Bio::Seq::IO probleme d'accession a as_feat.
Voila mon soucis est le suivant j'ai un fichier *gbf du type:
Code:
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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.
