{"action":"created","issue":{"url":"https://api.github.com/repos/biojava/biojava/issues/796","repository_url":"https://api.github.com/repos/biojava/biojava","labels_url":"https://api.github.com/repos/biojava/biojava/issues/796/labels{/name}","comments_url":"https://api.github.com/repos/biojava/biojava/issues/796/comments","events_url":"https://api.github.com/repos/biojava/biojava/issues/796/events","html_url":"https://github.com/biojava/biojava/issues/796","id":354774387,"node_id":"MDU6SXNzdWUzNTQ3NzQzODc=","number":796,"title":"GenbankSequenceParser - found unknown section key: CONTIG","user":{"login":"TorkelE","id":18099310,"node_id":"MDQ6VXNlcjE4MDk5MzEw","avatar_url":"https://avatars2.githubusercontent.com/u/18099310?v=4","gravatar_id":"","url":"https://api.github.com/users/TorkelE","html_url":"https://github.com/TorkelE","followers_url":"https://api.github.com/users/TorkelE/followers","following_url":"https://api.github.com/users/TorkelE/following{/other_user}","gists_url":"https://api.github.com/users/TorkelE/gists{/gist_id}","starred_url":"https://api.github.com/users/TorkelE/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/TorkelE/subscriptions","organizations_url":"https://api.github.com/users/TorkelE/orgs","repos_url":"https://api.github.com/users/TorkelE/repos","events_url":"https://api.github.com/users/TorkelE/events{/privacy}","received_events_url":"https://api.github.com/users/TorkelE/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2018-08-28T15:05:29Z","updated_at":"2018-08-28T23:35:12Z","closed_at":null,"author_association":"NONE","body":"I have downloaded a larger amount of sequce data from the refseq project. It is a bounce of genebank files.\r\n\r\nWhen I read these files using biojava and:\r\n```java\r\n    InputStream is = new FileInputStream(fileName);\r\n    if (fileName.substring(fileName.length()-3).equals(\".gz\")) {is = new GZIPInputStream(is); } \r\n    GenbankReader<DNASequence, NucleotideCompound> dnaReader = new GenbankReader<DNASequence, NucleotideCompound>(is, new GenericGenbankHeaderParser<DNASequence,NucleotideCompound>(),\r\n\t\t        new DNASequenceCreator(AmbiguityDNACompoundSet.getDNACompoundSet())\r\n\t\t        ); \r\n    LinkedHashMap<String, DNASequence> gbFile = dnaReader.process();\r\n```\r\n\r\nEverything runs fine, however I get a lot of information messages like:\r\n```java\r\n433147 [main] INFO org.biojava.nbio.core.sequence.io.GenbankSequenceParser - found unknown section key: CONTIG\r\n```\r\n(all in red)\r\n\r\nMy guess is that the reason can be found in this part of he genebank file, where the sequence has been designated as a contig (between the list of features and the actual nucleotide sequence).\r\n```\r\n...\r\n     CDS             complement(1934428..1936155)\r\n                     /locus_tag=\"MVOL_RS08690\"\r\n                     /old_locus_tag=\"Mvol_1722\"\r\n                     /inference=\"COORDINATES: similar to AA\r\n                     sequence:RefSeq:WP_013181105.1\"\r\n                     /note=\"Derived by automated computational analysis using\r\n                     gene prediction method: Protein Homology.