Various python scripts to deal with fasta-files and a like.

• blast_16S_besthit_api.py: blastn and get taxonomy for besthit. uses API to connect to NCBI, works for only handful seqs at a time.
• calc_seq_lengthy.py: given a multi-fasta file (.fna or .fasta), calculate sequence length for each DNA molecule.
• extract_sequences.py: subset a multi-fasta or genbank file given a list of ids. Spaces may be present in fasta header, but then the list of ids should match everything before.
• get_hits_hmmer3.py: given hmmsearch (hmmer3) output, filter Sequence ids for selected e-value threshold.
• lenfilter_fasta.py: filter a (multi-)fasta file based on sequence length.
• merge_multifasta.py: combine several multi-fasta into one file.
• parse_gbk_cds2fna.py: given a gbk file, extract the nucleotide sequences for all CDS into a fasta file using /locus_tag as headers.
• parse_gbk_df.py: given a folder with .gbk files, create a tidy df (.csv) with sequences and annotated features.
• reduce_identical_blast.py: given a blast_result with 100% identity hits kept and self-blasts removed, create a reduced set of unique sequences and map old Ids.
• replace_fasta_headers.py: given a multi-fasta file and a map of old and new ids, rename the fasta headers.
• split_fasta.py: split multi-fasta into smaller number of subset files.
• subset_notin_list.py: get items from longer list not in specified subset, e.g., use to get ids from unbinned contigs (not BioPython).
• translateKraken2.py: get full taxonomic lineage for NCBI tax IDs in Kraken2 standard output (need taxonkit.sif; script modified from https://raw.githubusercontent.com/microbialman/MetaSequencing/master/workflow/scripts/translateKraken2.py).