Open nbuso opened 6 years ago
Coding entries contains AH lines also in Standard data class. Errors are of the type:
Unknown line type: AH LOCAL_SPAN PRIMARY_IDENTIFIER PRIMARY_SPAN COMP
Example entry from file: std/cum_std_inv_01_r137.cds
ID DAB41761; SV 1; linear; genomic DNA; STD; INV; 1533 BP. XX PA BK010358.1 XX DT 16-JUL-2018 (Rel. 137, Created) DT 16-JUL-2018 (Rel. 137, Last updated, Version 1) XX DE Heliconius melpomene (postman butterfly) cytochrome P450 CYP405A4 XX KW TPA; TPA:inferential. XX OS Heliconius melpomene (postman butterfly) OC Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; OC Neoptera; Holometabola; Lepidoptera; Glossata; Ditrysia; Papilionoidea; OC Nymphalidae; Heliconiinae; Heliconiini; Heliconius. XX RN [1] RC Publication Status: Online-Only RP 1-5039 RX DOI; 10.1186/1471-2164-10-574. RX PUBMED; 19954531. RA Zagrobelny M., Scheibye-Alsing K., Jensen N.B., Moller B.L., Gorodkin J., RA Bak S.; RT "454 pyrosequencing based transcriptome analysis of Zygaena filipendulae RT with focus on genes involved in biosynthesis of cyanogenic glucosides"; RL BMC Genomics 10:574-574(2009). XX RN [2] RC Publication Status: Available-Online prior to print RP 1-5039 RX DOI; .1007/s00239-018-9854-8. RX PUBMED; 29974176. RA Zagrobelny M., Jensen M.K., Vogel H., Feyereisen R., Bak S.; RT "Evolution of the Biosynthetic Pathway for Cyanogenic Glucosides in RT Lepidoptera"; RL J. Mol. Evol. 86(6):379-394(2018). XX RN [3] RP 1-5039 RA Zagrobelny M., Jensen M.K., Vogel H., Feyereisen R., Bak S.; RT ; RL Submitted (17-NOV-2017) to the INSDC. RL Department of Plant and Environmental Sciences, University of Copenhagen, RL Thorvaldsensvej 40, Frederiksberg C, Copenhagen 1871, Denmark XX DR MD5; 0fdc51a4288be7834c8c4de6bbb12cab. XX AH LOCAL_SPAN PRIMARY_IDENTIFIER PRIMARY_SPAN COMP AS 1-160 CAEZ01010737.1 92003-92162 c AS 161-270 CAEZ01010737.1 92669-92778 c AS 271-364 CAEZ01010737.1 93023-93116 c AS 365-550 CAEZ01010737.1 94792-94977 c AS 551-620 CAEZ01010737.1 95076-95145 c AS 621-747 CAEZ01010737.1 95230-95356 c AS 748-957 CAEZ01010737.1 95438-95647 c AS 958-1201 CAEZ01010737.1 95870-96113 c AS 1202-1372 CAEZ01010737.1 96335-96505 c AS 1373-1533 CAEZ01010737.1 96881-97041 c XX FH Key Location/Qualifiers FH FT source 1..1533 FT /organism="Heliconius melpomene" FT /mol_type="genomic DNA" FT /db_xref="taxon:34740" FT CDS join(BK010358.1:1..160,BK010358.1:667..776, FT BK010358.1:1021..1114,BK010358.1:2790..2975, FT BK010358.1:3074..3143,BK010358.1:3228..3354, FT BK010358.1:3436..3645,BK010358.1:3868..4111, FT BK010358.1:4333..4503,BK010358.1:4879..5039) FT /codon_start=1 FT /gene="CYP405A4" FT /product="cytochrome P450 