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Correlate species traits.ipynb
Correlate species traits.ipynb
 
 
DeltaLFE calculation demonstration.ipynb
DeltaLFE calculation demonstration.ipynb
 
 
README.md
README.md
 
 
_distributed.py
_distributed.py
 
 
annotate_readthrough_efficiency.py
annotate_readthrough_efficiency.py
 
 
calculate_sliding_window_series.py
calculate_sliding_window_series.py
 
 
codon_randomization.py
codon_randomization.py
 
 
codonw.py
codonw.py
 
 
compare_updates.py
compare_updates.py
 
 
config.py
config.py
 
 
convert_webgester_list.py
convert_webgester_list.py
 
 
data_helpers.py
data_helpers.py
 
 
ensembl_ftp.py
ensembl_ftp.py
 
 
find_member_species.py
find_member_species.py
 
 
genome_model.py
genome_model.py
 
 
gff.py
gff.py
 
 
gff3_extract_coding_genes.py
gff3_extract_coding_genes.py
 
 
ingest_new_genome.py
ingest_new_genome.py
 
 
local_cache.py
local_cache.py
 
 
mfe_plots.py
mfe_plots.py
 
 
mysql_rnafold.py
mysql_rnafold.py
 
 
ncbi_entrez.py
ncbi_entrez.py
 
 
ncbi_taxa.py
ncbi_taxa.py
 
 
notify_pushover.py
notify_pushover.py
 
 
nucleic_compress.py
nucleic_compress.py
 
 
odb4.py
odb4.py
 
 
paxdb.py
paxdb.py
 
 
pcache.py
pcache.py
 
 
process_series_data.py
process_series_data.py
 
 
profile_plots.dev.py
profile_plots.dev.py
 
 
profile_plots.py
profile_plots.py
 
 
profile_plots_t2.py
profile_plots_t2.py
 
 
profile_plots_t3.py
profile_plots_t3.py
 
 
profile_plots_t4.py
profile_plots_t4.py
 
 
profiling.py
profiling.py
 
 
rate_limit.py
rate_limit.py
 
 
readthrough_test.py
readthrough_test.py
 
 
reference_trees.py
reference_trees.py
 
 
regulondb_tables.py
regulondb_tables.py
 
 
requeue_sequences_missing_energies_for_sliding_window.py
requeue_sequences_missing_energies_for_sliding_window.py
 
 
rnafold_vienna.py
rnafold_vienna.py
 
 
runningstats.py
runningstats.py
 
 
store_new_shuffles.py
store_new_shuffles.py
 
 
store_seqs_from_fasta.py
store_seqs_from_fasta.py
 
 
taxonomy.py
taxonomy.py
 
 
termfold.singularity
termfold.singularity
 
 
test_create_random_external_class.py
test_create_random_external_class.py
 
 
test_data_helpers.py
test_data_helpers.py
 
 
test_gff_extract_coding_genes.py
test_gff_extract_coding_genes.py
 
 

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rnafold-rts-public

Source code for RTS analysis. https://www.biorxiv.org/content/10.1101/2020.02.10.941153v1

Important files:

  • termfold.singularity - singularity recipe for container for running code (including jupyter notebooks).
  • DeltaLFE calculation demonstration.ipynb - jupyter notebook demonstrating the delta-LFE computation and allowing it to be easily run on new genomes. The input will be two fasta files, one with CDS sequences and one with matching 3'-UTR sequences. The results are the native, randomized and dLFE graphs.
  • config.py - configuration for database connections, etc.

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Source code for RTS analysis. https://www.biorxiv.org/content/10.1101/2020.02.10.941153v1

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