Bio::Seq::IO probleme d'accession a as_feat.

**loula427** · 08/12/2013, 04h44

Voila mon soucis est le suivant j'ai un fichier *gbf du type:

Code :

Sélectionner tout - Visualiser dans une fenêtre à part

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LOCUS       C_0                     5477 bp    DNA     circular     07-DEC-2013
DEFINITION  Genus species.
ACCESSION   
VERSION
KEYWORDS    .
SOURCE      Genus species
  ORGANISM  Genus species
            Unclassified.
REFERENCE   1  (bases 1 to 5477)
  AUTHORS   Last,F.
  TITLE     Direct Submission
  JOURNAL   Submitted (07-DEC-2013) Division, Affilation, Street, City,
            Province X9X 8Y8, Country
COMMENT     Complete genome.
FEATURES             Location/Qualifiers
     source          1..5477
                     /organism="Genus species"
                     /mol_type="genomic DNA"
                     /note="type: genomic"
     gene            728..1099
                     /gene="atp6"
     CDS             728..1099
                     /gene="atp6"
                     /EC_number="3.6.3.14"
                     /codon_start=1
                     /product="ATP synthase F0 subunit a"
                     /translation="MGSLTIGFINYGINFFSMFMPSGAPLALAPFLILIELLSYVARG
                     ISLGVRLAANITSGHILLTIIATFIFKMLNIGGIFIPLAFLTFALLFVLTILEMAIGA
                     IQAYVLGLLVTIYLNDSVHLH"
     gene            complement(1717..2238)
                     /gene="orf173"
     CDS             complement(1717..2238)
                     /gene="orf173"
                     /codon_start=1
                     /product="hypothetical protein"
                     /translation="MLGEMWGISYIPISYIPILYIPISYIPISYIPLSYIPDAHQPTF
                     LLTLRIFDPQCWIKDPKSGGFRIFQYRIFLFRIFHYCIFHFCIFQYRIFQLSIFQFST
                     FLYRIFQYRIFLYRIFQYRIYQYSIFQYRIYQYSIFQYRKYQYSIYQYSIFQYSKFQY
                     SIFQYRKFQIPHI"
....

Je souhaiterais convertir celui ci en format fasta ma premiere idee est d'utiliser Bio::SeqIO mon code est le suivant :

Code :

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$gbf = "${a}.gbf";
	my $seq_in = Bio::SeqIO->new(
                              -file   => "$gbf",
	                          -format => "GenBank",
                              );
 
	my $sqn2faaOut   = "$TMPDIR/sqn2faaOut";
	my $seq_out = Bio::SeqIO->new(
	                           -file   => ">$sqn2faaOut",
                               -format => "fasta",
                               );
 
	# write each entry in the input file to the output file
	while (my $inseq = $seq_in->next_seq) {
		print "$inseq\n";
	    $seq_out->write_seq($inseq);
	}

quand j'imprime $inseq j'obtiens:

Code :

