https://github.com/wwood/bbbin
Tip revision: b98a60ba36ad03c4dafc984b9b17ac2a318b5fe0 authored by Ben Woodcroft on 18 March 2024, 05:59:38 UTC
rust: Adjust for strange case.
rust: Adjust for strange case.
Tip revision: b98a60b
File | Mode | Size |
---|---|---|
plasmarithm | ||
ruby | ||
rust | ||
test | ||
testFiles | ||
.gitignore | -rw-r--r-- | 51 bytes |
16Samplicons_by_keyword.rb | -rw-r--r-- | 1.6 KB |
454UnscaffoldedContigs.rb | -rwxr-xr-x | 3.7 KB |
454contig_descriptions.rb | -rwxr-xr-x | 2.7 KB |
454scaffold_coverage_length.rb | -rwxr-xr-x | 5.7 KB |
COPYING | -rw-r--r-- | 34.3 KB |
DNAtoAminoAcid.pl | -rwxr-xr-x | 365 bytes |
JGI_chop_Tgf.pl | -rwxr-xr-x | 21 bytes |
JGI_to_Ensembl.pl | -rwxr-xr-x | 9.3 KB |
JGI_to_Ensembl_via_WormBase.pl | -rwxr-xr-x | 1.1 KB |
README.html | -rw-r--r-- | 332.2 KB |
README.txt | -rw-r--r-- | 900 bytes |
SNPRatios.pl | -rwxr-xr-x | 575 bytes |
TestingHelpers.pm | -rw-r--r-- | 1.7 KB |
acceptibleMatrices.pl | -rwxr-xr-x | 906 bytes |
ace2phylip.pl | -rwxr-xr-x | 399 bytes |
aceTraces.pl | -rwxr-xr-x | 739 bytes |
acidichydrophobic.matrix | -rw-r--r-- | 2.0 KB |
acidpolaritymatrix.rb | -rw-r--r-- | 1.5 KB |
alignment_trim.rb | -rwxr-xr-x | 3.4 KB |
alpha_diversity_from_ebd_file.rb | -rwxr-xr-x | 2.8 KB |
annotate_by_csv.rb | -rwxr-xr-x | 4.0 KB |
annotate_fasta.rb | -rwxr-xr-x | 2.3 KB |
annotate_fasta_length.rb | -rwxr-xr-x | 1.8 KB |
annotate_ncbi_tree.py | -rwxr-xr-x | 3.1 KB |
apicomplexan_blast_database_create.sh | -rwxr-xr-x | 11.5 KB |
apiloc | -rwxr-xr-x | 46 bytes |
apiloc_screen.sh | -rwxr-xr-x | 76 bytes |
assembly_combinatorially.rb | -rwxr-xr-x | 3.4 KB |
at_bias.rb | -rwxr-xr-x | 1.1 KB |
autoupdate_wallpaper.sh | -rwxr-xr-x | 610 bytes |
autoupdate_wallpaper_continuous.sh | -rwxr-xr-x | 80 bytes |
base.yml | -rw-r--r-- | 1.2 KB |
beta_diversity_comparison.rb | -rwxr-xr-x | 2.2 KB |
beta_diversity_squares.rb | -rwxr-xr-x | 2.2 KB |
bl2seqRebuid.pl | -rwxr-xr-x | 3.5 KB |
blast.rb | -rwxr-xr-x | 658 bytes |
blastYourself.pl | -rwxr-xr-x | 1.8 KB |
blast_and_extract_region.rb | -rwxr-xr-x | 2.3 KB |
blast_by_splits.rb | -rwxr-xr-x | 3.7 KB |
blast_evalue_grep.rb | -rwxr-xr-x | 719 bytes |
blast_evalue_grep_test.rb | -rw-r--r-- | 2.2 KB |
blast_mask.rb | -rwxr-xr-x | 3.0 KB |
blast_mask_test.rb | -rw-r--r-- | 2.8 KB |
blast_overlap_percentage.rb | -rwxr-xr-x | 2.6 KB |
blast_saturation.rb | -rwxr-xr-x | 4.5 KB |
blast_saturation_test.rb | -rw-r--r-- | 5.8 KB |
