Brief Description of Scripts

blast

Scripts and documents related to the use of NCBI BLAST+ 2.12.0.

Script	Description
blast_commands.txt	contains commonly used commands when working with the NCBI BLAST+ 2.12.0 program
generate_taxid_map.py	generate a taxid file from Genbank file containing all sequences of interest
process_genbank_db.py	generate both a .fasta file containing all sequences in Genbank file, as well as a metadata .csv file

examples

Examples of how we use common Python modules and documentation templates.

Script	Description
argparse_example.py	contains example implementation of argparse
docstrings_example.py	contains example docstring formats for our scripts
pathlib_example.py	contains commonly used code when working with pathlib module
slurm_scheduler_example.sh	contains example of slurm scheduler script
template.py	template of our Python scripts

miscellaneous

Miscellaneous scripts for dealing with common file types.

Script	Description
batch_rename.py	used to sanitize SeqStudio ab1 file names to fit the formats required for our scripts
batch_reverse_complement.py	generate reverse complements of several sequences
convert_gb_fasta.py	extract .fasta sequences from Genbank files
generate_sequence.py	in-silico generation of random DNA sequences
calc_ta.py	calculate melting temperatures of several primer sets

sanger-processing

Scripts related to working with SeqStudio ab1 files.

Script	Description
sanger_qc.py	automated QC of Sanger sequences
sanger_sequence_trim.py	automated trimming of Sanger sequences (SeqStudio ab1 files)
generate_seqstudio_qc.py	generate SeqStudio QC .csv file from solely the ab1 files (used if the original QC .csv is lost)

sequence-analysis

Scripts related to sequence analysis tasks.

Script	Description
species_aligner_analysis.py	from a Genbank file containing multiple entries, generate alignments for each species within the GenBank file.