Some useful sequence tools written in Python - Now updated for Python3 :

replace_heads.py

Given a txt file of new headers, replaces existing headers in an mf file.

heditor.py

Edits Genbank headers to include species name and accession number only.

find_seq_overlap.py

Gets position of overlapping sequences on a given target sequence.

gbk_to_proteome.py

Gets all protein sequences from a gbk file.

 splice.py

To get sequence based on positions.

longest_orf.py

To find the longest orf from all frames and identify presence of in-frame stop codons.

get_seq_go.py

Get sequence from a multifasta file based on id.

reverse_complement.py

Reverse complements a sequence.

phd_to_fasta.py

Gets fasta sequence from phd file.

mulif_to_singlef.py

Separates multi fasta file to single fasta files.

remove_duplicate_fasta.py

Removes identical sequences (with identical headers).

extract_exonerate_output.py

Separates exonerate output into gff, orf and cds.

exonerate_highest_score.py

Gets highest scoring sequence alignment from exonerate output (when you don't want to use bestn).

nhmmer_or_hmmsearch_to_fasta.py

Gets fasta sequence for protein hits from hmmsearch or hit regions(dna) from nhmmer.

unique_headers.py	

Removes characters ":,.()%*" from fasta file headers, truncates header after first white space and adds a unique id.

unique_ids.py

Removes existing headers in a fasta file and replaces them with unique ids for each sequence ( >1, >2, >3 ...)

split_fasta_ntimes.py

Splits multi-fasta file into smaller multi-fasta files by N sequences

get_by_size.py

Extracts all sequences from an mf file that are >= a desired length.

compare_txt.py

Compares two text files (e.g can use to compare accession ids) and prints any ids that are not in both text files.