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5.2 years ago
savscosta
•
0
Hello. I want to get from the fasta file only those sequences matching the name of gene from a name.txt file
Ex. Input.fasta
>lcl|CP001829.1_gene_1 [gene=dnaA] [locus_tag=CpC231_0001] [location=1..1812] [gbkey=Gene]
TTGTCGGAGGCTCCATCGACATGGAACGAGCGGTGGCAAGAAGTTACTAATGAGCTGCTGTCACAGTCTC
>lcl|CP001829.1_gene_2 [locus_tag=CpC231_0001a] [location=complement(1821..1967)] [gbkey=Gene]
GTGTCGAGTATCACTGAATTACAAGTTTGTAATTACACAGCGTGTATAACTCTGTGGACTACTTTTAAAA
>lcl|CP001829.1_gene_3 [gene=dnaN] [locus_tag=CpC231_0002] [location=2396..3583] [gbkey=Gene]
CCACGTGAATCTTGAACCGGCCACGTGAATCTTGAACCGGCCACGTGAATCTTGAACCGG
>lcl|CP001829.1_gene_4 [gene=recF] [locus_tag=CpC231_0003] [location=3650..4864] [gbkey=Gene]
GTGTACATTCGCGAGCTATCGCTCCGAGATTTTCGTTCGTGGGCAGACTGCCACGTGAATCTTGAACCGG
>lcl|CP001829.1_gene_5 [locus_tag=CpC231_0004] [location=4854..5426] [gbkey=Gene]
ATGAGCAATAAACCTGCTGATGCTGGATCAGAAGATCCCGTAGCAGAGGCATTTGCTGCTATTCGTGCGG
AAGCCCAGCGGCGCACAGGGCGCATCCCCGATCTCTCCGTCCAAGCTCCGCGTTCTGGTTTAAAGCTTAA
>lcl|CP001829.1_gene_6 [gene=gyrB] [locus_tag=CpC231_0005] [location=5566..7611] [gbkey=Gene]
GTGGCAACCGCTGAACATGAATATGGCGCCTCATCCATTACGATCCTTGAGGGTCTAGAGGCTGTACGTA
name.txt
recF
gyrB
output:
>lcl|CP001829.1_gene_6 [gene=gyrB] [locus_tag=CpC231_0005] [location=5566..7611] [gbkey=Gene]
GTGGCAACCGCTGAACATGAATATGGCGCCTCATCCATTACGATCCTTGAGGGTCTAGAGGCTGTACGTA
>lcl|CP001829.1_gene_4 [gene=recF] [locus_tag=CpC231_0003] [location=3650..4864] [gbkey=Gene]
GTGTACATTCGCGAGCTATCGCTCCGAGATTTTCGTTCGTGGGCAGACTGCCACGTGAATCTTGAACCGG
thanks for your help!