cct-examples (1:1.0.3-1build1)

Details

Core information at a glance
Distribution: ubuntu
Origin: ubuntu-stonking
Repository: https://nl.archive.ubuntu.com/ubuntu
Codename: stonking
Component: universe
Source: cct
Architecture: i386
Section: universe/science
Priority: optional
Maintainer: Ubuntu Developers <[email protected]>
Size & integrity

Byte sizes and integrity verification
Installed size: 101.3 kB
Size expected: 43.3 MB
Size actual: 43.3 MB
Size match
Dependencies

Required package dependencies
bioperl
cgview
Suggested packages

Recommended additional packages
None
Description

example data for testing the package cct
Homepage Download .deb
Checksums

Hash values and integrity verification status
Type	Expected	Actual
MD5	d04c6421…9c265e40	d04c6421…9c265e40
SHA-1	8daec82a…f61713c4	8daec82a…f61713c4
SHA-256	7d683e64…36b9a278	7d683e64…36b9a278
SHA-512	134897f2…176249dd	134897f2…176249dd
Files and directories included
.
usr
usr/share
usr/share/cct
usr/share/cct/lib
usr/share/cct/lib/scripts
usr/share/cct/lib/scripts/assign_cogs
usr/share/cct/lib/scripts/assign_cogs/sample_output
usr/share/cct/lib/scripts/assign_cogs/sample_output/sample_1.gff
usr/share/cct/lib/scripts/assign_cogs/sample_output/sample_1b.gff
usr/share/cct/lib/scripts/assign_cogs/sample_output/sample_2.gff
usr/share/cct/lib/scripts/assign_cogs/sample_output/sample_2b.gff
usr/share/cct/lib/scripts/assign_cogs/test_input
usr/share/cct/lib/scripts/assign_cogs/test_input/sample_1.gbk
usr/share/cct/lib/scripts/assign_cogs/test_input/sample_2.fna
usr/share/cct/lib/scripts/cgview_xml_builder
usr/share/cct/lib/scripts/cgview_xml_builder/test_input
usr/share/cct/lib/scripts/cgview_xml_builder/test_input/R_denitrificans.cogs
usr/share/cct/lib/scripts/cgview_xml_builder/test_input/R_denitrificans.gbk
usr/share/cct/lib/scripts/cgview_xml_builder/test_input/labels_to_show.txt
usr/share/cct/lib/scripts/cgview_xml_builder/test_input/prokka_multicontig.gbk
usr/share/cct/lib/scripts/convert_vcf_to_features
usr/share/cct/lib/scripts/convert_vcf_to_features/sample_output
usr/share/cct/lib/scripts/convert_vcf_to_features/sample_output/output_multiple_chromosomes_20
usr/share/cct/lib/scripts/convert_vcf_to_features/sample_output/output_multiple_chromosomes_20.tab
usr/share/cct/lib/scripts/convert_vcf_to_features/sample_output/output_multiple_chromosomes_21
usr/share/cct/lib/scripts/convert_vcf_to_features/sample_output/output_multiple_chromosomes_21.tab
usr/share/cct/lib/scripts/convert_vcf_to_features/sample_output/output_single_chromosome_20
usr/share/cct/lib/scripts/convert_vcf_to_features/sample_output/output_single_chromosome_20.tab
usr/share/cct/lib/scripts/convert_vcf_to_features/test_input
usr/share/cct/lib/scripts/convert_vcf_to_features/test_input/input_multiple_chromosomes.vcf
usr/share/cct/lib/scripts/convert_vcf_to_features/test_input/input_single_chromosome.vcf
usr/share/cct/lib/scripts/get_cds
usr/share/cct/lib/scripts/get_cds/sample_output
usr/share/cct/lib/scripts/get_cds/sample_output/R_denitrificans.cds.faa
usr/share/cct/lib/scripts/get_cds/sample_output/R_denitrificans.cds.fna
usr/share/cct/lib/scripts/get_cds/sample_output/prokka_multicontig.cds.faa
usr/share/cct/lib/scripts/get_cds/sample_output/prokka_multicontig.cds.fna
usr/share/cct/lib/scripts/get_cds/test_input
usr/share/cct/lib/scripts/get_cds/test_input/R_denitrificans.gbk
usr/share/cct/lib/scripts/get_cds/test_input/prokka_multicontig.gbk
usr/share/cct/lib/scripts/get_orfs
usr/share/cct/lib/scripts/get_orfs/sample_output
usr/share/cct/lib/scripts/get_orfs/sample_output/R_denitrificans.orfs.faa
usr/share/cct/lib/scripts/get_orfs/sample_output/R_denitrificans.orfs.fna
usr/share/cct/lib/scripts/get_orfs/sample_output/prokka_multicontig.orfs.faa
usr/share/cct/lib/scripts/get_orfs/sample_output/prokka_multicontig.orfs.fna
