how to filter a fasta file with seqs ID

Question

[chiara.conte91]

Hello everybody! I have to filter out some sequences from a fast file fasta is like

>0 RH1_6550
CAGCAGCCGCGGTAATACATAAACTCAAAGGAATTGACGGGCAGCAGCCGCGGTAATACGAAGGGGGCTAGCGTTGCTCGGAATTACTGGGCGTAAAGGGCGCGTAGGCGGACATTTAAGTCAGGGGTGAAATCCCAGAGCTCAACTCTGGAACTGCCTTTGATACTGGGTGTCTTGAGTGTGAGAGAGGTATGTGGAACTCCGAGTGTAGAGGTGAAATTCGTAGATATTCGGAAGAACACCAGTGGCGAAGGCGACATACTGGCTCATTACTGACGCTGAGGCGCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGATTGCTAGTTGTCGGGCTGCATGCAGTTCGGTGACGCAGCTAACGCATTAAGCAATCCGCCTGGGGAGTACGGTCGCAAGATTAAAACTCAAAGGAATTGACGG
>1 LH1_2535
CAGCAGCCGCGGTAATAGCAGCCGCGGTAATACGGAGGGTCCGAGCGTTAATCGGAATTACTGGGCGTAAAGCGTGCGCAGGCGGTTTGTTAAGCCAGATGTGAAATCCCCGGGCTCAACCTGGGAATTGCATTTGGAACTGGCGAACTAGAGTCTTGTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACAAAGACTGACGCTCATGCACGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGTCTACTCGGAGTTTGGTGTCTTGAACACTGGGCTCTCAAGCTAACGCATTAAGTAGACCGCCTGGGGAGTACGGCCGCAAGGTTAAAACTCAAAGGAATTGACG
>10 LPI1_10041
CAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTGTCCGGAATTACTGGGCGTAAAGCGTACGTAGGCGGATCAGAAAGTAGGGGGTGAAATCCCAGGGCTCAACCCTGGAACTGCCTCCTAAACTCCTGGTCTTGAGTTCGAGAGAGGTGAGTGGAATTCCAAGTGTAGAGGTGAAATTCGTAGATATTTGGAGGAACACCAGTGGCGAAGGCGGCTCACTGGCTCGATACTGACGCTGAGGTACGAAAGTGTGGGGAGCAAACAGGATTAGATACCCCGGTAGTCCACACCGTAAACGATGAATGCCAGTCGTCGGGCAGTATACTGTTCGGTGACACACCTAACGGATTAAGCATTCCGCCTGGGGAGTACGGTCGCAAGATTAAAACTCAAAGGAATTGACGG
>100 RH3_70592
CAGCAGCCGCGGTAATACGGGGGGTGCGAGCGTTATTCGGAATTACTGGGCGTAAAGAGCGCGTAGGCGGTCTCTTAAGTCAGGTGTGAAAGCCCGGGGCTCAACCCCGGAAGTGCACTTGAAACTAAGAGACTTGAGTATGGGAGAGGGAAGTGGAATTCCTGGTGTAGCGGTGAAATGCGTAGATATCAGGAGGAACATCAGTGGCGAAGGCGACTTCCTGGACCAATACTGACGCTGAGGCGCGAAGGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCAGTAAACGGTGAACACTAGGTGTAGCGGGTATTGACCCCTGCTGTGCCGCAGCAAACGCATTAAGTGTTCCGCCTGGGGAGTACGGCCGCAAGGTTAAAACTCAAAGGAATTGACGG
>1000 SHI1_76884
CAGCAGCCGCGGTAATACAGAGGTCCCGAGCGTTGTTCGGATTCACTGGGCGTAAAGGGAGCGTAGGCGGTCGGCAAAGTCTGATGTGAAATCTCCGGGCCCAACCCGGAAACTGCATCGGATACTGGTCGGCTAGAGGATTGGAGGGGGGACTGGAATTCTCGGTGTAGCAGTGAAATGCGTAGATATCGAGAGGAACACCAGTGGCGAAGGCGAGTCCCTGGACAATTCCTGACGCTGAGGCACGAAAGCTAGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCTAGCCGTAAATGGTGCACGCTTGCTGTGGGCGGAATCGACCCCGTCCGTGGCGTAGCTAACGCGTTAAGCGTGCCGCCTGGGGAGTACGACCGCAAGGTTGAAACTCAAAGGAATTGACGG

and I have a list of IDs to exclude (the number 0,10,100) or the entire identifier >0 RH1_6550.

I tried to use qiime1 filter_fasta.py -f inseqs.fasta -o list_filtered_seqs.fasta -s seqs_to_keep.txt but it returned empty fasta file.

Any clue of how to do it?

Thanks in advance!! Best, Chiara

Answer 1

[GenoMax]

faSomeRecords utility from Jim Kent is one of the best options. I linked linux version but macOS is also available. Add execute permissions after download chmod a+x faSomeRecords. You will want to use -exclude option with full fasta header.

faSomeRecords - Extract multiple fa records
usage:
   faSomeRecords in.fa listFile out.fa
options:
   -exclude - output sequences not in the list file.

[sunnykevin97]

Its not working. The out.fa generates empty file.