blast_to_blastclust.rb | -rwxr-xr-x | 2.0 KB |
blast_triangularise.rb | -rwxr-xr-x | 794 bytes |
blast_triangularise_test.rb | -rw-r--r-- | 1.3 KB |
blastbig.sh | -rwxr-xr-x | 668 bytes |
blastxml_split.rb | -rwxr-xr-x | 1.6 KB |
blastxml_split_test.rb | -rw-r--r-- | 1.1 KB |
blastxml_to_exonpart.pl | -rwxr-xr-x | 2.3 KB |
blastxml_to_gff.pl | -rw-r--r-- | 2.5 KB |
blastxml_to_html.pl | -rwxr-xr-x | 2.5 KB |
blastxml_to_microarray_csv.pl | -rwxr-xr-x | 4.0 KB |
blastxml_to_png.pl | -rwxr-xr-x | 4.1 KB |
blastxml_to_tab.pl | -rw-r--r-- | 1.3 KB |
blastxml_to_tab.rb | -rwxr-xr-x | 1.9 KB |
bp_classify_hits_kingdom_ben.pl | -rwxr-xr-x | 8.3 KB |
break_random_sequences.rb | -rwxr-xr-x | 4.2 KB |
brenda_soap.py | -rw-r--r-- | 571 bytes |
cap3_output.rb | -rwxr-xr-x | 4.5 KB |
cazy2fasta.rb | -rwxr-xr-x | 706 bytes |
classify_iontorrent_snps.rb | -rwxr-xr-x | 10.3 KB |
clustalw_simple.pl | -rwxr-xr-x | 800 bytes |
codeListing.pl | -rwxr-xr-x | 1.3 KB |
codon_usage.rb | -rwxr-xr-x | 2.6 KB |
comment_removal.pl | -rwxr-xr-x | 133 bytes |
conda_newest | -rwxr-xr-x | 3.0 KB |
consedToSNPs.pl | -rwxr-xr-x | 664 bytes |
contig_list_to_bed.rb | -rwxr-xr-x | 2.5 KB |
contig_recruiter.py | -rwxr-xr-x | 3.0 KB |
count_occurence.rb | -rwxr-xr-x | 2.6 KB |
count_sequences.rb | -rwxr-xr-x | 179 bytes |
coverage_regionwise.py | -rwxr-xr-x | 4.6 KB |
csv2fasta.rb | -rwxr-xr-x | 1.9 KB |
csv_newlines.rb | -rwxr-xr-x | 1.3 KB |
csv_to_tab.rb | -rwxr-xr-x | 1.0 KB |
csv_to_tab_test.rb | -rw-r--r-- | 347 bytes |
dNdS_2seqs.rb | -rwxr-xr-x | 721 bytes |
dcnls.rb | -rwxr-xr-x | 4.6 KB |
dereplicate_img.rb | -rwxr-xr-x | 3.0 KB |
describeFasta.pl | -rwxr-xr-x | 781 bytes |
dewobble.rb | -rwxr-xr-x | 1.2 KB |
distinctMatch.pl | -rwxr-xr-x | 610 bytes |
draw_gene_structure.pl | -rwxr-xr-x | 1.9 KB |
elegans.sh | -rwxr-xr-x | 70 bytes |
ensembl_genes_ids_to_orthomcl_group.rb | -rwxr-xr-x | 5.4 KB |
ensembl_species_id_prefixes_autogenerated.rb | -rw-r--r-- | 3.1 KB |
ensembl_species_id_prefixes_autogenerator.rb | -rwxr-xr-x | 3.8 KB |
entrez.py | -rwxr-xr-x | 1.9 KB |
entrez.rb | -rwxr-xr-x | 475 bytes |
entrez_proteins_from_nucleotide_ids.rb | -rwxr-xr-x | 3.2 KB |
enzyme_matcher.rb | -rwxr-xr-x | 2.2 KB |
eupathdb_gene_information_file_extractor.rb | -rwxr-xr-x | 1.2 KB |
eupathdb_genomic_sequence_extractor.rb | -rwxr-xr-x | 3.2 KB |
eupathdb_gff_to_tandem_descriptions.rb | -rwxr-xr-x | 3.4 KB |
