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stage for v1.6.0 release
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Jon Palmer committed Jul 30, 2019
1 parent 16500bc commit 58d2600
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Showing 4 changed files with 37 additions and 27 deletions.
28 changes: 14 additions & 14 deletions bin/funannotate-test.py
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Original file line number Diff line number Diff line change
Expand Up @@ -17,7 +17,7 @@ def __init__(self,prog):
epilog="""Written by Jon Palmer (2016-2018) [email protected]""",
formatter_class = MyFormatter)
parser.add_argument('-t','--tests', required=True, nargs='+',
choices=['all', 'clean', 'mask', 'predict', 'annotate', 'busco', 'rna-seq', 'compare'],
choices=['all', 'clean', 'mask', 'predict', 'annotate', 'rna-seq', 'compare'],
help='select which tests to run')
parser.add_argument('--cpus', default=2, type=int, help='Number of CPUs to use')
args=parser.parse_args()
Expand Down Expand Up @@ -165,7 +165,7 @@ def runPredictTest():
print("#########################################################")
#check results
try:
assert 1500 <= countGFFgenes(os.path.join(tmpdir, 'annotate', 'predict_results', 'Awesome_testicus.gff3')) <= 1700
assert 1500 <= countGFFgenes(os.path.join(tmpdir, 'annotate', 'predict_results', 'Awesome_testicus.gff3')) <= 1800
print('SUCCESS: `funannotate predict` test complete.')
shutil.rmtree(tmpdir)
except AssertionError:
Expand All @@ -182,7 +182,7 @@ def runBuscoTest():
lib.log.error("$AUGUSTUS_CONFIG_PATH environmental variable not found, set to continue.")
return
if os.path.isdir(os.path.join(AUGUSTUS, 'species', 'awesome_busco')):
shutil.rmtree(os.path.join(AUGUSTUS, 'species', 'awesome_busco'))
shutil.rmtree(os.path.join(AUGUSTUS, 'species', 'awesome_busco'))
tmpdir = 'test-busco_'+pid
os.makedirs(tmpdir)
inputFasta = 'test.softmasked.fa'
Expand All @@ -201,7 +201,7 @@ def runBuscoTest():
print("#########################################################")
#check results
try:
assert 1500 <= countGFFgenes(os.path.join(tmpdir, 'annotate', 'predict_results', 'Awesome_busco.gff3')) <= 1700
assert 1500 <= countGFFgenes(os.path.join(tmpdir, 'annotate', 'predict_results', 'Awesome_busco.gff3')) <= 1800
print('SUCCESS: `funannotate predict` BUSCO-mediated training test complete.')
shutil.rmtree(tmpdir)
except AssertionError:
Expand Down Expand Up @@ -259,7 +259,7 @@ def runCompareTest():
shutil.copyfile(input3, os.path.join(tmpdir, input3))
#run predict
runCMD(['funannotate', 'compare',
'-i', input1, input2, input3,
'-i', input1, input2, input3,
'-o', 'compare', '--cpus', str(args.cpus),
'--run_dnds', 'estimate', '--outgroup', 'botrytis_cinerea.dikarya'], tmpdir)
print("#########################################################")
Expand All @@ -273,7 +273,7 @@ def runCompareTest():
except AssertionError:
print('ERROR: `funannotate compare` test failed - check logfiles')
print("#########################################################\n")
def runRNAseqTest():
print("#########################################################")
print('Running funannotate RNA-seq training/prediction unit testing')
