Skip to content

Instantly share code, notes, and snippets.

@martenson

martenson/MTS Secret

Created February 1, 2017 18:35
Show Gist options
  • Star 0 You must be signed in to star a gist
  • Fork 0 You must be signed in to fork a gist
  • Save martenson/b31b09e66890653bb7171e33a36eb1fa to your computer and use it in GitHub Desktop.
Save martenson/b31b09e66890653bb7171e33a36eb1fa to your computer and use it in GitHub Desktop.
Download ZIP
Raw
MTS
$ grep -i -n -r "galaxy_utils.sequence" *
000/repo_830/fastq_paired_end_splitter.py:3:from galaxy_utils.sequence.fastq import fastqReader, fastqWriter, fastqSplitter
000/repo_816/fastq_filter.py:3:from galaxy_utils.sequence.fastq import fastqReader, fastqWriter
000/repo_794/fastq_paired_end_joiner.py:7:import galaxy_utils.sequence.fastq as fq
000/repo_820/fastq_to_tabular.py:3:from galaxy_utils.sequence.fastq import fastqReader
000/repo_813/fastq_trimmer.py:3:from galaxy_utils.sequence.fastq import fastqReader, fastqWriter
000/repo_810/fastq_paired_end_deinterlacer.py:3:from galaxy_utils.sequence.fastq import fastqReader, fastqWriter, fastqNamedReader, fastqJoiner
000/repo_54/tools/venn_list/venn_list.py:59: from galaxy_utils.sequence.fastq import fastqReader
000/repo_797/fastq_manipulation.py:4:from galaxy_utils.sequence.fastq import fastqReader, fastqWriter
000/repo_220/cgatools/lib/galaxy/datatypes/completegenomics.py:17:import galaxy_utils.sequence.vcf
000/repo_811/fastq_to_fasta.py:3:from galaxy_utils.sequence.fastq import fastqReader
000/repo_811/fastq_to_fasta.py:4:from galaxy_utils.sequence.fasta import fastaWriter
000/repo_41/tools/seq_rename/seq_rename.py:112: from galaxy_utils.sequence.fasta import fastaReader, fastaWriter
000/repo_41/tools/seq_rename/seq_rename.py:117: from galaxy_utils.sequence.fastq import fastqReader, fastqWriter
000/repo_349/deseq/fonctionsNGS/differential_expression_analysis_pipeline_for_rnaseq_data/DiffExpAnal/fastq_groomer_parallel.py:8:from galaxy_utils.sequence.fastq import fastqReader, fastqVerboseErrorReader, fastqAggregator, fastqWriter
000/repo_827/fastq_stats.py:3:from galaxy_utils.sequence.fastq import fastqReader, fastqAggregator
000/repo_16/tools/fasta_tools/fasta_filter_by_id.py:22:from galaxy_utils.sequence.fasta import fastaReader, fastaWriter
000/repo_805/fastq_trimmer_by_quality.py:3:from galaxy_utils.sequence.fastq import fastqReader, fastqWriter
000/repo_823/fastq_combiner.py:3:from galaxy_utils.sequence.fastq import fastqWriter, fastqSequencingRead, fastqCombiner, fastqFakeFastaScoreReader
000/repo_823/fastq_combiner.py:4:from galaxy_utils.sequence.fasta import fastaReader, fastaNamedReader
000/repo_396/tools/seq_primer_clip/seq_primer_clip.py:34:from galaxy_utils.sequence.fasta import fastaReader, fastaWriter
000/repo_396/tools/seq_primer_clip/seq_primer_clip.py:35:from galaxy_utils.sequence.fastq import fastqReader, fastqWriter
000/repo_793/fastq_masker_by_quality.py:4:from galaxy_utils.sequence.fastq import fastqReader, fastqWriter
000/repo_219/cgatools/lib/galaxy/datatypes/completegenomics.py:17:import galaxy_utils.sequence.vcf
000/repo_250/fastq_groomer_parallel.py:13:from galaxy_utils.sequence.fastq import fastqReader, fastqVerboseErrorReader, fastqAggregator, fastqWriter