eupathdb_go_term_positives_negatives.rb | -rwxr-xr-x | 1.6 KB |
eupathdb_id_only_fasta_files.rb | -rwxr-xr-x | 598 bytes |
eupathdb_tandem_gene_csv_to_conserved_pairs.rb | -rwxr-xr-x | 2.4 KB |
evalue_graph.rb | -rwxr-xr-x | 1.4 KB |
exonerate2gbrowseGff.rb | -rwxr-xr-x | 718 bytes |
exonerate2gff.rb | -rwxr-xr-x | 574 bytes |
extractTracesFromDetailsFile.pl | -rwxr-xr-x | 2.5 KB |
extract_from_fasta.pl | -rwxr-xr-x | 6.0 KB |
extract_from_fasta_test.pl | -rw-r--r-- | 19 bytes |
facil_codon_table_for_inspection.rb | -rwxr-xr-x | 982 bytes |
falciparum_unconserved_regions.rb | -rwxr-xr-x | 2.4 KB |
fasta2phylip.py | -rwxr-xr-x | 2.6 KB |
fasta_alignment_unknownify_at_end.rb | -rwxr-xr-x | 1.7 KB |
fasta_concat.pl | -rwxr-xr-x | 977 bytes |
fasta_files_to_otu_tables.rb | -rwxr-xr-x | 3.4 KB |
fasta_first_word.rb | -rwxr-xr-x | 130 bytes |
fasta_hmmsearch.pl | -rwxr-xr-x | 933 bytes |
fasta_screen.pl | -rwxr-xr-x | 1.4 KB |
fasta_screen_test.pl | -rw-r--r-- | 1.8 KB |
fasta_separate.pl | -rwxr-xr-x | 474 bytes |
fasta_split.rb | -rwxr-xr-x | 2.1 KB |
fasta_to_fastq.rb | -rwxr-xr-x | 1.4 KB |
fasta_to_html.pl | -rwxr-xr-x | 883 bytes |
fasta_to_phylip.rb | -rw-r--r-- | 145 bytes |
fasta_to_sqlite_csv_upload.rb | -rwxr-xr-x | 3.7 KB |
fastacmd_taxonomy_to_single_line.rb | -rwxr-xr-x | 669 bytes |
fastq_count.sh | -rwxr-xr-x | 153 bytes |
fastq_split.rb | -rwxr-xr-x | 3.7 KB |
figtree | -rwxr-xr-x | 79 bytes |
fill_taxonomy.py | -rwxr-xr-x | 5.4 KB |
findNs.pl | -rwxr-xr-x | 847 bytes |
first_blast_result.rb | -rwxr-xr-x | 354 bytes |
foam_ko_to_hmm_name.rb | -rw-r--r-- | 1.9 KB |
formatGenbank.rb | -rw-r--r-- | 219 bytes |
fq2fa.sh | -rwxr-xr-x | 73 bytes |
gag_scatterplot.rb | -rwxr-xr-x | 9.5 KB |
gc.rb | -rwxr-xr-x | 2.2 KB |
gc_content_vs_coverage.rb | -rwxr-xr-x | 2.9 KB |
gc_content_vs_coverage2.rb | -rwxr-xr-x | 4.3 KB |
gccorrect_preparation.py | -rwxr-xr-x | 2.4 KB |
gem_server | -rwxr-xr-x | 53 bytes |
gem_server_screen.sh | -rwxr-xr-x | 11 bytes |
genbank_newer_accession.rb | -rwxr-xr-x | 2.7 KB |
genbank_species_to_beginning.rb | -rwxr-xr-x | 366 bytes |
genbank_summariser.rb | -rwxr-xr-x | 3.5 KB |
gene_call_update_matcher.rb | -rwxr-xr-x | 3.4 KB |
gene_wise_transcriptome_directionality.rb | -rwxr-xr-x | 3.6 KB |
genscanMultiFasta.pl | -rwxr-xr-x | 2.4 KB |
genscan_to_gff.pl | -rwxr-xr-x | 1.6 KB |
gff_exonerate_est2genome_gff2ps.pl | -rwxr-xr-x | 2.8 KB |
gff_remove_orientation.pl | -rwxr-xr-x | 1.1 KB |
