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in reply to Re^3: Size of sequences in fastafile
in thread Size of sequences in fastafile

This is my data:
>NM_030643.4 Homo sapiens apolipoprotein L4 (APOL4) GAGGTGCTGGGGAGCAGCGTGTTTGCTGTGCTTGATTGTGAGCTGCTGGGAAGTTGTGACTTTCATTTTA CCTTTCGAATTCCTGGGTATATCTTGGGGGCTGGAGGACGTGTCTGGTTATTATATAGGTGCACAGCTGG AGGTGAGATCCACACAGCTCAGACCAGCTGGATCTTGCTCAGTCTCTGTCAGAGGAAGATCCCTTGGAGG AGGCCCCGCAGCGACATGGAGGGAGCTGCTTTGCTGAAAATCTTTGTCGTCTGCATCTGGAACCAAAATC >NM_001198855.1 Homo sapiens cytochrome P450 family 2 subfamily C memb +er 8 (CYP2C8) ACATGTCAAAGAGACACACACTAAATTAGCAGGGAGTGTTATAAAAACTTTGGAGTGCAAGCTCACAGCT GTCTTAATAAGAAGAGAAGGCTTCAATGGAACCTTTTGTGGTCCTGGTGCTGTGTCTCTCTTTTATGCTT CTCTTTTCACTCTGGAGACAGAGCTGTAGGAGAAGGAAGCTCCCTCCTGGCCCCACTCCTCTTCCTATTA >NR_029834.1 Homo sapiens microRNA 200a (MIR200A), microRNA CCGGGCCCCTGTGAGCATCTTACCGGACAGTGCTGGATTTCCCAGCTTGACTCTAACACTGTCTGGTAAC GATGTTCAAAGGTGACCCGC >AC067940.1 Homo sapiens clone RP11-818E9, LOW-PASS SEQUENCE SAMPLING AAATACAACTTTAAATCAAAACGGTAAAAATTCCACTCTTTCATACTAACTTCAAAAGTATTTGCTTTAA AAAAAAAGNNNNNNNNNNAAACTGAATTTCTATTAAGCATCTATTTATAGAAGAGAGTAAACACCCCGTG AATAAAAGACAGAGAATTGTAGCAGCCCGAAGTCCCTTTTCTCTCCTCCCAAGCATTTGGCTCTGGTCCA AATTCACATATCCTGCTCCGTAAAACAAAGTGCCTTGGTTAACCTAACGTTATTCCTTGAACAGTAGTTT AGTGATCAACTAGTTTTTGTTGTTGTTGTTGTTTGAGACAGAGTCTCACTCTGTCGCCCAGGCTGGAGTG CAGTGGCGAGATCTCAGCTCACTGCAACCTCTGCTGCCCAGGTTCAAGGGATTCTCCTGCCTCAGCCTCC CAAGTAGCTGGTATTACAGGCACCTGCCACCGCGCCTGGCTAATTTTTTTTTTTTTTTTTTTTTGTATTT
The question is, how can I find out the sequence length of each sequence and extract those of a specific length? I have tried both to put the data in an array, which puts each line in one element, and also to put it in a scalar and tried to use the > to separate each seq, but I am stuck.

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Re^5: Size of sequences in fastafile
by zubenel0 (Sexton) on Mar 01, 2020 at 12:39 UTC
    This code should work but you will need to install BioPerl module Bio::SeqIO.
    use Bio::SeqIO; # Setting minimum length to 250 my $min_len = 250; # Reading the input fasta file my $seqio_in = Bio::SeqIO->new(-file => "Genes.fasta", -format => "fasta" ); # Creating the output fasta file my $seqio_out = Bio::SeqIO->new(-file => ">Genes_filt_250.fasta", -format => "fasta" ); # Saving sequences to the output if length > min_len while ( my $seq = $seqio_in->next_seq ) { if ( $seq->length > $min_len ) { $seqio_out->write_seq($seq); } }
    The sequences with length higher than 250 should be saved in file "Genes_filt_250.fasta":
    >NM_030643.4 Homo sapiens apolipoprotein L4 (APOL4) GAGGTGCTGGGGAGCAGCGTGTTTGCTGTGCTTGATTGTGAGCTGCTGGGAAGTTGTGAC TTTCATTTTACCTTTCGAATTCCTGGGTATATCTTGGGGGCTGGAGGACGTGTCTGGTTA TTATATAGGTGCACAGCTGGAGGTGAGATCCACACAGCTCAGACCAGCTGGATCTTGCTC AGTCTCTGTCAGAGGAAGATCCCTTGGAGGAGGCCCCGCAGCGACATGGAGGGAGCTGCT TTGCTGAAAATCTTTGTCGTCTGCATCTGGAACCAAAATC >AC067940.1 Homo sapiens clone RP11-818E9, LOW-PASS SEQUENCE SAMPLING AAATACAACTTTAAATCAAAACGGTAAAAATTCCACTCTTTCATACTAACTTCAAAAGTA TTTGCTTTAAAAAAAAAGNNNNNNNNNNAAACTGAATTTCTATTAAGCATCTATTTATAG AAGAGAGTAAACACCCCGTGAATAAAAGACAGAGAATTGTAGCAGCCCGAAGTCCCTTTT CTCTCCTCCCAAGCATTTGGCTCTGGTCCAAATTCACATATCCTGCTCCGTAAAACAAAG TGCCTTGGTTAACCTAACGTTATTCCTTGAACAGTAGTTTAGTGATCAACTAGTTTTTGT TGTTGTTGTTGTTTGAGACAGAGTCTCACTCTGTCGCCCAGGCTGGAGTGCAGTGGCGAG ATCTCAGCTCACTGCAACCTCTGCTGCCCAGGTTCAAGGGATTCTCCTGCCTCAGCCTCC CAAGTAGCTGGTATTACAGGCACCTGCCACCGCGCCTGGCTAATTTTTTTTTTTTTTTTT TTTTGTATTT