[Tutor] FASTA FILE SUB-SEQUENCE EXTRACTION
syed zaidi
syedzaidi85 at hotmail.co.uk
Tue Mar 8 02:33:23 EST 2016
Hello all,
I am stuck in a problem, I hope someone can help me out. I have a FASTA file with multiple sequences and another file with the gene coordinates. SAMPLEFASTA FILE:
>EBM_revised_C2034_1 length=611GCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGGAGGAAGGGAGTAAAGTTAATACCTTTGCTCATTGACGTTACCCGCAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATCTGATACTGGCAAGCTTGAGTCTCGTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACGAAGACTGACGCTCAGGTGCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGTCGACTTGGAGGTTGTGCCCTTGAGGCGTGGCTTCCGGAGCTAACGCGTTAAGTCGACCGCCTGGGGAGTACGGCCGCAAGGTTAAAACTCAAATGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATT>EBM_revised_C2104_1 length=923TCCGAGGGCGGTGGGATGTTGGTGCTGCAGCGGCTTTCGGATGCGCGGCGGTTGGGTCATCCGGTGTTGGCGGTGGTGGTCGGGTCGGCGGTTAATCAGGATGGGGCGTCGAATGGGTTGACCGCGCCTAATGGTCCTTCGCAGCAGCGGGTGGTGCGGGCGGCGTTGGCCAATGCCGGGTTGAGCGCGGCCGAGGTGGATGTGGTGGAGGGGCATGGGACCGGGACCACGTTGGGGGATCCGATTGAGGCTCAGGCGTTGTTGGCCACTTATGGGCAAGATCGGGGGGAGCCGGGAGAACCTTTGTGGTTGGGGTCGGTGAAGTCGAATATGGGTCATACGCAGGCCGCGGCGGGGGTGGCCGGGGTGATCAAGATGGTGTTGGCGATGCGCCATGAGCTGTTGCCGGCGACGTTGCACGTGGATGTGCCTAGCCCGCATGTGGATTGGTCGGCGGGGGCGGTGGAGTTGTTGACCGCGCCGCGGGTGTGGCCTGCTGGTGCTCGGACGCGTCGTGCGGGGGTGTCGTCGTTTGGGATTAGTGGCACTAATGCGCATGTGATTATCGAGGCGGTGCCGGTGGTGCCGCGGCGGGAGGCTGGTTGGGCGGGGCCGGTGGTGCCGTGGGTGGTGTCGGCGAAGTCGGAGTCGGCGTTGCGGGGGCAGGCGGCTCGGTTGGCCGCGTACGTGCGTGGCGATGATGGCCTCGATGTTGCCGATGTGGGGTGGTCGTTGGCGGGTCGTTCGGTTTTTGAGCATCGGGCGGTGGTGGTTGGCGGGGACCGTGATCGGTTGTTGGCCGGGCTCGATGAGCTGGCGGGTGACCAGTTGGGCGGCTCGGTTGTTCGGGGCACGGCGACTGCGGCGGGTAAGACGGTGTTCGTCTTCCCCGGCCAAGGCTCCCAATGGCTGGGCATGGGAAT
GENE COORD FILEScaf_name Gene_name DS_St DS_EnEBM_revised_C2034_1 gene1_1 33 99EBM_revised_C2034_1 gene1_1 55 100EBM_revised_C2034_1 gene1_1 111 150EBM_revised_C2104_1 gene1_1 44 70
I want to perform the following steps:compare the scaf_name with the header of fasta sequenceif header matches then process the sequence and extract the sequence by the provided start and end positions.
I would appreciate if someone can help
Thanks
Best Regards
Ali
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