gff_to_exonpart.pl | -rwxr-xr-x | 2.0 KB |
gly_sliding_window.rb | -rwxr-xr-x | 3.6 KB |
greengenes_to_taxtastic.rb | -rwxr-xr-x | 3.4 KB |
grinder_orientations_fix.rb | -rwxr-xr-x | 2.8 KB |
gtdb_genome_id_to_file.py | -rwxr-xr-x | 3.7 KB |
gtdb_tree_to_taxonomy.py | -rwxr-xr-x | 3.3 KB |
guix-add.rb | -rwxr-xr-x | 3.2 KB |
guix-deploy.py | -rwxr-xr-x | 7.3 KB |
guix-import-ruby.rb | -rwxr-xr-x | 241 bytes |
guix-update.rb | -rwxr-xr-x | 2.9 KB |
hmm_explode.rb | -rwxr-xr-x | 3.5 KB |
hmmalign_right.rb | -rwxr-xr-x | 1.9 KB |
hmmsearch_and_codons.rb | -rwxr-xr-x | 7.3 KB |
hydrophobicity_profile.rb | -rwxr-xr-x | 911 bytes |
img_cog_matrix.rb | -rwxr-xr-x | 3.1 KB |
img_gene_id_list_to_tree.rb | -rwxr-xr-x | 7.6 KB |
in | -rw-r--r-- | 21 bytes |
in.err | -rw-r--r-- | 0 bytes |
in.out | -rw-r--r-- | 24 bytes |
insert_size.py | -rwxr-xr-x | 2.0 KB |
join_unsorted.rb | -rwxr-xr-x | 3.3 KB |
kawaii | -rwxr-xr-x | 237 bytes |
kawaii_screen.sh | -rwxr-xr-x | 56 bytes |
kegg_single_connections.rb | -rwxr-xr-x | 3.0 KB |
kmer_counter.rb | -rw-r--r-- | 158 bytes |
kmers_count_parallel.rb | -rwxr-xr-x | 5.7 KB |
m_orf_filter.rb | -rwxr-xr-x | 236 bytes |
margo | -rwxr-xr-x | 3.2 KB |
mask_eupathdb_domains.rb | -rwxr-xr-x | 2.0 KB |
mask_eupathdb_domains_test.rb | -rw-r--r-- | 1.0 KB |
mask_fasta_with_xstream_spreadsheet.rb | -rwxr-xr-x | 1.4 KB |
mask_fasta_with_xstream_spreadsheet_test.rb | -rw-r--r-- | 807 bytes |
matchToRealityCheck.pl | -rwxr-xr-x | 714 bytes |
median_contig_coverage.rb | -rwxr-xr-x | 1023 bytes |
memory_watcher.rb | -rwxr-xr-x | 1.4 KB |
merge.pl | -rw-r--r-- | 1.0 KB |
merge_and_summarise_otu_tables.rb | -rwxr-xr-x | 5.3 KB |
metagenome_otus.py | -rwxr-xr-x | 11.2 KB |
microscopy_automate | -rwxr-xr-x | 9.5 KB |
microscopy_automate.rb | l--------- | 19 bytes |
microscopy_automate_dv.rb | -rwxr-xr-x | 2.9 KB |
mismatching_primer_counts.rb | -rwxr-xr-x | 1.9 KB |
mob | -rwxr-xr-x | 163 bytes |
molecular_weights.rb | -rwxr-xr-x | 359 bytes |
monophyly_finder.py | -rwxr-xr-x | 4.9 KB |
mumer_coords_to_blast_output_format.rb | -rwxr-xr-x | 1.2 KB |
myblastparser_tophit.pl | -rwxr-xr-x | 2.0 KB |
myblastparser_tophit_test.pl | -rw-r--r-- | 144 bytes |
neuropeptide_filter.rb | -rwxr-xr-x | 856 bytes |
orf_finder.rb | -rwxr-xr-x | 11.9 KB |
orf_finder_test.rb | -rw-r--r-- | 7.4 KB |
orthomcl_filter.rb | -rwxr-xr-x | 1.9 KB |
orthomcl_species_jumper.rb | -rwxr-xr-x | 5.8 KB |
