• scripts/group-text.py
• Line correspond to the same group should be consecutive
• scripts/group-text.py -i pairwise.0309.txt -e 'lambda x:x.split(":GCF")[0]' -r 'lambda x,n:x.split(":")[0] +"-" + str(n).zfill(5)' -wh -od pairwise.0309

subsetting fasta by sequence id: scripts/subsetting-fasta.py

• similar to seqtk subseq seq-ids.txt

remove sequence very similar to that present in another set:scripts/extract-non-representative-segments.py

remove nearly identical sequence by minimap2 search: scripts/reduce-redundancy.py

drop sequence with the same id: scripts/drop-sequence-with-same-id.py

rename sequence in input fasta file scripts/rename-fasta.py

convert proteins predicted by prodigal to bed format prodigal-faa2bed.py

Homolog search with mmseqs

• RNA search: scripts/RNA-homolog-search.py
• protein search: scripts/protein-homolog-search.py

filter mmseqs hits in blast+ format

• scripts/filter-hits.py

clustering pairwise search results with MCL algorithm

• scripts/mcl-clustering.py

clustering pairwise search results with leiden algorithm

• scripts/leiden-partitioning.py

reformat cd-hit/cd-hit-est clustering results

• scripts/cd-hit-to-clustering-table.py

reformat MCL clustering results

• scripts/mcl-to-clustering-table.py

group sequence by clustering table

• scripts/group-sequences.py

Annotate genomic context of specified interval in a prokaryote genome given gene bed file

• scripts/annotate-intervals.py

Pick local max of overlapping intervals

• seems not implement by bed tools
• scripts/pick-local-max.py

Pick local max from bedgraph like format

• scripts/pick-local-max-all-bins.py

Select mutual closest features in 2 bed files, now used for transcription unit determination

• scripts/extract-transcription-unit-from-genome.py

count kmer frequency: scripts/kmer-frequency-fitter.py

simulate sequence from kmer frequency: scripts/kmer-emitter.py

classify sequences with kmer composition:

• kmer-profile-classification.py
• scripts/kmer-profile-inference.py