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0  Bio::Seq::RichSeq=HASH(0xb5c0480)
   '_annotation' => Bio::Annotation::Collection=HASH(0xb5b3120)
      '_annotation' => HASH(0xb483c30)
         'comment' => ARRAY(0xb59ef30)
            0  Bio::Annotation::Comment=HASH(0xb59ef6c)
               '_root_verbose' => 0
               'text' => 'Complete genome.'
         'keyword' => ARRAY(0xb5c03b8)
            0  Bio::Annotation::SimpleValue=HASH(0xb5c04a8)
               '_root_verbose' => 0
               'tagname' => 'keyword'
               'value' => ''
         'reference' => ARRAY(0xb59ec10)
            0  Bio::Annotation::Reference=HASH(0xb59edb4)
               'authors' => 'Last,F.'
               'end' => 5477
               'location' => 'Submitted (07-DEC-2013) Division, Affilation, Street, City, Province X9X 8Y8, Country'
               'start' => 1
               'title' => 'Direct Submission'
      '_typemap' => Bio::Annotation::TypeManager=HASH(0xb59e7c4)
         '_type' => HASH(0xb5b310c)
            'comment' => 'Bio::Annotation::Comment'
            'dblink' => 'Bio::Annotation::DBLink'
            'keyword' => 'Bio::Annotation::SimpleValue'
            'reference' => 'Bio::Annotation::Reference'
   '_as_feat' => ARRAY(0xb5c0458)
      0  Bio::SeqFeature::Generic=HASH(0xb59f0c0)
         '_gsf_seq' => Bio::PrimarySeq=HASH(0xb5caa9c)
            '_root_verbose' => 0
            '_seq_length' => undef
            'alphabet' => 'dna'
            'desc' => 'Genus species.'
            'display_id' => 'C_0'
            'is_circular' => 1
            'seq' => 'TCTAATTGGTCATAATTTCATGTCTATCTAAATGGTCATGATCATTATTGTAATTTCATGTCTATCTAAATGGTCATGATCATTATTGTAATTTCATGTCTATCTAAATGGTCATGATCATTATTGTAATTTCATGTCTATCTAAATGGTCATGATTATTATTGTAATTTCATGTCTATCTAAATGGTCGTGATTATTATTGTAATTTCATGTCTATCTAAATGGTCGTGATTATTATTGTAATTTCATGTCTATCTAGGTAAGTTTATAGGTAAGTTTATAGGTAAATTTAAAAAATAACCAAAACCAATATTAGGAATCTATGATTACAGCATTACTAGCATCTCCAGTTGAACAATTCCAAGTAATTCCATATTTTGGATTGGTTACACTTGGTAATGTAGATTTTTCTTATTCAAATGTAGTATGAGTATTATTATTATTATTATTAACTTTAGCTAATATATCATTATTATTAGGAAAAAGAAGCAATATATCTGAATCTAAGGTAGTTCAAAATAATTGACAAAGAATGATTACTAAAGTAGGTACATTTGTAAATGATATGTCTCAAGATACTATAGGATCAGAAGGTAGAAGATATGTAAATATTATCTTAGGATTGTTCGTTTTTGTTTTATTATTAAACATTTTAGGAATGATACCATATAGTTTTGCTATAACATCTCAAATCGTAGTAACATTATGAATATCATGAGGTGTATGATTGGGTTCATTAACTATTGGTTTTATTAATTATGGAATAAATTTCTTTAGTATGTTTATGCCAAGTGGAGCTCCATTAGCATTAGCACCATTTTTAATTTTAATTGAATTATTAAGTTATGTTGCAAGAGGAATATCATTAGGAGTGCGATTAGCAGCTAATATTACTTCTGGACATATTTTATTAACAATTATAGCAACATTCATATTTAAAATGTTAAATATAGGTGGAATATTTATTCCTTTAGCTTTCTTAACATTTGCTTTATTATTTGTTTTAACAATTTTAGAAATGGCAATTGGTGCAATCCAAGCCTATGTTTTAGGATTATTAGTAACAATATATTTAAATGACTCTGTGCATTTACATTAATTCATAATATATGGTCATTTTCTGCTATATATTATAATTTTATGATTAAATTCAGCCTATATTGTTTTTAACAACATAGGCCTTTTGATTATATTAGTATTCTAATTTGATACTGAGTACCATTTTAGGTATTGAGTATACTGAGTTAACTCTCAGTACCATTTTAGGTAATGAGTATTTTATATTAATACTCAGTACCAATATAGGTATTGAGTATTCTATATAGGTACTCAGTACCAATTTAAGTAATGAGTATTCTATATTAATACACAGTACCATTTTAGGTAATGAGTATTCTATATTAACACACAATACCAATTTAGTATATTACTACATAGGTATTAAGTATTATATGTTAATGGATATTAGAAAATACTACAGATATTGGATATACGAAACCCCTCTACAATTCACCTAACAATTAAGATCAAAGATCCTAAATGTAGGATCAATGATCCTAAATGTGGGCTTTGCAGCGGGAATATAGAGGCGATATAATAAACCCCTACAACTAATGTGTCGAGAATGTATTGGTATATACTCGATGCGCATAGCGCATCAGCCCACTTTTCACTTAACAATTAGGATCAAAGATCCTAATTGTTGGATCAAAGATCCTAAATGTGGGGGATTTGGAATTTACGATATTGGAATATACTATATTGGAATTTACTATATTGAAATATACTATATTGGTATATACTATATTGGTATTTACGATATTGGAATATACTATATTGGTATATACGATATTGGAATATACTATATTGGTATATACGATATTGGAATATACGATATAGGAATATACGATATTGGAATATACGATATAGGAATGTACTAAATTGGAATATACTTAATTGGAATATACGATATTGGAATATACAAAAATGGAATATACAATAATGGAATATACGAAATAGGAATATACGATATTGGAATATACGAAATCCCCCACTTTTAGGATCTTTGATCCAACATTGAGGATCAAAGATCCTCAATGTTAGGAGAAAAGTGGGCTGATGCGCATCGGGAATATACGATAATGGAATATACGAAATAGGAATATACGAAATAGGAATATACAATATAGGAATATACGAAATAGGAATATACGAAATCCCCCACATTTCACCTAACATTGAGGATCAAAGATCCTCAATGTTGGATCAAAGATCCTAAATGTGGGCTGATGCGCATCGGGTATATACGAAATCCCCACATTTCTCCTAACATTGAGGATCAAAGATCCTCAATGTTGGATCAAAGAACCTAAATGTGGGCTGATGCGCATCGGGAATATACAAAATTGGAATATATAGGCAATATACTATATTGGAATATATAGGCTATATATTATATTGGAATATATAGGCAATATACTATATTGGAATATATAGGCAATATACTATATTGAAATATATAGGCTATATATTATATTGGTATATATAGGCAATATACTACATAGGAATATATGATATTGGTATATACTATATTGGTATATACGATATTGGAATATACGAAATAGGAATATACGAAAATGGAATATATAGGCTATATACTATATTAAAATATATGAAATAGGAATATACGATATTGGTATATACGATAATGGAATATACGATATTGGAATATACGATATTGGAATATACGAAAATGGAATATACGAAAATGGAATATATAGGCAATATACTATATTGGAATATATAGGCTATATAGGCAATATAATATATTGGAATATATAGGCTATATACTATATTGGAATATATAGGCTATATACAAAATGGAATATATAGGCAATATACTATATTGTAATATATAGGCTATATAGGCAATATAATATATTGGAATATATAGGCTATATACGAAATTGGAATATATGATATTGGAATATACGGTATTGGAATATATGAAAATGGTATATATAGGCTATATATGATATTGGAATATATAGGCAATATACTATATTGGAATATATAGGCAATATACTATATTGGAATATATTGGCTATATACTATATTGGAATATATGATATTGGAATATACGATATTGGAATATATAAGCTATATACGAAATTGGAATATATAGGCTATATACAAAATGGAATATATAGGCTATATACAAAATGGAATATATAGGCTATATACGAAAATGGAATATATAGGCAATATACTATATTGGAATATATGAAATCCCCCACATTTCTCCTAACATTGAGGATCAAAGATCCTCAATGTTGGATCAAAGATCCTAAATGTGGGCTGATGCGCATCGGGTATATACTATATTGGAATATACGAAATCCTCCACAACTAGGTTCAATGAACCTAGTTGTGGACTGATGTGCCATGCGCATCGGGTATATACGAAATTGGTACATAGCCTATATATTATATTGGAATATATAGGCAATATACTATATTAGAATATATAGGCTATATACTATATTGGAATATATGATAAATATATTATGAAAATAATATACAGGTTATTTATAAGTACCACAAATACAGGATAAATAAAGAGCTATGTTTTTAAAATATACATTTATAAAACAGACATGTAAAATATAGATTTATAAAATATTTATGTTTATATGGCTTAATAAGCCACATAAAAATATAGATATATAAAATATTTATGTTTTTATATGACTTGTTTAGCCATATAACATTTTCCCTTGTTGGAAAATATGTCATATTTACCTCTTAATTGCATAAGGTGCAACCTTGAAATTTGCAATTGATGCTTGTTTAGCCATATAACATTTTCCCTTGTTGGGAAATATGTCACAATTACCCCTTAATTGCGTAAGGTGCAACCTTGAAATTTGCCAATTGATATTTCCGATACACAATTTGTATCCACCCCTAGAATTAGGATCAAAGATCCAATATTTAGGATCTTTGATTTAATATTTAGGATCTTTGATCCTAATAGTTAGGTGAAAAGTTAGGTAAATTGTTAGGTGATTTGTAGGGGTATGGCTATCATGGCTAAATCACCATCACGGCTAAATCACCATCACAATTAGAGCAGTAGGTTATATTATAACGCCACTTTTTAACTCATGAAATATAAAATTTTTTTAGAAATACAAGGAGTATTATCAATAACTAATAACGATGGCATAAATCAATTATGTTCAATCTATAGATTAGGAAAAATAGAGACAACAATATTAATACCAGCTTCAATAAGCATTTTCATGTTAAGTGAAGGAGCAACAAGTACATATGTATTAGTTTCAACATTAGAAGAATCAAGTATTGTTGATAAATTAGTAACAAAATTGAACAATTTAGATAAAACTTTTAGTGTTAAAATAAAGGTAACAGGAACAGCTTTAAAAATTGAAAAAATAAATAAAGAAGAAATTAAAGAAGAACAGATAAAAATTGGTAGTCACAGATATGAATTAAAACCATTAGGTATAGATGAAAAAGAATTGACTAATAAATGAAAAATTTCAAAAATATCTAAACATGCTCAAATACCGACATTTTTAAATAAAGCTAAGTCAAATTTATGATGACAACTTTTACAAATTGAACAGGGGATCAAAGATCCAGTGTTACAAATTGCAGCTAAAAAAGAAATAAAGGGTACTTTTGCAAAAGTAGTTACAGATCAAATTCAAACTAATTTGCAAAAAAACATGATAAAAGAAAATTTTGTAACATTTAAATCTGGATTAAATGAAATTTCATTATGTTTAATATCTGATCAAGTACAGGTTACATCACAAAGTGGTTACCATGAATTAATAAGTAAAAATAAGGACTTGGTAAAAAAAATTGGTAATGATTTTGTAAAGTTAAAACCACGAGAACCATATAAAGGTAAAGGTATTGGATTTTTAAAAGCCCCATTCAAATTAAAACAAAGAAAGAAAAAATAATATACATGTAGAGAGGTCTACATGTAGAGAGGTCTACATAGCAACGTCTTTTGTGTAAACATTTATACATGTAGAGAGGTCTACATAGCAATGTCTTTTGCGTAAACATCTTTTGCATAAGCATCTTTTGCATTAGCATCTTTTGCATTAGCATCTTTTGTGTAAGCATATTTTGCGTTAGCATCTTTTGTGTAAGCATATTTTGCGTAAGCATCTTTTGCATTAGCATCTTTTGCATTAGCATCTTTTGTGTAAGCATATTTTGCGTAAGCATCTTTTGCATTAGCATCTTTTGTGTAAGCATATTATGCGTAAGCATCTTTTGCATTAACATCTTTTGTGTAAGCATATTATGCGTAAACATCTTTTGCATTAGCATCTTATGCATGAGCATCTTTTGCATTAGCATCTTTTGCATTAGCATCTTTTGTGTAAGCATATTATGCGTAAGCATCTTGTGTGTAAGCATCTTTTGATTGT'
         '_gsf_seq_id' => 'C_0'
         '_gsf_tag_hash' => HASH(0xb59f340)
            'mol_type' => ARRAY(0xb59f368)
               0  'genomic DNA'
            'note' => ARRAY(0xb5bb224)
               0  'type: genomic'
            'organism' => ARRAY(0xb59f3a4)
               0  'Genus species'
         '_location' => Bio::Location::Simple=HASH(0xb5bb314)
            '_end' => 5477
            '_location_type' => 'EXACT'
            '_root_verbose' => 0
            '_seqid' => 'C_0'
            '_start' => 1
            '_strand' => 1
         '_primary_tag' => 'source'
         '_source_tag' => 'EMBL/GenBank/SwissProt'
      1  Bio::SeqFeature::Generic=HASH(0xb59f0d4)
         '_gsf_seq' => Bio::PrimarySeq=HASH(0xb5caa9c)
            -> REUSED_ADDRESS
         '_gsf_seq_id' => 'C_0'
         '_gsf_tag_hash' => HASH(0xb59f250)
            'gene' => ARRAY(0xb59f2b4)
               0  'atp6'
         '_location' => Bio::Location::Simple=HASH(0xb5bc110)
            '_end' => 1099
            '_location_type' => 'EXACT'
            '_root_verbose' => 0
            '_seqid' => 'C_0'
            '_start' => 728
            '_strand' => 1
         '_primary_tag' => 'gene'
         '_source_tag' => 'EMBL/GenBank/SwissProt'
      2  Bio::SeqFeature::Generic=HASH(0xb59f188)
         '_gsf_seq' => Bio::PrimarySeq=HASH(0xb5caa9c)
            -> REUSED_ADDRESS
         '_gsf_seq_id' => 'C_0'
         '_gsf_tag_hash' => HASH(0xb5bbad0)
            'EC_number' => ARRAY(0xb5bd5ec)
               0  '3.6.3.14'
            'codon_start' => ARRAY(0xb5bc1ec)
               0  1
            'gene' => ARRAY(0xb5bd45c)
               0  'atp6'
            'product' => ARRAY(0xb5bd330)
               0  'ATP synthase F0 subunit a'
            'translation' => ARRAY(0xb5bd40c)
               0  'MGSLTIGFINYGINFFSMFMPSGAPLALAPFLILIELLSYVARGISLGVRLAANITSGHILLTIIATFIFKMLNIGGIFIPLAFLTFALLFVLTILEMAIGAIQAYVLGLLVTIYLNDSVHLH'
         '_location' => Bio::Location::Simple=HASH(0xb5bd484)
            '_end' => 1099
            '_location_type' => 'EXACT'
            '_root_verbose' => 0
            '_seqid' => 'C_0'
            '_start' => 728
            '_strand' => 1
         '_primary_tag' => 'CDS'
         '_source_tag' => 'EMBL/GenBank/SwissProt'