usr/share/cct/lib/scripts/get_orfs/test_input
usr/share/cct/lib/scripts/get_orfs/test_input/R_denitrificans.gbk
usr/share/cct/lib/scripts/get_orfs/test_input/prokka_multicontig.gbk
usr/share/cct/lib/scripts/local_blast_client
usr/share/cct/lib/scripts/local_blast_client/sample_output
usr/share/cct/lib/scripts/local_blast_client/sample_output/results_blastn.txt
usr/share/cct/lib/scripts/local_blast_client/sample_output/results_blastp.txt
usr/share/cct/lib/scripts/local_blast_client/sample_output/results_blastx.txt
usr/share/cct/lib/scripts/local_blast_client/sample_output/results_tblastn.txt
usr/share/cct/lib/scripts/local_blast_client/sample_output/results_tblastx.txt
usr/share/cct/lib/scripts/local_blast_client/test_input
usr/share/cct/lib/scripts/local_blast_client/test_input/test_dna_database.fasta
usr/share/cct/lib/scripts/local_blast_client/test_input/test_input_dna.fasta
usr/share/cct/lib/scripts/local_blast_client/test_input/test_input_protein.fasta
usr/share/cct/lib/scripts/local_blast_client/test_input/test_protein_database.fasta
usr/share/cct/lib/scripts/ncbi_search
usr/share/cct/lib/scripts/ncbi_search/sample_output
usr/share/cct/lib/scripts/ncbi_search/sample_output/NC_009933.gbk
usr/share/cct/lib/scripts/ncbi_search/sample_output/NC_009934.gbk
usr/share/cct/lib/scripts/ncbi_search/sample_output/combined.gbk
usr/share/cct/lib/scripts/sequence_to_multi_fasta
usr/share/cct/lib/scripts/sequence_to_multi_fasta/sample_output
usr/share/cct/lib/scripts/sequence_to_multi_fasta/sample_output/output1.fasta
usr/share/cct/lib/scripts/sequence_to_multi_fasta/sample_output/output2.fasta
usr/share/cct/lib/scripts/sequence_to_multi_fasta/sample_output/output3.fasta
usr/share/cct/lib/scripts/sequence_to_multi_fasta/sample_output/test_seq.fasta
usr/share/cct/lib/scripts/sequence_to_multi_fasta/sample_output/test_seq_multi.fasta
usr/share/cct/lib/scripts/sequence_to_multi_fasta/sample_output/test_seq_multi_s100_v5.fasta
usr/share/cct/lib/scripts/sequence_to_multi_fasta/sample_output/test_seq_multi_v5.fasta
usr/share/cct/lib/scripts/sequence_to_multi_fasta/sample_output/test_seq_s100_v5.fasta
usr/share/cct/lib/scripts/sequence_to_multi_fasta/sample_output/test_seq_v5.fasta
usr/share/cct/lib/scripts/sequence_to_multi_fasta/test_input
usr/share/cct/lib/scripts/sequence_to_multi_fasta/test_input/test_seq.fasta
usr/share/cct/lib/scripts/sequence_to_multi_fasta/test_input/test_seq_multi.fasta
usr/share/cct/test_projects
usr/share/cct/test_projects/test_blastn
usr/share/cct/test_projects/test_blastn/comparison_genomes
usr/share/cct/test_projects/test_blastn/comparison_genomes/match_end_of_orf.fasta
usr/share/cct/test_projects/test_blastn/comparison_genomes/match_end_of_orf_rev_comp.fasta
usr/share/cct/test_projects/test_blastn/comparison_genomes/match_start_of_orf.fasta
usr/share/cct/test_projects/test_blastn/comparison_genomes/match_start_of_orf_rev_comp.fasta
usr/share/cct/test_projects/test_blastn/project_settings.conf
usr/share/cct/test_projects/test_blastn/reference_genome
usr/share/cct/test_projects/test_blastn/reference_genome/two_copies_of_long_ORF_opposite_directions.fasta
usr/share/cct/test_projects/test_blastp
usr/share/cct/test_projects/test_blastp/comparison_genomes
usr/share/cct/test_projects/test_blastp/comparison_genomes/match_end_of_orf.fasta
usr/share/cct/test_projects/test_blastp/comparison_genomes/match_start_of_orf.fasta
usr/share/cct/test_projects/test_blastp/project_settings.conf
usr/share/cct/test_projects/test_blastp/reference_genome
usr/share/cct/test_projects/test_blastp/reference_genome/two_copies_of_long_ORF_opposite_directions.fasta
usr/share/cct/test_projects/test_blastx
usr/share/cct/test_projects/test_blastx/comparison_genomes
usr/share/cct/test_projects/test_blastx/comparison_genomes/match_end_of_orf.fasta
