upDownStreamSeqsFromGbk

Set requirements

pip install -r requirements.txt

upDownStreamSeqsFromgbk.py

Input files:

Genbank file to search the gene positions and extended sequences.

gbk_filename = "/home/agustin/Tatroviride_IMI206040_0.gb" # <-Please change->

Fasta of query sequences to take de gene id or txt with gene ids in the first colum (columns separated by \t). The first line of the txt(header of file) is avoid. Include file name and "fasta" or "txt" file type:

input_file_name_type=["/home/agustin/IDcluster10.txt","txt"] # <-Please change->

Output file:

The output is a fasta file format with the original sequences and the extended upstream and downstream sequences. Set the name of the output file:

fna_filename = "UpDownStream.fna" # <-Please change->

How much to extend.

Select how much base pairs extend to upstream or downastream side from the original genes start and end:

upstream=1500 # <-Please change->
downstream=0  # <-Please change->

Run.

python3 upDownStreamSeqsFromgbk.py

Extract extended fasta

bash expand_fasta.sh < UpDownStream.fna

Extract original fasta

bash original_fasta.sh < UpDownStream.fna

Extract extended region from upstream

awk '{if (/^>/) print $0; else print(substr($1,1,1500)) }' extended.fasta

Extract extended region from downstream

awk '{if (/^>/) print $0; else print(substr($1, length($1)-1500, length($1))) }' extended.fasta

Run the GUI output parser

bash parserApp.sh

AgustinPardo/upDownStreamSeqsFromGbk

upDownStreamSeqsFromGbk

Set requirements