\"\r\n                     /codon_start=1\r\n                     /transl_table=11\r\n                     /product=\"oxaloacetate decarboxylase subunit alpha\"\r\n                     /protein_id=\"WP_013181105.1\"\r\n                     /db_xref=\"GeneID:9276977\"\r\n                     /translation=\"MVKSVKITDTTFRDAHQSLMATRLRLSDMLPIAEKMDEVGFYSM\r\n                     EVWGGATFDSCIRFLNEDPWERLRELKKKITETPLQMLLRGQNLVGYRHYSDDVVEKF\r\n                     VKKSVENGIDIIRIFDALNDVRNLEYPIKVAVECGAHVQGAISYTTSPVHTIDQYIEL\r\n                     ARNFEEHKCDSICIKDMAGLLTPFDAKELIKRLKEEVSIPIDLHSHCTAGIAPMTYIT\r\n                     SVEAGIDILNCAISPLSMGTSQPPIESMVASLKDTEYDTGLNLVALTEIRDYFDEIRN\r\n                     KYKYLINPISERVDARILRYQVPGGMLSNLVSQLKEQGAIDKFEEVLNEIPNVRKDLG\r\n                     YPPLVTPTSQIVGTQAVMNVLTGERYRIITNEVSNYVRGYYGKAPASIDRDLIKRVLK\r\n                     TGEKRIECRPADLLEPEYEKRAKEAKEKGLIRNEKYEVEDILTYTLYPQVAVKFLRGE\r\n                     AEEEPIPEEKEVSKFSEIPTKYVVEVDGEAYEVKVEPVYGSEYKKPKTEKIDSETEGA\r\n                     VNSPFRGMVTKVNVKEGAEVKAGDTIITLEAMKMENPVECPVDGKVEKIIVHEGQSVS\r\n                     VGDILMIVK\"\r\nCONTIG      join(CP002057.1:1..1936387)\r\nORIGIN      \r\n        1 aatttaaaga ttaaaattag tagactgtcg atttacaata tcatatttat gagtaatgat\r\n...\r\n```\r\nHowever, there shouldn't really be anything noteworthy with the file containing sequences classified as contigs?\r\n\r\nIs there something strange going on here, or can I just proceed as everything worked out fine?\r\n"},"comment":{"url":"https://api.github.com/repos/biojava/biojava/issues/comments/416774335","html_url":"https://github.com/biojava/biojava/issues/796#issuecomment-416774335","issue_url":"https://api.github.com/repos/biojava/biojava/issues/796","id":416774335,"node_id":"MDEyOklzc3VlQ29tbWVudDQxNjc3NDMzNQ==","user":{"login":"josemduarte","id":6000474,"node_id":"MDQ6VXNlcjYwMDA0NzQ=","avatar_url":"https://avatars3.githubusercontent.com/u/6000474?v=4","gravatar_id":"","url":"https://api.github.com/users/josemduarte","html_url":"https://github.com/josemduarte","followers_url":"https://api.github.com/users/josemduarte/followers","following_url":"https://api.github.com/users/josemduarte/following{/other_user}","gists_url":"https://api.github.com/users/josemduarte/gists{/gist_id}","starred_url":"https://api.github.com/users/josemduarte/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/josemduarte/subscriptions","organizations_url":"https://api.github.com/users/josemduarte/orgs","repos_url":"https://api.github.com/users/josemduarte/repos","events_url":"https://api.github.com/users/josemduarte/events{/privacy}","received_events_url":"https://api.github.com/users/josemduarte/received_events","type":"User","site_admin":false},"created_at":"2018-08-28T23:35:12Z","updated_at":"2018-08-28T23:35:12Z","author_association":"CONTRIBUTOR","body":"The message is simply an over-verbose way of saying that the parsing of that CONTIG section is not supported. I think it can safely be ignored.\r\n\r\nAs a note you can fully configure the verbosity of the logger via providing a log4j2.xml file in your classpath, for instance with the following everything will be logged at INFO level except for the GenbankSequenceParser which will be logged at WARN level (avoiding the messages):\r\n\r\n```xml\r\n<?xml version=\"1.0\" encoding=\"UTF-8\"?>\r\n<configuration status=\"WARN\">\r\n\t<appenders>\r\n\t\t<File name=\"TheLogFile\" fileName=\"application.log\" append=\"false\">\r\n        \t\t<PatternLayout pattern=\"%d{yyyy-MM-dd HH:mm:ss} %-5level - %msg%n\"/>\r\n    \t\t</File>\t\t\r\n\t</appenders>\r\n\t<loggers>\r\n\t\t<root level=\"info\">\r\n\t\t\t<appender-ref ref=\"TheLogFile\" level=\"info\"/>\r\n\t\t</root>\r\n\r\n\t\t<Logger name=\"org.biojava.nbio.core.sequence.io.GenbankSequenceParser\" level=\"warn\" additivity=\"false\">\r\n\t\t\t<appender-ref ref=\"ConsoleStdErr\"/>\r\n\t\t</Logger>\r\n\r\n\t</loggers>\r\n</configuration>\r\n```\r\n\r\nFull reference here: https://logging.apache.org/log4j/2.x/manual/configuration.html"}}
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