How can I extract sequences from FASTA file using OTUs ID?
I have one FASTA file with sequences and headers, and one OTUs table. What I want to do is replace the current headers in the FASTA file with just the OTU IDs from the .txt file. The files look like something like this:
FASTA file:
>9d4544fa-322a-4fac-bcf5-f8ca410c7e8a runid=b48dcb2029ef589b8cdb55fe529d93b3baadbc7c sampleid=28012021COVID3 read=57150 ch=310 start_time=2021-01-28T18:23:35Z
TCAGTTACGTATTGCTGGTGCTGAAGAAAGTTGTCGGTGTCTTTGTGTTAACCTTTCTGTTGGTGCTGATATTGCAGTCGCCCCCACCTCCTTGGATCCGCCAGGTTAAACACCCAAGCAGACGCCGAAGATAGAGCGACAGGCAAGTAGGTTAACACAAAGACACCGACAACTTTTCTTCCAGCACCAGCAGCCCGTAACT
>a8d321b9-97f1-42aa-a17a-fa1c4609e60e runid=b48dcb2029ef589b8cdb55fe529d93b3baadbc7c sampleid=28012021COVID3 read=46034 ch=83 start_time=2021-01-28T18:24:16Z
CGTTCGGTGCGTATTGCTGGTGCTGAAGAAAGTTGTCCGGTGTCTTTGTGTTAACCTTTCTGTTGGTGCTGATATTGCGGCGTCTGGCAGGTGTTAACCTGGCCTCGAGAGAGTTTGATCCTGGCTGGGATGAACGCTGACGTGCCTAATACATGCAAGTAG
>6d97cca8-6795-4c59-b4d1-05880735b957 runid=b48dcb2029ef589b8cdb55fe529d93b3baadbc7c sampleid=28012021COVID3 read=46363 ch=227 start_time=2021-01-28T18:24:08Z
GTTCAGTGCATATTGCTGTGGTGCTGCGAAAGTTTGTGGTGTCTTTGTGTTAACGCTTTCTGTTGGTGCTGATATTGCGGCGGCGTCTGCGCGGTGTTTAACCTGGCGGATCAAGGAGGTGTTCAGCCGCACCTTCCGTTTTGACTACGCCATTACGACTGCCCAATCTGTTTTACCCTAGGCCCGATCCTTGCGGTCACGGACTTCAGGCACCCCCGGCTTTCATGGCTTGACAGGCGGTGTGTACAAGGCCCGGGAACATTCACCCGCGCCATGGCTGATGCGCGATTACTAGCGAATCCCAGCTTCACGGGTCGGGTTGCA
>772e0bef-fad4-4767-b0e6-d88e6f16b2ed runid=b48dcb2029ef589b8cdb55fe529d93b3baadbc7c sampleid=28012021COVID3 read=49763 ch=349 start_time=2021-01-28T18:24:10Z
CGTTCAGTTACGTATTGCTGGTGCTGAAGAAAGTTGTCGGTGTCTTTAGGTTAACCTTTCTGTTGGTGCTGATATTGCGGCGTCTGCTTGGGTGTTTAACCTGGCCTCGAGAAGTTTGATCCTGGCTCAGGATGAACGCTAGCTTCTGAGCTTAACATGCAGAGTCCAGGGCAGCATGGAAGAAACTGCTTCTTCTGATGGCGACAACGCACGGGTGCATGCGCGTATCAAACCTGCCTCATA
>2b673c48-69c9-48a4-995b-4ad630e23502 runid=b48dcb2029ef589b8cdb55fe529d93b3baadbc7c sampleid=28012021COVID3 read=71966 ch=124 start_time=2021-01-28T18:24:11Z
OTUs table:
OTU ID IA1 IA2 IA3 IA4 IA5 IS6
otu500 7 10 3 0 5 0
otu502 7 8 4 0 11 1
otu504 4 5 6 2 4 2
otu505 4 4 6 2 8 3
and my desired output is that the .fasta file would look like this:
>otu500
tggggaatcttagacaatgggcgcaagcctgatctagccatgccg
>otu502
tgaggaatattggtcaatggaggcaactctgaaccagccatgccttggtcaatggaggc
>otu504
gcgaacaggattagataccctggtagtccacgccgtaaacttggtcaatggaggc
>otu505
ttggtcaatggaggcttggtcaatggaggctaccctggttaccctggt
>otu506
• 1,086 views
•
link
written
by
twinklemishra0892 •
1 answer
You can use one of the solutions here if you need to extract fasta sequence of specific ID's from a large file :
Extract fasta sequences based on ids file
Log in to answer this question.
More posts like this
