Finding sequence from FASTA file, help?

Question

[Athena]

I have a list of sequence ID as sequenceID.fasta

TRINITY_DN0_c0_g1_i1.p1
TRINITY_DN0_c0_g2_i3.p1
TRINITY_DN10002_c0_g1_i1.p1
TRINITY_DN10002_c0_g1_i2.p1
TRINITY_DN10002_c1_g1_i1.p1
TRINITY_DN10006_c0_g1_i1.p1
TRINITY_DN10006_c0_g1_i4.p1
TRINITY_DN10007_c0_g1_i2.p1
TRINITY_DN1000_c0_g1_i15.p1
TRINITY_DN1000_c0_g1_i31.p1
TRINITY_DN1000_c0_g1_i40.p2
TRINITY_DN1000_c0_g2_i1.p1
TRINITY_DN10012_c2_g1_i1.p1
TRINITY_DN10014_c0_g2_i1.p1
TRINITY_DN10014_c2_g1_i1.p1
TRINITY_DN10014_c2_g2_i1.p1

And I have a trinity_out.Trinity.fasta file which has nucleotide sequence

>TRINITY_DN36054_c0_g1_i1 len=279 path=[0:0-278]
CAGTCAATAATTTTGACGTACTTTTCAAAACATTTCTTGCTGTTTCTTCAAAACTCTTAT
CTAATTTTTTGTTTTTCAGAAGGTTAAAAGTATATTGAAAAGTTTCTCGATTTTCAGTGG
TTAGTCTAGGATTGCTATTATTTTCAATTTGGTGTTTGCATTCTTCAAACATTACCATCA
GATCATATCGTGTTATTTCATACTGCATTTCTTTGATTTCCTGCTTTGACAAAGTTGTTA
TCGATTTTTTCATCCTGTTTCTTAATTTTGTCAAACCAT
>TRINITY_DN36094_c0_g1_i1 len=250 path=[0:0-249]
AGGAAAGTACTTAGTGAGTACATACCTGACAGTGATCACGGTTTTACGAAAAGATACATT
GAAAGAAGAATACTTCAACCTCCATTAAAACGATACACGTATTGCTTGCTCACTTCCATG
TCTTATGGCGCTTCAGACTGCTATGATCCAAATTTTTGCGGTCCCATCTTTGGTAAACGA
AATTGTTACAAGCGGTCCAAATTTACAGATAATCATTTCCCAGATATAAATCTCGGCGGG
AAACTTCATC
>TRINITY_DN36018_c0_g1_i2 len=1265 path=[0:0-408 1:409-443 2:444-1264]
AAAAGCTCCAATTGTTTGGTGGACTCCCGCTGGCTAGTCAGGATAACAGATTACGGTCTG
CCAAGTTTTAGTAGCGGCCAGTTTTTTGACGAATCAGAACAAGATGCATATAGACGTAAA
CTTTGGACCGCCCCAGAATTATTGAGGGAGAACATACCCCCTAAGAACGGTTCCCAAAAG
GGTGACGTATACAGTTTCGCCATAGTGGCGTACGAGATTATAACAAGGTCTGAACCATTT
CCCTTTGATTTAATGACTGCCAGAGACGCGGTAAATAGGGTAAGAAACGGTGAAAGCATC
CCGTTCAGACCATGCCTACCCGAGACAACGGATGTTGGCAAAGCTGTCCTTGACCTCTTG
CGAGCTTGTTGGCATGAGGTTCCAGAACACAGACCCAACTTCAACCAGGTTCGAACTGTT
[....]

I wanted to extract the corresponding nucleotides from the ID list from the trinity fasta file. I have tried

grep -Fwf sequence_id.fasta -A1 trinity_out.Trinity.fasta > NRCDS_nuc.fasta

but when I run more to see if I got the correct output, it came out empty. Not sure where I got it wrong.

I could do samtools faidx trinity_out.Trinity.fasta and manually put all the id's from the list but that seems taxing so I'm looking for a way to automate this process.

Any help would be appreciated. Thank you!

Answer 1

[GenoMax]

Use the solutions in --> Excluding sequences from fasta based on a id list - faSomeRecords not working

Do the opposite of what is being discussed in that thread since you want to keep records based on your ID.

faSomeRecords - Extract multiple fa records
usage:
   faSomeRecords in.fa listFile out.fa