Please can anyone help with this.
I am trying to make a fasta file, created in a Linux NGS pipeline more windows friendly.
I have a fasta file with several sequences in it generated by an NGS pipeline.
I'd really like to reformat the file doing several things, I currently do this manually with a text editor and want to speed things up. Im pretty new to Linux and scripts but guess this could be done much more efficiently. my fasta files looks a bit like this for each gene.
>gene-name-iter4\n somesequence\n somesequnece\n somesequence\n >gene2name-iter4\n somesequence\n somesequence\n
At the moment I remove all \n style line breaks then replace all > with \r\n> to put in windows style carriage returns replace all iter4 with iter4\r\n delete the one carriage return that is now before my first sequence, and add a carriage return to the end of the very last line.
Please can someone show me how to make this easier in Linux, I have access to centos virtual machine, but then move the output consensus fasta file from whole genome sequencing to windows computers.
Thank you James