000/repo_250/README:34: from galaxy_utils.sequence.fastq import fastqReader, fastqVerboseErrorReader, fastqAggregator, fastqWriter
000/repo_817/fastq_groomer.py:3:from galaxy_utils.sequence.fastq import fastqReader, fastqVerboseErrorReader, fastqAggregator, fastqWriter
000/repo_17/tools/fastq/fastq_filter_by_id.py:25:from galaxy_utils.sequence.fastq import fastqReader, fastqWriter
000/repo_804/fastq_paired_end_interlacer.py:3:from galaxy_utils.sequence.fastq import fastqReader, fastqWriter, fastqNamedReader, fastqJoiner
001/repo_1876/lib/galaxy/datatypes/completegenomics.py:18:import galaxy_utils.sequence.vcf
Raw
TTS
$grep -i -n -r "galaxy_utils.sequence" *
000/repo_809/fastq_combiner.py:3:from galaxy_utils.sequence.fastq import fastqWriter, fastqSequencingRead, fastqCombiner, fastqFakeFastaScoreReader
000/repo_809/fastq_combiner.py:4:from galaxy_utils.sequence.fasta import fastaReader, fastaNamedReader
000/repo_816/fastq_paired_end_splitter.py:3:from galaxy_utils.sequence.fastq import fastqReader, fastqWriter, fastqSplitter
000/repo_802/fastq_filter.py:3:from galaxy_utils.sequence.fastq import fastqReader, fastqWriter
000/repo_813/fastq_stats.py:3:from galaxy_utils.sequence.fastq import fastqReader, fastqAggregator
000/repo_799/fastq_trimmer.py:3:from galaxy_utils.sequence.fastq import fastqReader, fastqWriter
000/repo_123/cgatools/lib/galaxy/datatypes/completegenomics.py:17:import galaxy_utils.sequence.vcf
000/repo_54/tools/venn_list/venn_list.py:59: from galaxy_utils.sequence.fastq import fastqReader
000/repo_797/fastq_to_fasta.py:3:from galaxy_utils.sequence.fastq import fastqReader
000/repo_797/fastq_to_fasta.py:4:from galaxy_utils.sequence.fasta import fastaWriter
000/repo_780/fastq_paired_end_joiner.py:7:import galaxy_utils.sequence.fastq as fq
000/repo_115/cgatools/lib/galaxy/datatypes/completegenomics.py:17:import galaxy_utils.sequence.vcf
000/repo_115/CG_cgatools/lib/galaxy/datatypes/completegenomics.py:17:import galaxy_utils.sequence.vcf
000/repo_796/fastq_paired_end_deinterlacer.py:3:from galaxy_utils.sequence.fastq import fastqReader, fastqWriter, fastqNamedReader, fastqJoiner
000/repo_138/fastq_groomer_parallel.py:13:from galaxy_utils.sequence.fastq import fastqReader, fastqVerboseErrorReader, fastqAggregator, fastqWriter
000/repo_138/README:38: from galaxy_utils.sequence.fastq import fastqReader, fastqVerboseErrorReader, fastqAggregator, fastqWriter
000/repo_803/fastq_groomer.py:3:from galaxy_utils.sequence.fastq import fastqReader, fastqVerboseErrorReader, fastqAggregator, fastqWriter
000/repo_105/cgatools_suite/cgatools/lib/galaxy/datatypes/completegenomics.py:17:import galaxy_utils.sequence.vcf
000/repo_105/cgatools/lib/galaxy/datatypes/completegenomics.py:17:import galaxy_utils.sequence.vcf
000/repo_553/fastq_groomer_parallel.py:9:from galaxy_utils.sequence.fastq import fastqReader, fastqVerboseErrorReader, fastqAggregator, fastqWriter
000/repo_791/fastq_trimmer_by_quality.py:3:from galaxy_utils.sequence.fastq import fastqReader, fastqWriter
000/repo_806/fastq_to_tabular.py:3:from galaxy_utils.sequence.fastq import fastqReader