orthomcl_species_jumper_faster.rb | -rwxr-xr-x | 6.2 KB |
otu_table_renamer.rb | -rwxr-xr-x | 3.1 KB |
out | -rw-r--r-- | 5 bytes |
pI.rb | -rwxr-xr-x | 345 bytes |
parseConreal.pl | -rwxr-xr-x | 1.6 KB |
parseMatInspector.pl | -rwxr-xr-x | 1.8 KB |
parseMatInspector2.pl | -rwxr-xr-x | 3.5 KB |
parseMatch.pl | -rwxr-xr-x | 1.1 KB |
parse_fasta.rb | -rwxr-xr-x | 1.4 KB |
parsedChop.pl | -rwxr-xr-x | 527 bytes |
parsedToDomainDraw.pl | -rwxr-xr-x | 1.2 KB |
pc2.pl | -rwxr-xr-x | 1.6 KB |
pileup_consensus.rb | -rwxr-xr-x | 1.7 KB |
pileup_subset.rb | -rwxr-xr-x | 2.4 KB |
plasmit_screenscraper.rb | -rwxr-xr-x | 1.4 KB |
plotManualCoverage.pl | -rwxr-xr-x | 3.5 KB |
plotManualQuality.pl | -rwxr-xr-x | 1.9 KB |
plotManualSNPs.pl | -rwxr-xr-x | 1.5 KB |
plotManualSNPs3.pl | -rwxr-xr-x | 195 bytes |
plotManualSNPs4.pl | -rwxr-xr-x | 1.1 KB |
predictmnls | -rwxr-xr-x | 825 bytes |
primer_design_for_toxoplasma_ku80_prime_replacement.rb | -rwxr-xr-x | 16.8 KB |
prottest | -rwxr-xr-x | 876 bytes |
ps2pdf.pl | -rwxr-xr-x | 121 bytes |
pseudogene_extract_proteins.rb | -rwxr-xr-x | 1.3 KB |
pwmConsensus.pl | -rwxr-xr-x | 2.5 KB |
pwmConsensusJaspar.pl | -rwxr-xr-x | 1.4 KB |
qa_shotgun_reads.rb | -rwxr-xr-x | 2.4 KB |
randomFasta.pl | -rwxr-xr-x | 586 bytes |
rare_codons.rb | -rwxr-xr-x | 722 bytes |
reality_check.pl | -rwxr-xr-x | 505 bytes |
reduceSet.pl | -rwxr-xr-x | 623 bytes |
reduceSetByName.pl | -rwxr-xr-x | 483 bytes |
reduceSetToAppendix.pl | -rwxr-xr-x | 852 bytes |
redundant_sequences.rb | -rwxr-xr-x | 1.0 KB |
regex_fasta.rb | -rwxr-xr-x | 711 bytes |
remove_alignment_from_fasta.pl | -rwxr-xr-x | 885 bytes |
remove_short_sequences.rb | -rwxr-xr-x | 330 bytes |
renameHtml.pl | -rwxr-xr-x | 758 bytes |
reverseFasta.pl | -rwxr-xr-x | 591 bytes |
reverseGnuplot.pl | -rwxr-xr-x | 592 bytes |
rget.pl | -rwxr-xr-x | 701 bytes |
rpbs.rb | -rwxr-xr-x | 3.8 KB |
rpbs_test.rb | -rw-r--r-- | 1.1 KB |
rq_env.rb | -rwxr-xr-x | 369 bytes |
runmb.sh | -rwxr-xr-x | 42 bytes |
sam_to_percent_identities.rb | -rwxr-xr-x | 3.2 KB |
search_overview.pl | -rwxr-xr-x | 4.4 KB |
sequenceChop.pl | -rwxr-xr-x | 4.4 KB |
sequenceChopTest.pl | -rw-r--r-- | 1.2 KB |
sequenceNamer.pl | -rwxr-xr-x | 257 bytes |
sequence_chunks.rb | -rwxr-xr-x | 3.8 KB |
sequence_cleaner.rb | -rwxr-xr-x | 263 bytes |
shorten_blast_result.rb | -rwxr-xr-x | 729 bytes |
silica_sliding_window.rb | -rwxr-xr-x | 2.3 KB |
sim_reads.py | -rwxr-xr-x | 4.1 KB |