CYP405A4" FT /protein_id="DAB41761.1" FT /translation="MFFLLLVLLVISLILIQDFVKKRGYKWKKLSEFPGDRPLPLVGNG FT LDIGFDADEASFRLIKMWEKHGKQNFRLSVGSEDWLMLCEPEDIKVLLNDNFELSKPLE FT RNAAMKPFFGYSVSTSEGERWKSVRKLMTPSFHFKALDRAADDFGKHTQTLFELIDSYE FT GKSPVNIYTYLKPYMLDMLSVNLFGVEKNYLKNRDHPYIKSSSKMIKIITYNYFSYWRN FT NSYLVRFTPLHTEMQNIIRDVKQNSSDIITQRRKILNKMIEETKSNNKNIDLNYDTFIE FT DKLAGGCLLDRFILSVSPNGDPEKDAIINEEITLTLFTGHLTTSMTMCNAMYLMSLYPE FT VQQKVLDEQKAIFGKDLNRQATTQDLNDMKYLEALIKETIRFIPTIPRIGRQLQKDLKL FT SDGRVAPAGTSVIVFFNAAARNPRTYTEPEKFMPERFFDTTMHPFAFVPFSAGPRNCVA FT FRYAWIVLKATLSNIIRRYEILPGPEPKFAFRLITESTNGLHLHYKKRDICA" XX SQ Sequence 1533 BP; 510 A; 288 C; 302 G; 433 T; 0 other; atgtttttct tactgttagt tctgctcgtt atatctttaa tattgatcca agattttgtc 60 aagaaacgtg ggtacaaatg gaagaagctt tcagaatttc ccggtgacag accgttacca 120 ttggtcggga atggcctaga catcggattc gatgcagacg aagcgtcttt tagattgatt 180 aaaatgtggg aaaaacatgg aaaacaaaat ttccgtctgt ctgttggatc cgaggactgg 240 ctcatgctgt gcgaacctga agacattaag gtacttctaa acgacaattt tgagctttcg 300 aaacctctag agagaaatgc agccatgaaa ccattctttg gctactccgt atccacttct 360 gagggagaaa gatggaaatc agtgagaaag ctgatgactc caagttttca ctttaaagct 420 ttggaccgag ctgctgacga tttcggcaaa cacactcaaa cactctttga gctcatagat 480 tcttatgaag gcaagagtcc agtcaatata tacacatatt tgaagccgta catgctcgat 540 atgttaagcg ttaatctttt tggagttgaa aagaattacc ttaaaaaccg tgatcatcca 600 tatattaagt ccagcagcaa aatgattaag attataacat acaattactt ttcctactgg 660 agaaataata gttacttagt aagatttact ccattgcaca ctgaaatgca gaatattatt 720 agagacgtca aacaaaacag ttcagatata attacgcaaa gaagaaaaat tttgaacaaa 780 atgatagaag aaaccaagag caacaataag aacatcgact tgaactatga tactttcata 840 gaagataagc ttgctggtgg ttgcttgttg gacagattta tattaagcgt gtcgccaaat 900 ggtgatcctg agaaggatgc gatcattaat gaagaaataa cattaacctt atttactgga 960 catctaacga catcaatgac gatgtgcaac gcaatgtacc tgatgtcatt gtacccagaa 1020 gtacaacaga aagttctaga tgaacagaag gctatatttg gtaaagactt gaacagacaa 1080 gcgactacac aagatttaaa tgacatgaaa tatcttgaag cgctaataaa ggagactata 1140 aggttcattc ctacaattcc cagaattggg agacaactac aaaaagactt aaagttatct 1200 gatggtcgtg tagctcctgc tggaacgtct gtaattgttt tcttcaatgc cgctgccaga 1260 aatcccagga cttacacaga accagaaaaa tttatgcctg aacgattctt tgacacaaca 1320 atgcatccat ttgcttttgt tcctttcagt gccggaccta ggaactgcgt agctttccgc 1380 tatgcgtgga ttgttctgaa ggcgacttta tcgaacatta tacggagata tgaaattctt 1440 cctggtcctg aacccaaatt tgccttccgt ctgatcacgg aatctaccaa tggattgcat 1500 ctacactaca agaagagaga tatatgtgct taa 1533 //
Coding entries contains AH lines also in Standard data class. Errors are of the type:
Unknown line type: AH LOCAL_SPAN PRIMARY_IDENTIFIER PRIMARY_SPAN COMP
Example entry from file: std/cum_std_inv_01_r137.cds