usr/share/cct/test_projects/test_blastx/comparison_genomes/match_start_of_orf.fasta
usr/share/cct/test_projects/test_blastx/project_settings.conf
usr/share/cct/test_projects/test_blastx/reference_genome
usr/share/cct/test_projects/test_blastx/reference_genome/two_copies_of_long_ORF_opposite_directions.fasta
usr/share/cct/test_projects/test_orfs
usr/share/cct/test_projects/test_orfs/project_settings.conf
usr/share/cct/test_projects/test_orfs/reference_genome
usr/share/cct/test_projects/test_orfs/reference_genome/random.fasta
usr/share/cct/test_projects/test_plots
usr/share/cct/test_projects/test_plots/project_settings.conf
usr/share/cct/test_projects/test_plots/reference_genome
usr/share/cct/test_projects/test_plots/reference_genome/test.fasta
usr/share/cct/test_projects/test_tblastn
usr/share/cct/test_projects/test_tblastn/comparison_genomes
usr/share/cct/test_projects/test_tblastn/comparison_genomes/match_end_of_orf.fasta
usr/share/cct/test_projects/test_tblastn/comparison_genomes/match_end_of_orf_rev_comp.fasta
usr/share/cct/test_projects/test_tblastn/comparison_genomes/match_start_of_orf.fasta
usr/share/cct/test_projects/test_tblastn/comparison_genomes/match_start_of_orf_rev_comp.fasta
usr/share/cct/test_projects/test_tblastn/project_settings.conf
usr/share/cct/test_projects/test_tblastn/reference_genome
usr/share/cct/test_projects/test_tblastn/reference_genome/two_copies_of_long_ORF_opposite_directions.fasta
usr/share/cct/test_projects/test_tblastx
usr/share/cct/test_projects/test_tblastx/comparison_genomes
usr/share/cct/test_projects/test_tblastx/comparison_genomes/match_end_of_orf.fasta
usr/share/cct/test_projects/test_tblastx/comparison_genomes/match_end_of_orf_rev_comp.fasta
usr/share/cct/test_projects/test_tblastx/comparison_genomes/match_start_of_orf.fasta
usr/share/cct/test_projects/test_tblastx/comparison_genomes/match_start_of_orf_rev_comp.fasta
usr/share/cct/test_projects/test_tblastx/project_settings.conf
usr/share/cct/test_projects/test_tblastx/reference_genome
usr/share/cct/test_projects/test_tblastx/reference_genome/two_copies_of_long_ORF_opposite_directions.fasta
usr/share/doc
usr/share/doc/cct
usr/share/doc/cct/examples
usr/share/doc/cct/examples/sample_projects
usr/share/doc/cct/examples/sample_projects/sample_project_1
usr/share/doc/cct/examples/sample_projects/sample_project_1/comparison_genomes
usr/share/doc/cct/examples/sample_projects/sample_project_1/comparison_genomes/NC_007717.gbk.gz
usr/share/doc/cct/examples/sample_projects/sample_project_1/comparison_genomes/NC_007718.gbk.gz
usr/share/doc/cct/examples/sample_projects/sample_project_1/comparison_genomes/NC_007720.gbk.gz
usr/share/doc/cct/examples/sample_projects/sample_project_1/labels_to_show.txt
usr/share/doc/cct/examples/sample_projects/sample_project_1/project_settings_a.conf
usr/share/doc/cct/examples/sample_projects/sample_project_1/project_settings_b.conf
usr/share/doc/cct/examples/sample_projects/sample_project_1/project_settings_c.conf
usr/share/doc/cct/examples/sample_projects/sample_project_1/reference_genome
usr/share/doc/cct/examples/sample_projects/sample_project_1/reference_genome/NC_007719.gbk.gz
usr/share/doc/cct/examples/sample_projects/sample_project_2
usr/share/doc/cct/examples/sample_projects/sample_project_2/comparison_genomes
usr/share/doc/cct/examples/sample_projects/sample_project_2/comparison_genomes/Methanococcus_maripaludis.gbk.gz
usr/share/doc/cct/examples/sample_projects/sample_project_2/comparison_genomes/Methanosarcina_acetivorans.gbk.gz
usr/share/doc/cct/examples/sample_projects/sample_project_2/comparison_genomes/Thermococcus_kodakaraensis.gbk.gz
usr/share/doc/cct/examples/sample_projects/sample_project_2/project_settings_a.conf
usr/share/doc/cct/examples/sample_projects/sample_project_2/project_settings_b.conf