      3  Bio::SeqFeature::Generic=HASH(0xb5bc124)
         '_gsf_seq' => Bio::PrimarySeq=HASH(0xb5caa9c)
            -> REUSED_ADDRESS
         '_gsf_seq_id' => 'C_0'
         '_gsf_tag_hash' => HASH(0xb5bd704)
            'gene' => ARRAY(0xb5bd664)
               0  'orf173'
         '_location' => Bio::Location::Simple=HASH(0xb5bd808)
            '_end' => 2238
            '_location_type' => 'EXACT'
            '_root_verbose' => 0
            '_seqid' => 'C_0'
            '_start' => 1717
            '_strand' => '-1'
         '_primary_tag' => 'gene'
         '_source_tag' => 'EMBL/GenBank/SwissProt'
      4  Bio::SeqFeature::Generic=HASH(0xb5bb2d8)
         '_gsf_seq' => Bio::PrimarySeq=HASH(0xb5caa9c)
            -> REUSED_ADDRESS
         '_gsf_seq_id' => 'C_0'
         '_gsf_tag_hash' => HASH(0xb5bd768)
            'codon_start' => ARRAY(0xb5bd970)
               0  1
            'gene' => ARRAY(0xb5bd7f4)
               0  'orf173'
            'product' => ARRAY(0xb5be078)
               0  'hypothetical protein'
            'translation' => ARRAY(0xb5bd880)
               0  'MLGEMWGISYIPISYIPILYIPISYIPISYIPLSYIPDAHQPTFLLTLRIFDPQCWIKDPKSGGFRIFQYRIFLFRIFHYCIFHFCIFQYRIFQLSIFQFSTFLYRIFQYRIFLYRIFQYRIYQYSIFQYRIYQYSIFQYRKYQYSIYQYSIFQYSKFQYSIFQYRKFQIPHI'
         '_location' => Bio::Location::Simple=HASH(0xb5bdfec)
            '_end' => 2238
            '_location_type' => 'EXACT'
            '_root_verbose' => 0
            '_seqid' => 'C_0'
            '_start' => 1717
            '_strand' => '-1'
         '_primary_tag' => 'CDS'
         '_source_tag' => 'EMBL/GenBank/SwissProt'
      5  Bio::SeqFeature::Generic=HASH(0xb5bd718)
         '_gsf_seq' => Bio::PrimarySeq=HASH(0xb5caa9c)
            -> REUSED_ADDRESS
         '_gsf_seq_id' => 'C_0'
         '_gsf_tag_hash' => HASH(0xb5bd754)
            'gene' => ARRAY(0xb5bb300)
               0  'orf130'
         '_location' => Bio::Location::Simple=HASH(0xb5be244)
            '_end' => 4559
            '_location_type' => 'EXACT'
            '_root_verbose' => 0
            '_seqid' => 'C_0'
            '_start' => 4167
            '_strand' => 1
         '_primary_tag' => 'gene'
         '_source_tag' => 'EMBL/GenBank/SwissProt'
      6  Bio::SeqFeature::Generic=HASH(0xb5bd650)
         '_gsf_seq' => Bio::PrimarySeq=HASH(0xb5caa9c)
            -> REUSED_ADDRESS
         '_gsf_seq_id' => 'C_0'
         '_gsf_tag_hash' => HASH(0xb5bd9c0)
            'codon_start' => ARRAY(0xb5be0dc)
               0  1
            'gene' => ARRAY(0xb5be1b8)
               0  'orf130'
            'product' => ARRAY(0xb5bf6ac)
               0  'hypothetical protein'
            'translation' => ARRAY(0xb5bf6d4)
               0  'MKYKIFLEIQGVLSITNNDGINQLCSIYRLGKIETTILIPASISIFMLSEGATSTYVLVSTLEESSIVDKLVTKLNNLDKTFSVKIKVTGTALKIEKINKEEIKEEQIKIGSHRYELKPLGIDEKELTNK'
         '_location' => Bio::Location::Simple=HASH(0xb5bf648)
            '_end' => 4559
            '_location_type' => 'EXACT'
            '_root_verbose' => 0
            '_seqid' => 'C_0'
            '_start' => 4167
            '_strand' => 1
         '_primary_tag' => 'CDS'
