seqtools is a suite of python modules for sequence manipulation, including:

• general read/write csv and biological processes such as translation and reverse complement
• retrieval of sequence files
• extraction of sequences and metadata
• annotation of sequences in genbank format

seqtools requires:

• biopython:

pip install biopython

• CLUSTALW2
• Needle

(available with module load bioinfo)

General biology tools and file manipulation.

• load_csv: Lightweight delimited file loader. If headers not provided, first line will be used as header row
• write_csv: Write a list of dicts to a delimited file. If headers are not provided it will use the keys of the first dict. If the keys are not consistent throughout the list it will error.
• translate: translate DNA sequence into 1 or 3 letter amino acid sequence
• transcribe: transcribe DNA sequence into RNA sequence
• rc: return reverse complement of DNA sequence. Ambiguous characters are tolerated.

Get sequence files using NCBI Entrez API for GenBank/GenPept files or retrive Uniprot flat files.

• get_data_entrez: return GenBank or GenPept files using RefSeq Accession
• get_uniprot: return Uniprot flat file using accession
• get_exons_from_gb: return exon positions from genbank file, including just coding exon regions if cds=True
• get_domain_details_from_gb: extract feature locations from GenBank file. This returns any features labelled as 'misc_feature'
• get_domain_details_from_protein: return feature positions from Uniprot or GenPept file. Uniprot features defined using up_feature_types. GenPept returns all labelled with 'Region' or 'Site'

Get transcript/gene information from GTF file

• gtf_to_gene_length: Get gene lengths from a GTF file, using either the longest transcript, combined length of all unique sequence or total length of all transcripts.
• get_transcripts: Get fasta files for all transcript or protein sequences for an ENS gene ID

Run global alignment algorithms

• run_clustalw2: Run CLUSTALW2 multiple sequernce alignment. Return alignment object or specify output file
• run_needle: Run Needle pairwise sequernce alignment. Return alignment object or specify output file
• get_contigs_from_clustal: Return regions of homology using coordinates of top sequence or base_sequence if specified

Find and add annotations to GenBank files

• get_sequence_from_genbank: Return sequence from GenBank file. (whole sequence or just CDS)
• get_sequence_from_uniprot: Return sequence from GenBank file. (whole sequence or just CDS)
• clean_sequence: Remove modification characters - return DNA sequence
• find_sirna_and_annotate_genbank: find sequence in ref_seq and return cooordinates
• annotate: Takes a list of sequences, searches for them in the GenBank file and adds annotations

Find regions of homology between orthologues, perform alignments and annotate homology regions. Requires a manually completed accessions.csv file to specify which transcripts/proteins to use

• protein: retrieves GenPept files from accessions.csv file and performs multiple sequence alignment
• mrna: retrieves GenBank files from accessions.csv, performs multiple sequence alignment and pairwise alignment, then annotates regions of homology on genbank file.