Hi there, I got a fasta file which looks like below, and I also have a list of genes (DDB0234326, DDB0182333, etc). Could someone give me some suggestions on how to extract the sequences according to the gene list?
Thanks a lot for your help in advance!
>DDB0190058|JC1V2_0_00886|1|-1|2161867|2162448
ATCTAAAAAAAAAAAATATCAAAAATTTAAGAGTTTTAATAAATTATATGGATAATCATTATTATTATATTTTTTTTTTT
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTGATTTATATGTGGTATTTAATATTTAAAAAATATTTTGTTTGTTTTTATTT
GTTTTTTGTTATTTTTTTATCCTTTTATCTTTTTATTTTTGTTTTTTTTTTTAGTTCTAATTTTATCTTTTTTCTTTCTT
TTGTTATTTTTTATAAAAAAAAAAAATAAAAATAAAAATAAAAAAAAAATAAAAATAAAAAAAAAATAAAAATAAAAATA
AAAATTTGAAAAAAAAAATAAAAATTATTTCAAATTTGCTATTATTTCAAATATTCCACGAAATCATGAAATAATCAAAA
ATATCTCAAGTGATTTTTTTTTTTTTGTTTTGCTGAAAAAAAAAAATTATTTTTACTTTTTTTTTTTTATTTTCATTTTT
CTTTTTTTAAAATAATAATAGTAGTAAAAGAAATAAAAATAAAAAAATAAAAAAAAAAATAACCATAAACAAATAATAAT
AATAATAAAAAAATTTATTTCC
>DDB0190067|JC1V2_0_00895|1|-1|2192202|2192651
ACTGGTTATAAAAAAAAAAAAAAAAAAAAACAGAATGATTACATTCATTTTTTTTTTTTTATATCATTTTGTGTATTTTG
ATTACTCTATATTTATGTTATTTTATTCAATAAAAAAAAATTCCATTATTTTTTTTAGAAATTTAAGTTATTATTTTTTT
TTTTTTTTTTTGTATTTTCATTGGTTGGTTGGTTGTTTTATTAATTTTTAAAATGAGATTTTAACTGAAAAAAAAAAAAA
AAAATATCTTTTCTTCGATTTGCATTATAATTTAATTTTTTTTTTTTTTTTTTTTTATTTTTTTTAAATTTTTCTTGATT
TTGGGAGAGATTTATGATTAAATTTAATTTTTAATTTTTTTTTTTTTTTTTTGATGATAATTAAATTTTTTTTTACAATT
TATAAAAAAAAAAAAAAACTATTTATTTATTATAAAAAAAAAATAAAAAA
>DDB0190069|JC1V2_0_00897|1|1|2193205|2194305
TTTTTTTTTTTTAATGAATGAAATTTTTTTTTTTTATGATTTAAATAAAAATTTAATTTTACTATAATCAAAATAAAAAT
AAATAAAAAAAACTAAATAAAATAAATTTAAAATAGATCACCCAATACTTTAGTGAATATTTTTTTTTTTTTTTTTTTTT
TTAAAAAATAATTTGTTTTATTTTAATTTAATTTTTTTGTTTTGTTAATTTTATCACAAATAAATGTACAACAAAATAAC
ACCACTTTTTTCTGTGCACACCTTACCAAATTAAATGAAAATTACAAAAAGGGAAGAAAATAACAGTTTGTTAAAAAAAA
ATATATATATTTTAAAATTTAATTATTATTTTTTTTTTCCTTTTTGTTCCATTTTAATATTATTTTTTATATCCAATTCA
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bright602 •
2 answers
There are many ways do get sequences from a FASTA file. Some (like the Kent utility) are more efficient than others (reading all sequences into memory and writing them back out). I made a Python library that's designed to be efficient (creates and operates on the same index .fai files that samtools faidx uses), has a Python API similar to a dict object, and has a command-line utility (faidx) that covers most of the common FASTA operations.
When I die I will stop telling people they should use it.
$ pip install pyfaidx
$ dos2unix gene_list.txt
$ faidx -d '|' genes.fasta $(tr '\n' ' ' < gene_list.txt) > selected_genes.fasta
This splits the headers in your FASTA file on the "pipe" (-d '|') character so that your gene list doesn't have to be an exact match, and converts your gene list to arguments to pass into faidx. You could also do this in a bash loop:
$ while read gene; do
faidx -d '|' genes.fasta $gene >> selected_genes.fasta;
done < gene_list.txt
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Hands down the fastest method to extracts records from a file using a list of ID''s: C: Retrieve a subset of FASTA from large multi-FASTA file
Thread linked here has multiple other options.
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