Expand All @@ -284,7 +284,7 @@ def runRNAseqTest():
lib.log.error("$AUGUSTUS_CONFIG_PATH environmental variable not found, set to continue.")
return
if os.path.isdir(os.path.join(AUGUSTUS, 'species', 'awesome_rna')):
shutil.rmtree(os.path.join(AUGUSTUS, 'species', 'awesome_rna'))
shutil.rmtree(os.path.join(AUGUSTUS, 'species', 'awesome_rna'))
tmpdir = 'test-rna_seq_'+pid
os.makedirs(tmpdir)
inputFasta = 'test.softmasked.fa'
Expand All @@ -296,7 +296,7 @@ def runRNAseqTest():
download(download_links.get('rna-seq'), 'test-rna_seq.tar.gz')
subprocess.call(['tar', '-zxf', 'test-rna_seq.tar.gz'])
for f in [inputFasta, protEvidence, illumina, nanopore]:
shutil.copyfile(f, os.path.join(tmpdir, f))
shutil.copyfile(f, os.path.join(tmpdir, f))
#run train
runCMD(['funannotate', 'train', '-i', inputFasta,
'--single', illumina, '--nanopore_mrna', nanopore,
Expand All @@ -313,7 +313,7 @@ def runRNAseqTest():
print("#########################################################")
print('Now running `funannotate update` to run PASA-mediated UTR addition and multiple transcripts')
runCMD(['funannotate', 'update', '-i', 'rna-seq',
'--cpus', str(args.cpus)], tmpdir)
'--cpus', str(args.cpus)], tmpdir)
print("#########################################################")
#check results
try:
Expand All @@ -332,11 +332,11 @@ def runRNAseqTest():
runMaskTest()
if 'predict' in args.tests or 'all' in args.tests:
runPredictTest()
if 'busco' in args.tests or 'all' in args.tests:
runBuscoTest()
#if 'busco' in args.tests or 'all' in args.tests:
# runBuscoTest()
if 'rna-seq' in args.tests or 'all' in args.tests:
runRNAseqTest()
runRNAseqTest()
if 'annotate' in args.tests or 'all' in args.tests:
runAnnotateTest()
runAnnotateTest()
if 'compare' in args.tests or 'all' in args.tests:
runCompareTest()
runCompareTest()
6 changes: 3 additions & 3 deletions dockerbuild/Dockerfile-base
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Original file line number Diff line number Diff line change
Expand Up @@ -31,7 +31,7 @@ RUN wget --quiet https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86
sudo /bin/bash ~/miniconda.sh -b -p /home/linuxbrew/conda && rm ~/miniconda.sh && sudo chown -R linuxbrew: /home/linuxbrew/conda && \
conda update -y conda && conda config --add channels r && conda config --add channels defaults && \
conda config --add channels etetoolkit && conda config --add channels conda-forge && conda config --add channels bioconda && \
conda install -y numpy pandas scipy matplotlib seaborn natsort scikit-learn psutil biopython requests \
conda install -y numpy pandas scipy matplotlib seaborn natsort scikit-learn psutil biopython requests snap glimmerhmm=3.0.4=pl526h0a44026_3 \
goatools fisher bedtools blat hmmer exonerate diamond tbl2asn hisat2 ucsc-pslcdnafilter stringtie perl-dbd-sqlite \
samtools raxml trimal mafft phyml kallisto bowtie2 infernal perl-threaded perl-db-file perl-bioperl perl-dbd-mysql \
perl-app-cpanminus mummer ete3 ete_toolchain minimap2 salmon=0.9.1 jellyfish htslib nano perl-text-soundex perl-scalar-util-numeric && \
Expand Down Expand Up @@ -100,5 +100,5 @@ RUN wget --quiet https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86

