https://github.com/wwood/bbbin
History
Tip revision: b98a60ba36ad03c4dafc984b9b17ac2a318b5fe0 authored by Ben Woodcroft on 18 March 2024, 05:59:38 UTC
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

README.txt

back to top