I have a list of gene names which I know are present in a genbank file. I want to order these genes based on the order of their presence in the genbank. This should also account for whether they are on the positive or negative strand. So for example I have four genes; genes_1? are on the positive strand and genes_2? are negative
>nano Gene_names.txt gene_1A #assume this is the first gene for positive strand gene_1B gene_2A #assume this is first gene for negative strand gene_2B >nano Desired_out.txt gene_1A gene_2B gene_1B gene_2A
The genbank would be the standard flat file as linked below by terdon. The gene names are from a text list file and I have edited them now to reflect this.Im not exactly sure how to approach the strandness issue but I would imagine the complement would be helpful. I am unsure as to the strandness of the genes as is.
A working example of my work is to get the order of SpoI-V and other sporulation genes from C. difficile 630
e.g. sigE, sigG, spoIIE, sleC