         '_source_tag' => 'EMBL/GenBank/SwissProt'
      7  Bio::SeqFeature::Generic=HASH(0xb5bd8a8)
         '_gsf_seq' => Bio::PrimarySeq=HASH(0xb5caa9c)
            -> REUSED_ADDRESS
         '_gsf_seq_id' => 'C_0'
         '_gsf_tag_hash' => HASH(0xb5bf60c)
            'gene' => ARRAY(0xb5be208)
               0  'orf165'
         '_location' => Bio::Location::Simple=HASH(0xb5bf814)
            '_end' => 5466
            '_location_type' => 'EXACT'
            '_root_verbose' => 0
            '_seqid' => 'C_0'
            '_start' => 4969
            '_strand' => '-1'
         '_primary_tag' => 'gene'
         '_source_tag' => 'EMBL/GenBank/SwissProt'
      8  Bio::SeqFeature::Generic=HASH(0xb5bd9ac)
         '_gsf_seq' => Bio::PrimarySeq=HASH(0xb5caa9c)
            -> REUSED_ADDRESS
         '_gsf_seq_id' => 'C_0'
         '_gsf_tag_hash' => HASH(0xb5bf670)
            'codon_start' => ARRAY(0xb5bf97c)
               0  1
            'gene' => ARRAY(0xb5bf774)
               0  'orf165'
            'product' => ARRAY(0xb5bfa94)
               0  'hypothetical protein'
            'translation' => ARRAY(0xb5bf864)
               0  'MLTHKMLTHNMLTQKMLMQKMLMQKMLMHKMLMQKMFTHNMLTQKMLMQKMLTHNMLTQKMLMQKMLTQNMLTQKMLMQKMLMQKMLTQNMLTQKMLTQNMLTQKMLMQKMLMQKMLMQKMFTQKTLLCRPLYMYKCLHKRRCYVDLSTCRPLYMYIIFSFFVLI'
         '_location' => Bio::Location::Simple=HASH(0xb5bfa08)
            '_end' => 5466
            '_location_type' => 'EXACT'
            '_root_verbose' => 0
            '_seqid' => 'C_0'
            '_start' => 4969
            '_strand' => '-1'
         '_primary_tag' => 'CDS'
         '_source_tag' => 'EMBL/GenBank/SwissProt'
   '_dates' => ARRAY(0xb5c0174)
        empty array
   '_division' => '07-DEC-2013'
   '_molecule' => 'DNA'
   '_root_verbose' => 0
   '_secondary_accession' => ARRAY(0xb5c04d0)
        empty array
   'primary_seq' => Bio::PrimarySeq=HASH(0xb5caa9c)
      -> REUSED_ADDRESS
   'species' => Bio::Species=HASH(0xb59eb98)
      '_classification' => ARRAY(0xb40420c)
         0  'species'
         1  'Genus'
         2  'Unclassified'
      '_common_name' => 'Genus species'

J'aimerais acceder au tableau qui se trouve dans la section as_feat de la Hash seulement quand je fait $inseq->as_feat() cela ne fonctionne pas je ne sais pas ou je me trouve je souhaiterais passer dans chaque element du tableau et pour chaque élément de celui créer une entrée dans mon fichier fasta.

Si vous connaissais programme perl qui fait c que je souhaite je suis preneuse aussi, bien que je veuille savoir comment faire.

**Lolo78** · 08/12/2013, 10h51

Je ne connais rien en bioinformatique, mais je remarque que la section s'appelle "_as_feat", pas "as_feat".

**Gardyen** · 09/12/2013, 12h19

hum à quelle(s) séquence(s) tu veux accéder exactement ?
le code que tu as donné permet d'avoir l'entrée GenBank en FASTA comme prévu, cela inclut donc les sub-features dans la séquence

si tu veux les sub-features séparément, alors vérifie la doc pour les objets Bio::Seq

Bio::Seq::IO probleme d'accession a as_feat.

Bioinformatique Perl

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