000/repo_41/tools/seq_rename/seq_rename.py:133: from galaxy_utils.sequence.fasta import fastaReader, fastaWriter
000/repo_41/tools/seq_rename/seq_rename.py:138: from galaxy_utils.sequence.fastq import fastqReader, fastqWriter
000/repo_114/cgatools/lib/galaxy/datatypes/completegenomics.py:17:import galaxy_utils.sequence.vcf
000/repo_16/tools/fasta_tools/fasta_filter_by_id.py:16:from galaxy_utils.sequence.fasta import fastaReader, fastaWriter
000/repo_779/fastq_masker_by_quality.py:4:from galaxy_utils.sequence.fastq import fastqReader, fastqWriter
000/repo_790/fastq_paired_end_interlacer.py:3:from galaxy_utils.sequence.fastq import fastqReader, fastqWriter, fastqNamedReader, fastqJoiner
000/repo_144/testing_cgatools-982e19c29ec0/cgatools/lib/galaxy/datatypes/completegenomics.py:17:import galaxy_utils.sequence.vcf
000/repo_118/cgatools/lib/galaxy/datatypes/completegenomics.py:17:import galaxy_utils.sequence.vcf
000/repo_783/fastq_manipulation.py:4:from galaxy_utils.sequence.fastq import fastqReader, fastqWriter
000/repo_271/tools/seq_primer_clip/seq_primer_clip.py:34:from galaxy_utils.sequence.fasta import fastaReader, fastaWriter
000/repo_271/tools/seq_primer_clip/seq_primer_clip.py:35:from galaxy_utils.sequence.fastq import fastqReader, fastqWriter
000/repo_124/cgatools/lib/galaxy/datatypes/completegenomics.py:17:import galaxy_utils.sequence.vcf
000/repo_17/tools/fastq/fastq_filter_by_id.py:25:from galaxy_utils.sequence.fastq import fastqReader, fastqWriter
001/repo_1674/tools/fastq_pair_names/fastq_pair_names.py:19:from galaxy_utils.sequence.fastq import fastqReader
001/repo_1858/galaxy/tools/maf/vcf_to_maf_customtrack.py:4:import galaxy_utils.sequence.vcf
001/repo_1858/galaxy/tools/maf/vcf_to_maf_customtrack.py:89: vcf_files.append( PopulationVCFParser( galaxy_utils.sequence.vcf.Reader( open( filename ) ), pop_name ) )
001/repo_1858/galaxy/tools/maf/vcf_to_maf_customtrack.py:94: vcf_files.append( SampleVCFParser( galaxy_utils.sequence.vcf.Reader( open( filename ) ) ) )
001/repo_1858/galaxy/tools/meme/fimo_wrapper.py:8:from galaxy_utils.sequence.transform import DNA_reverse_complement
001/repo_1858/galaxy/doc/source/lib/galaxy_utils.sequence.rst:7:.. automodule:: galaxy_utils.sequence.fasta
001/repo_1858/galaxy/doc/source/lib/galaxy_utils.sequence.rst:15:.. automodule:: galaxy_utils.sequence.fastq
001/repo_1858/galaxy/doc/source/lib/galaxy_utils.sequence.rst:23:.. automodule:: galaxy_utils.sequence.sequence
001/repo_1858/galaxy/doc/source/lib/galaxy_utils.sequence.rst:31:.. automodule:: galaxy_utils.sequence.transform
001/repo_1858/galaxy/doc/source/lib/galaxy_utils.sequence.rst:39:.. automodule:: galaxy_utils.sequence.vcf
001/repo_1858/galaxy/doc/source/lib/galaxy_utils.rst:9: galaxy_utils.sequence
001/repo_1858/galaxy/lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.py:12:import galaxy_utils.sequence.vcf
001/repo_1858/galaxy/lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.py:23: reader = galaxy_utils.sequence.vcf.Reader( open( in_file ) )
001/repo_1843/fimo_wrapper.py:8:from galaxy_utils.sequence.transform import DNA_reverse_complement
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment