoreMin', '1', '--outFilterMatchNmin', '1', '--outFilterMismatchNmax', '2', '--chimSegmentMin', '15', '--chimScoreMin', '15', '--chimScoreSeparation', '10', '--chimJunctionOverhangMin', '15']

pre-computed index and annotation files

GENOME_INDEX = "../indexes/hisat2/CFLAR_HIPK3"

SEGEMEHL_INDEX = "../indexes/segemehl/CFLAR_HIPK3.idx"

BWA_INDEX = "../indexes/bwa/CFLAR_HIPK3"

BOWTIE2_INDEX = "../indexes/bowtie2/CFLAR_HIPK3"

BOWTIE_INDEX = "../indexes/bowtie/CFLAR_HIPK3"

STAR_INDEX = "../indexes/star/CFLAR_HIPK3"

GENEPRED = "../annotation/CFLAR_HIPK3.genePred.wgn"

LIN_COUNTER = 'ccp' #'dcc'

DCC_EXTRA_PARAMS = ['-fg', '-M', '-Nr', 1, 1, '-F', '-ss'] TESTREALIGN_PARAMS = ['-q', 'median_1'] ## suggested 'median_40' CE2_PARAMS = ['--no-fix'] #suggested not to set '--no-fix' in real datasets FINDCIRC_EXTRA_PARAMS = ['--best-qual', '0'] #suggested '40' FIX_READ_HEADER = 'True' SAM_SORT_MM = '1G'

BYPASS = 'linear'

[egaffo]

I've just realized you are posting in the old version of CirComPara! Please, use the new CirComPara2 (https://github.com/egaffo/circompara2). Many issues have been fixed there and I no longer support this repo.