STAT5_GAS-project-

This code first fetch the fasta sequence(chromosome specific fasta file ) and the get the co_cordinates of genes from gff/gtf file (here I have made Zebra_output.txt from gff file, can see as example)and find a pattern with python RegEx. Finally, it generates the output file. A sample output file is also shown. Particularly, I made this code for my friend for his PhD. It fetches the match.group by this python RegEx TTC[TC][ATGCN][GA]GAA Examples of sequences
TTCAGGGAA
TTTTAGGAA
TTCGGGGAA
TTTTAGGAA
TTCTNGGAA
TTTTAAGAA
TTCTTGAAA
TTTTGGGAA
TTCTCGAAA
TTTTNGAAA
TTCTAGGAA
TTTTTGAAA
TTCTGGAAA
TTTTCGAAA
TTCTNGAAA
TTTTGGGAA ... and few more
Requires three arguments a fasta file, a gene info file (bed file), chromosome number _____________________________________________ $ python3 chromosome.fa zebra_output.txt 7