[Artemis-users] Bitten by multiFASTA annotation bug
Hi, I was trying Artemis to view some annotations I have in a multiFASTA and GFF3 file. In my use case, it is not common to have this type of data. I noticed a problem though, in that Artemis assigns all the GFF features to the first sequence in the FASTA file (see attached screenshot). After some research, I found that this issue has been reported 2-3 years ago: http://www.mail-archive.com/artemis-users@sanger.ac.uk/msg00468.html http://www.mail-archive.com/artemis-users@sanger.ac.uk/msg00401.html Any chance that this will be fixed? Regards, Florent PS/ I attached a subset of the contigs and annotations that illustrate the bug. ##gff-version 3 NODE_11_length_1349_cov_136.672348 Prodigal_v2.50 CDS 1 114 24.0- 0 ID=8_1;cscore=7.85;partial=10;rbs_motif=AGGAG;rbs_spacer=5-10bp;rscore=14.24;score=24.0,24.0,25.17;sscore=17.32;start_type=ATG;tscore=3.88;uscore=-1.94 NODE_13_length_11123_cov_152.177734 FIG CDS 25 153 . + 1 ID=fig|666.7046.peg.4;Name=hypothetical protein NODE_11_length_1349_cov_136.672348 GAAAGTTGCTGGCGGGCCAGCTCGACCACGGTGCCAGCGCCTTGAACGGTGTAGCC GCTCGGGTCGGTGTAGGTTAGAACGGTGGCGGTGTTGGCGGGTTGCTTGTGCATGTCGGT CTCTCCTTAAACCACAGCGTCGGCTTCAACCGCATCGCTGTATGCTTCTGCGTAGGCCTC GCAGGCGTCTTGCAGTTGCAGCGAAGCGATGCGGATTCGCCCTTGCACGCCTTCCCAGCG CTCGTCCTGCGTGTCGTAAGCCAGCAGGTCCGTAACACAGCGGTCCAGGAACGCGCGGCG CACCTTAACTTCTTCAGCGGCCTTGTTAAGGTTGAAGCGAGCGATTTCAGCGAGGGTAGC CATTTCGGTCTCCAGTGCGTTTGCGTCTATGCA NODE_13_length_11123_cov_152.177734 GCGCCGGCTTCCATCTCCGAAGCGATGGAGATCGGCAAGGCCCGCAGCCTGAACGAAGCC AACATGCGCGCTGAATACGCTCGCTGGCGGAAGTTCCACGGCATCAGCGGCCGTATCTCG GCGCCGAAGCCTGAGGCTGCTACCGAGGGCTTCTAGCCTCGCTGCCCGAAACCTGC TATTGCCGGCAATAGCCACCTCCCGGAGCTCGATATGACCTTCACGGT CAATACTCAGCCCATCGGCGTGTGTCGCAGAGGGCAAGCTGTCTGTTCACAG CATCTTCTACACAATCCAAGGTGAGGGACCGTTCTGCGGCACGCCGGCGGTCTTTATTCG TCTTGCTGCAACCTCCAGTGCCCGGGCTGCGACACCGAATACACTTCCGCCG GGAGGCGGGAGCTTATGAGATCCTGTTCGAGGTCGATAAACTGATCCGCAAGGATGGGTG GAGAAACTGGTCGTAATCACCGGCAACCTTTCCGTCAGGACATCGGAGACCT GATCAACGTCCTGACACTTCACGGATATTACGTCCAGATCGAATCGAACGGCACGCTGCC CCCGCTGTCCTATGGAACCACAACACCGCCGTTCGGAGCGGTGCCTATCTGGTGAT CAGCCCGAAGACAGGCAAGATTAATCCGCTGTCACTGGCCGCAGCGTGCGCGCTCAAGTA TGTCAATCGACCTTGCCGAGGACGACGGGTTGCCCAACCATGCGCTCCGCCA CACCGCCAACGGCTTGCGCGGCTGAGGGCTGGGAGCGCCCAATCTACCTCCA GCCTATGGACGGCAAGGACGAAGCGGGCAACCGCGCGAACCTCGAGGCGTGCGTCGCGTC GTGCATGTCCAAAGGCTACATCCTCCAGCTGCAAATCCACAAACTCATCGGAGCTGAA attachment: Screenshot.png___ Artemis-users mailing list Artemis-users@sanger.ac.uk http://lists.sanger.ac.uk/mailman/listinfo/artemis-users
Re: [Artemis-users] Bitten by multiFASTA annotation bug
Hi Tim, Thank you for your feedback. I will definitely try the two workarounds you described for this dataset. However, in the future, it would be great if Artemis were capable of handling all use-cases, including the one where the multiple sequences are loaded before the GFF3 features. Regards, Florent On 02/08/11 01:37, Tim Carver wrote: Hi Florent Actually I need to correct myself. I did fix this for GFF files. If you add the sequence to the end of the GFF file (see attached GFF changes to your example) then it should correctly offset the features to the correct sequence. For other file formats (EMBL, GenBank) this has not been implemented. Regards Tim On 8/1/11 2:47 PM, Tim Carvert...@sanger.ac.uk wrote: Hi Florent Apologies for not getting round to this. It has not been a priority here as the EMBOSS application 'union' does this. I shall try and promote it up the todo list. Regards Tim On 8/1/11 7:28 AM, Florent Anglyflorent.an...@gmail.com wrote: Hi, I was trying Artemis to view some annotations I have in a multiFASTA and GFF3 file. In my use case, it is not common to have this type of data. I noticed a problem though, in that Artemis assigns all the GFF features to the first sequence in the FASTA file (see attached screenshot). After some research, I found that this issue has been reported 2-3 years ago: http://www.mail-archive.com/artemis-users@sanger.ac.uk/msg00468.html http://www.mail-archive.com/artemis-users@sanger.ac.uk/msg00401.html Any chance that this will be fixed? Regards, Florent PS/ I attached a subset of the contigs and annotations that illustrate the bug. ___ Artemis-users mailing list Artemis-users@sanger.ac.uk http://lists.sanger.ac.uk/mailman/listinfo/artemis-users ___ Artemis-users mailing list Artemis-users@sanger.ac.uk http://lists.sanger.ac.uk/mailman/listinfo/artemis-users ___ Artemis-users mailing list Artemis-users@sanger.ac.uk http://lists.sanger.ac.uk/mailman/listinfo/artemis-users
