Some python programs to extract data from .gbk files
Given the gene name (must be an exact match to the /gene=[Name]) will produce an alignment-ready text file containing the DNA code from -100 to the end of the gene, as it’s labelled on the .gbk file.
Searches all .gbk files in the program's directory
inputs: gene name i.e. groL output: .txt file with >filename-productOfGene (DNA sequence of gene from position[-100] to end, with starting codon capitalized)
ex: result.txt with gene searched groL
>mygbkfile.gbk-60 kDa chaperonin gttgctgctccataacatcaaacatcgacccacggcgtaacgcgcttgctgcttggatgcccgaggcatagactgtacaaaaaaacagtcataacaagccATGaaaaccgccactgcgccgttaccaccgctgcgttcggtcaaggttctggaccagttgcgtgagcgcatacgctacttgcattacagcttaccaaccgaacaggcttatgtccactgggttcgtgccttcatccgtttccacggtgtgcgtcacccggcaaccttgggcagcagcgaagtcgaggcatttctgtcctggctggcgaacgagcgcaaggtttcggtctccacgcatcgtcaggcattggcggccttgctgttcttctacggcaaggtgctgtgcacggatctgccctggcagggcatcaacgaagaccagaacctgggcatcgccatcacccgccgtgcgctggaagccccgctgcgcgccatcgtggccaacgccggtgaagaaccgagcgtgatcgtggccaacgtcaaggccggcgaaggcagctacggctacaacgccgccaccggcgagttcggcgacatgatcgccatgggcatcctggacccgaccaaggtgacccgctcggccctgcagcacgccgcttccgtcgccggccttgcgatcacgaccgaagtggtcgtggccgaagtgccgaagaaggaagagccggccatgccgggtgctggcggtatgggcggtatgggcggcatgggcggcatggatttctga
etc...
Given the gene name (must be an exact match to the /gene=[Name]) will produce the names of the products of the x genes up and downstream of your query. Useful for identifying gene insertions or deletions, or finding transposable elements.
Searches all .gbk files in the program's directory
inputs: gene name i.e. pse1 depth: the number of genes or products to search for either direction of the gene
output: .csv file with searched gene at position 0, and all found genes/products at positions -depth to depth
-Set program in same directory with .gbk files to analyse
-Run program