usr/share/doc/cct/examples/sample_projects/sample_project_2/project_settings_c.conf
usr/share/doc/cct/examples/sample_projects/sample_project_2/reference_genome
usr/share/doc/cct/examples/sample_projects/sample_project_2/reference_genome/Methanobacterium_thermoautotrophicum.gbk.gz
usr/share/doc/cct/examples/sample_projects/sample_project_3
usr/share/doc/cct/examples/sample_projects/sample_project_3/comparison_genomes
usr/share/doc/cct/examples/sample_projects/sample_project_3/comparison_genomes/NC_000913.gbk.gz
usr/share/doc/cct/examples/sample_projects/sample_project_3/project_settings_a.conf
usr/share/doc/cct/examples/sample_projects/sample_project_3/project_settings_b.conf
usr/share/doc/cct/examples/sample_projects/sample_project_3/project_settings_c.conf
usr/share/doc/cct/examples/sample_projects/sample_project_3/reference_genome
usr/share/doc/cct/examples/sample_projects/sample_project_3/reference_genome/NC_004463.gbk.gz
usr/share/doc/cct/examples/sample_projects/sample_project_4
usr/share/doc/cct/examples/sample_projects/sample_project_4/analysis
usr/share/doc/cct/examples/sample_projects/sample_project_4/analysis/analysis_1.gff
usr/share/doc/cct/examples/sample_projects/sample_project_4/analysis/analysis_2.gff
usr/share/doc/cct/examples/sample_projects/sample_project_4/comparison_genomes
usr/share/doc/cct/examples/sample_projects/sample_project_4/comparison_genomes/L09136.gbk.gz
usr/share/doc/cct/examples/sample_projects/sample_project_4/comparison_genomes/L09137.gbk.gz
usr/share/doc/cct/examples/sample_projects/sample_project_4/features
usr/share/doc/cct/examples/sample_projects/sample_project_4/features/features_1.gff
usr/share/doc/cct/examples/sample_projects/sample_project_4/features/features_2.gff
usr/share/doc/cct/examples/sample_projects/sample_project_4/project_settings_a.conf
usr/share/doc/cct/examples/sample_projects/sample_project_4/project_settings_b.conf
usr/share/doc/cct/examples/sample_projects/sample_project_4/project_settings_c.conf
usr/share/doc/cct/examples/sample_projects/sample_project_4/reference_genome
usr/share/doc/cct/examples/sample_projects/sample_project_4/reference_genome/X52329.gbk.gz
usr/share/doc/cct/examples/sample_projects/sample_project_5
usr/share/doc/cct/examples/sample_projects/sample_project_5/comparison_genomes
usr/share/doc/cct/examples/sample_projects/sample_project_5/comparison_genomes/Arabidopsis_mito.gbk.gz
usr/share/doc/cct/examples/sample_projects/sample_project_5/comparison_genomes/E_coli.gbk.gz
usr/share/doc/cct/examples/sample_projects/sample_project_5/comparison_genomes/Human_mito.gbk.gz
usr/share/doc/cct/examples/sample_projects/sample_project_5/project_settings_a.conf
usr/share/doc/cct/examples/sample_projects/sample_project_5/project_settings_b.conf
usr/share/doc/cct/examples/sample_projects/sample_project_5/project_settings_c.conf
usr/share/doc/cct/examples/sample_projects/sample_project_5/reference_genome
usr/share/doc/cct/examples/sample_projects/sample_project_5/reference_genome/NC_001823.gbk.gz
usr/share/doc/cct/examples/sample_projects/sample_project_6
usr/share/doc/cct/examples/sample_projects/sample_project_6/comparison_genomes
usr/share/doc/cct/examples/sample_projects/sample_project_6/comparison_genomes/fem.fasta
usr/share/doc/cct/examples/sample_projects/sample_project_6/project_settings_a.conf
usr/share/doc/cct/examples/sample_projects/sample_project_6/project_settings_b.conf
usr/share/doc/cct/examples/sample_projects/sample_project_6/project_settings_c.conf
usr/share/doc/cct/examples/sample_projects/sample_project_6/reference_genome
usr/share/doc/cct/examples/sample_projects/sample_project_6/reference_genome/ref.fas.gz
usr/share/doc/cct/run-unit-test
usr/share/doc/cct-examples
usr/share/doc/cct-examples/changelog.Debian.gz
usr/share/doc/cct-examples/copyright
usr/share/doc/cct/examples/test_projects