COPY pasa_conf.txt /home/linuxbrew/PASApipeline/pasa_conf/conf.txt

RUN wget https://github.com/nextgenusfs/funannotate/archive/1.5.3.tar.gz && \
tar -zxvf 1.5.3.tar.gz && rm 1.5.3.tar.gz && mv funannotate-1.5.3 funannotate
RUN wget https://github.com/nextgenusfs/funannotate/archive/1.6.0.tar.gz && \
tar -zxvf 1.6.0.tar.gz && rm 1.6.0.tar.gz && mv funannotate-1.6.0 funannotate
2 changes: 1 addition & 1 deletion funannotate.py
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Original file line number Diff line number Diff line change
Expand Up @@ -421,7 +421,7 @@ def fmtcols(mylist, cols):
you cannot download from the machine funannotate is installed at - then download
the 7 tar.gz files from https://osf.io/bj7v4/files/ and run script from directory
Arguments: -t, --tests Test sets to run. [all,clean,mask,predict,busco,rna-seq,annotate,compare]
Arguments: -t, --tests Test sets to run. [all,clean,mask,predict,rna-seq,annotate,compare]
--cpus Number of cpus to use. Default: 2
Written by Jon Palmer (2016-2018) [email protected]
Expand Down
28 changes: 19 additions & 9 deletions util/check_modules.py
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Original file line number Diff line number Diff line change
Expand Up @@ -91,6 +91,8 @@ def check_version2(name):
elif name == 'mafft':
vers = subprocess.Popen([name, '--version'], stdout=subprocess.PIPE, stderr=subprocess.PIPE).communicate()[1]
vers = vers.strip()
elif name == 'emapper.py':
vers = subprocess.Popen([name, '--version'], stdout=subprocess.PIPE).communicate()[0].split('\n')[1].replace('emapper-', '')
else:
vers = subprocess.Popen([name, '--version'], stdout=subprocess.PIPE).communicate()[0].split('\n')[0]
if 'exonerate' in vers:
Expand Down Expand Up @@ -158,11 +160,19 @@ def check_version5(name):
vers = subprocess.Popen([name], stdout=subprocess.PIPE, stderr=subprocess.PIPE).communicate()
vers = 'no way to determine'
elif name == 'CodingQuarry':
vers = subprocess.Popen([name], stdout=subprocess.PIPE).communicate()
v = vers[0].split('\n')
for i in v:
if 'CodingQuarry v.' in i:
vers = i.split('v. ')[-1]
vers = subprocess.Popen([name], stdout=subprocess.PIPE).communicate()
v = vers[0].split('\n')
for i in v:
if 'CodingQuarry v.' in i:
vers = i.split('v. ')[-1]
elif name == 'snap':
vtmp = subprocess.Popen(['snap'], stderr=subprocess.STDOUT, stdout=subprocess.PIPE).communicate()[0].rstrip().split('\n')
for i in vtmp:
if i.startswith('SNAP'):
vers = i.split('(version ')[-1].rstrip(')')
elif name == 'glimmerhmm':
vtmp = subprocess.Popen(['snap'], stderr=subprocess.STDOUT, stdout=subprocess.PIPE).communicate()[0].rstrip().split('\n')
vers = '3.0.4'
except OSError as e:
if e.errno == os.errno.ENOENT:
return False
Expand Down Expand Up @@ -207,12 +217,12 @@ def check_version6(name):

programs1 = ['tblastn', 'makeblastdb', 'rmblastn', 'java'] #-version
programs2 = ['exonerate', 'bedtools', 'bamtools', 'augustus',
'samtools', 'gmap', 'hisat2', 'Trinity', 'nucmer',
'tbl2asn', 'emapper.py', 'minimap2', 'mafft',
'trimal', 'stringtie'] #--version
'samtools', 'gmap', 'hisat2', 'Trinity', 'nucmer',
'tbl2asn', 'emapper.py', 'minimap2', 'mafft',
'trimal', 'stringtie', 'salmon'] #--version
programs3 = ['RepeatModeler', 'RepeatMasker'] #-v
programs4 = ['diamond', 'ete3', 'kallisto'] #version
programs5 = ['gmes_petap.pl', 'blat', 'pslCDnaFilter', 'fasta', 'CodingQuarry'] #no version option at all, a$$holes
programs5 = ['gmes_petap.pl', 'blat', 'pslCDnaFilter', 'fasta', 'CodingQuarry', 'snap', 'glimmerhmm'] #no version option at all, a$$holes
programs6 = ['hmmsearch', 'hmmscan', 'tRNAscan-SE'] #-h
programs7 = ['signalp'] # -V

Expand Down

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