simpleCutoff.pl | -rwxr-xr-x | 559 bytes |
simpleCutoffHistogram.pl | -rwxr-xr-x | 583 bytes |
simpleCutoffPipeline.pl | -rwxr-xr-x | 770 bytes |
simulate_fasta.rb | -rwxr-xr-x | 1010 bytes |
simulation_fastq_cleanup.rb | -rwxr-xr-x | 3.0 KB |
single_linkage_cluster.rb | -rwxr-xr-x | 1.5 KB |
slovakian_extract.rb | -rwxr-xr-x | 747 bytes |
snpCsvCheck.pl | -rwxr-xr-x | 1.6 KB |
splitGnuplot.pl | -rwxr-xr-x | 386 bytes |
split_Pfam_ls.pl | -rwxr-xr-x | 1.4 KB |
sra_keywords.rb | -rwxr-xr-x | 1.7 KB |
sra_lites_to_blastdb.rb | -rwxr-xr-x | 3.6 KB |
sra_pyrotag_accessions_by_keyword.rb | -rwxr-xr-x | 1.9 KB |
sra_run_describer.rb | -rwxr-xr-x | 2.0 KB |
t2t_fix.py | -rwxr-xr-x | 5.7 KB |
takeOutSNPs.pl | -rwxr-xr-x | 578 bytes |
tblastn_tab_to_protein.rb | -rwxr-xr-x | 877 bytes |
test.fasta | -rw-r--r-- | 29 bytes |
test.pl | -rwxr-xr-x | 425 bytes |
test_enzyme_matcher.rb | -rw-r--r-- | 357 bytes |
test_primer_design_extras.rb | -rw-r--r-- | 4.2 KB |
test_silica_sliding_window.rb | -rw-r--r-- | 2.3 KB |
text_multiline_to_inkscape_svg.rb | -rwxr-xr-x | 634 bytes |
topbash | -rwxr-xr-x | 28 bytes |
transeq_nucl.rb | -rwxr-xr-x | 1.8 KB |
transfacHash.pl | -rwxr-xr-x | 1.4 KB |
transfacReducedSet.pl | -rwxr-xr-x | 1.3 KB |
transfacToPajek.pl | -rwxr-xr-x | 863 bytes |
translate_funky.rb | -rwxr-xr-x | 1.5 KB |
tree_divider.rb | -rwxr-xr-x | 528 bytes |
trees | -rwxr-xr-x | 3.2 KB |
trees_bayesian | -rwxr-xr-x | 323 bytes |
trees_distance | -rwxr-xr-x | 3.4 KB |
trees_distance_hpc | -rwxr-xr-x | 1.9 KB |
trees_ml | -rwxr-xr-x | 2.0 KB |
trees_ml_hpc | -rw-r--r-- | 1.9 KB |
trees_parsimony | -rwxr-xr-x | 2.8 KB |
trees_parsimony_hpc | -rw-r--r-- | 1.9 KB |
trimpoly.rb | -rwxr-xr-x | 4.2 KB |
trimpoly_test.rb | -rw-r--r-- | 7.2 KB |
uba_ncbi_accessions.tsv | -rw-r--r-- | 403.2 KB |
uniq.rb | -rw-r--r-- | 424 bytes |
uniq_test.rb | -rw-r--r-- | 415 bytes |
uniqify_fasta.rb | -rwxr-xr-x | 335 bytes |
uniqify_phylip.rb | -rwxr-xr-x | 1.4 KB |
uniqify_tree.rb | -rwxr-xr-x | 447 bytes |
unscaffold.rb | -rwxr-xr-x | 2.7 KB |
ununiqify_ensembl_tree.rb | -rwxr-xr-x | 5.7 KB |
ununiqify_standard_tree.rb | -rwxr-xr-x | 6.8 KB |
ununiqify_tree.rb | -rwxr-xr-x | 1.6 KB |
velvet_graph_to_coverages.rb | -rwxr-xr-x | 1.5 KB |
vias | -rwxr-xr-x | 310 bytes |
window_acidic_count.pl | -rwxr-xr-x | 1.5 KB |
window_simple_count.pl | -rw-r--r-- | 2.6 KB |
winzeler_tiling_map_to_tpmap.rb | -rwxr-xr-x | 1.1 KB |
yagenome.rb | -rwxr-xr-x | 3.4 KB |