726a662c2c
This PR converts ISO-8859 encoding to UTF-8 encoding for three scripts in repeatmasker. - the main RepeatMasker script - SimpleBatcher.pm - wublastToCrossmatch.pl The ISO-8859 encoding prevented the sbang replacement of long paths when spack uses python3.
100 lines
3.4 KiB
Python
100 lines
3.4 KiB
Python
# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
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# Spack Project Developers. See the top-level COPYRIGHT file for details.
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#
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# SPDX-License-Identifier: (Apache-2.0 OR MIT)
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from spack import *
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import glob
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class Repeatmasker(Package):
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"""RepeatMasker is a program that screens DNA sequences for interspersed
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repeats and low complexity DNA sequences."""
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homepage = "http://www.repeatmasker.org"
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url = "http://www.repeatmasker.org/RepeatMasker-open-4-0-7.tar.gz"
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version('4.0.9', sha256='8d67415d89ed301670b7632ea411f794c6e30d8ed0f007a726c4b0a39c8638e5')
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version('4.0.7', sha256='16faf40e5e2f521146f6692f09561ebef5f6a022feb17031f2ddb3e3aabcf166')
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variant('crossmatch', description='Enable CrossMatch search engine',
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default=False)
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depends_on('perl', type=('build', 'run'))
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depends_on('perl-text-soundex', type=('build', 'run'))
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depends_on('hmmer')
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depends_on('ncbi-rmblastn')
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depends_on('trf')
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depends_on('phrap-crossmatch-swat', type=('build', 'run'),
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when='+crossmatch')
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patch('utf8.patch')
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def url_for_version(self, version):
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url = 'http://www.repeatmasker.org/RepeatMasker-open-{0}.tar.gz'
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return url.format(version.dashed)
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def install(self, spec, prefix):
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# Config questions consist of:
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#
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# <PRESS ENTER TO CONTINUE>
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# Enter perl path
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# Enter where repeatmasker is being configured from
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# Enter trf path
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# Add a Search Engine:
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# 1. CrossMatch
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# 2. RMBlast - NCBI Blast with RepeatMasker extensions
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# 3. WUBlast/ABBlast (required by DupMasker)
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# 4. HMMER3.1 & DFAM
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# 5. Done
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# Enter RMBlast path
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# Do you want RMBlast to be your default search engine for
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# Repeatmasker? (Y/N)
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# Add a Search Engine: Done
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config_answers = []
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if spec.satisfies('@4.0.9:'):
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# 4.0.9 removes a bunch of the interactive options
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config_answers.append('')
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else:
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config_answers.extend(['',
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self.spec['perl'].command.path,
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self.stage.source_path,
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self.spec['trf'].prefix.bin.trf])
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# add crossmatch search
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if '+crossmatch' in spec:
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crossmatch = self.spec['phrap-crossmatch-swat'].prefix.bin
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config_answers.extend(['1', crossmatch, 'N'])
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# set default BLAST search
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config_answers.extend(['2',
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self.spec['ncbi-rmblastn'].prefix.bin,
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'Y'])
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# set non-default HMMER search
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config_answers.extend(['3',
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self.spec['hmmer'].prefix,
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'N'])
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# end configuration
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config_answers.append('5')
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config_answers_filename = 'spack-config.in'
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with open(config_answers_filename, 'w') as f:
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f.write('\n'.join(config_answers))
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with open(config_answers_filename, 'r') as f:
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perl = which('perl')
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perl('configure', input=f)
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# fix perl paths
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# every sbang points to perl, so a regex will suffice
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for f in glob.glob('*.pm'):
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filter_file('#!.*', '#!%s' % spec['perl'].command, f)
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install_tree('.', prefix.bin)
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