class Bio::FastaFormat

Treats a FASTA formatted entry, such as:

>id and/or some comments                    <== definition line
ATGCATGCATGCATGCATGCATGCATGCATGCATGC        <== sequence lines
ATGCATGCATGCATGCATGCATGCATGCATGCATGC
ATGCATGCATGC

The precedent ‘>’ can be omitted and the trailing ‘>’ will be removed automatically.

Examples ↑

fasta_string = <<END_OF_STRING
>gi|398365175|ref|NP_009718.3| Cdc28p [Saccharomyces cerevisiae S288c]
MSGELANYKRLEKVGEGTYGVVYKALDLRPGQGQRVVALKKIRLESEDEGVPSTAIREISLLKELKDDNI
VRLYDIVHSDAHKLYLVFEFLDLDLKRYMEGIPKDQPLGADIVKKFMMQLCKGIAYCHSHRILHRDLKPQ
NLLINKDGNLKLGDFGLARAFGVPLRAYTHEIVTLWYRAPEVLLGGKQYSTGVDTWSIGCIFAEMCNRKP
IFSGDSEIDQIFKIFRVLGTPNEAIWPDIVYLPDFKPSFPQWRRKDLSQVVPSLDPRGIDLLDKLLAYDP
INRISARRAAIHPYFQES
END_OF_STRING

f = Bio::FastaFormat.new(fasta_string)

f.entry #=> ">gi|398365175|ref|NP_009718.3| Cdc28p [Saccharomyces cerevisiae S288c]\n"+
# MSGELANYKRLEKVGEGTYGVVYKALDLRPGQGQRVVALKKIRLESEDEGVPSTAIREISLLKELKDDNI\n"+
# VRLYDIVHSDAHKLYLVFEFLDLDLKRYMEGIPKDQPLGADIVKKFMMQLCKGIAYCHSHRILHRDLKPQ\n"+
# NLLINKDGNLKLGDFGLARAFGVPLRAYTHEIVTLWYRAPEVLLGGKQYSTGVDTWSIGCIFAEMCNRKP\n"+
# IFSGDSEIDQIFKIFRVLGTPNEAIWPDIVYLPDFKPSFPQWRRKDLSQVVPSLDPRGIDLLDKLLAYDP\n"+
# INRISARRAAIHPYFQES"

Methods related to the name of the sequence ↑

A larger range of methods for dealing with Fasta definition lines can be found in FastaDefline, accessed through the FastaFormat#identifiers method.

f.entry_id #=> "gi|398365175"
f.first_name #=> "gi|398365175|ref|NP_009718.3|"
f.definition #=> "gi|398365175|ref|NP_009718.3| Cdc28p [Saccharomyces cerevisiae S288c]"
f.identifiers #=> Bio::FastaDefline instance
f.accession #=> "NP_009718"
f.accessions #=> ["NP_009718"]
f.acc_version #=> "NP_009718.3"
f.comment #=> nil

Methods related to the actual sequence ↑

f.seq #=> "MSGELANYKRLEKVGEGTYGVVYKALDLRPGQGQRVVALKKIRLESEDEGVPSTAIREISLLKELKDDNIVRLYDIVHSDAHKLYLVFEFLDLDLKRYMEGIPKDQPLGADIVKKFMMQLCKGIAYCHSHRILHRDLKPQNLLINKDGNLKLGDFGLARAFGVPLRAYTHEIVTLWYRAPEVLLGGKQYSTGVDTWSIGCIFAEMCNRKPIFSGDSEIDQIFKIFRVLGTPNEAIWPDIVYLPDFKPSFPQWRRKDLSQVVPSLDPRGIDLLDKLLAYDPINRISARRAAIHPYFQES"
f.data #=> "\nMSGELANYKRLEKVGEGTYGVVYKALDLRPGQGQRVVALKKIRLESEDEGVPSTAIREISLLKELKDDNI\nVRLYDIVHSDAHKLYLVFEFLDLDLKRYMEGIPKDQPLGADIVKKFMMQLCKGIAYCHSHRILHRDLKPQ\nNLLINKDGNLKLGDFGLARAFGVPLRAYTHEIVTLWYRAPEVLLGGKQYSTGVDTWSIGCIFAEMCNRKP\nIFSGDSEIDQIFKIFRVLGTPNEAIWPDIVYLPDFKPSFPQWRRKDLSQVVPSLDPRGIDLLDKLLAYDP\nINRISARRAAIHPYFQES\n"
f.length #=> 298
f.aaseq #=> "MSGELANYKRLEKVGEGTYGVVYKALDLRPGQGQRVVALKKIRLESEDEGVPSTAIREISLLKELKDDNIVRLYDIVHSDAHKLYLVFEFLDLDLKRYMEGIPKDQPLGADIVKKFMMQLCKGIAYCHSHRILHRDLKPQNLLINKDGNLKLGDFGLARAFGVPLRAYTHEIVTLWYRAPEVLLGGKQYSTGVDTWSIGCIFAEMCNRKPIFSGDSEIDQIFKIFRVLGTPNEAIWPDIVYLPDFKPSFPQWRRKDLSQVVPSLDPRGIDLLDKLLAYDPINRISARRAAIHPYFQES"
f.aaseq.composition #=> {"M"=>5, "S"=>15, "G"=>21, "E"=>16, "L"=>36, "A"=>17, "N"=>8, "Y"=>13, "K"=>22, "R"=>20, "V"=>18, "T"=>7, "D"=>23, "P"=>17, "Q"=>10, "I"=>23, "H"=>7, "F"=>12, "C"=>4, "W"=>4}
f.aalen #=> 298

A less structured fasta entry ↑

f.entry #=> ">abc 123 456\nASDF"

f.entry_id #=> "abc"
f.first_name #=> "abc"
f.definition #=> "abc 123 456"
f.comment #=> nil
f.accession #=> nil
f.accessions #=> []
f.acc_version #=> nil

f.seq #=> "ASDF"
f.data #=> "\nASDF\n"
f.length #=> 4
f.aaseq #=> "ASDF"
f.aaseq.composition #=> {"A"=>1, "S"=>1, "D"=>1, "F"=>1}
f.aalen #=> 4

References ↑