<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">All,<br class=""><br class="">I noticed that BioPython, like the versions of BioPerl in CPAN, does not handle GenBank structured comments (<a href="http://www.ncbi.nlm.nih.gov/genbank/structuredcomment" class="">http://www.ncbi.nlm.nih.gov/genbank/structuredcomment</a>) in the ideal way. Here’s an example structured comment:<br class=""><br class="">COMMENT ##FluData-START##<br class=""> EPI_ISOLATE_ID :: EPI_ISL_77637<br class=""> NAME :: A/California/07/2009<br class=""> TYPE :: H1N1<br class=""> Segment_name :: M'<br class=""> HOST_AGE :: 54<br class=""> HOST_GENDER :: F'<br class=""> PASSAGE :: M1/C1 (2009-04-24)<br class=""> LOCATION :: United States / California'<br class=""> COLLECT_DATE :: 09-Apr-2009<br class=""> Lineage :: A(H1N1)pdm09<br class=""> RESIST_TO_ADAMANTANES :: Resistant'<br class=""> RESIST_TO_OSELTAMIVIR :: Sensitive'<br class=""> RESIST_TO_ZANAMVIR :: Sensitive'<br class=""> SPECIMEN_ID :: H13596<br class=""> SENDER_LAB :: Naval Health Research Center'<br class=""> SEQLAB_SAMPLE_ID :: 2009712111<br class=""> EPI_SEQUENCE_ID :: EPI273604<br class=""> ##FluData-END##<br class=""><br class="">Or here: <a href="http://www.ncbi.nlm.nih.gov/nuccore/291609868" class="">http://www.ncbi.nlm.nih.gov/nuccore/291609868</a><br class=""><br class="">A table, with tag/value pairs. A fair number of bacterial genomes in GenBank use the structured comment to hold MIGS/MIMS data. The comment() method should return something like this, which is easily parsed:<br class=""><br class="">##FluData-START##<br class="">EPI_ISOLATE_ID :: EPI_ISL_77637<br class="">NAME :: A/California/07/2009<br class="">TYPE :: H1N1<br class="">Segment_name :: M'<br class="">HOST_AGE :: 54<br class="">HOST_GENDER :: F'<br class="">PASSAGE :: M1/C1 (2009-04-24)<br class="">LOCATION :: United States / California'<br class="">COLLECT_DATE :: 09-Apr-2009<br class="">Lineage :: A(H1N1)pdm09<br class="">RESIST_TO_ADAMANTANES :: Resistant'<br class="">RESIST_TO_OSELTAMIVIR :: Sensitive'<br class="">RESIST_TO_ZANAMVIR :: Sensitive'<br class="">SPECIMEN_ID :: H13596<br class="">SENDER_LAB :: Naval Health Research Center'<br class="">SEQLAB_SAMPLE_ID :: 2009712111<br class="">EPI_SEQUENCE_ID :: EPI273604<br class="">##FluData-END##<br class=""><br class="">Rather than this, which is what it currently returns:<br class=""><br class="">##FluData-START## EPI_ISOLATE_ID :: EPI_ISL_77637 NAME :: A/California/07/2009 TYPE :: H1N1 Segment_name :: M' HOST_AGE :: 54 HOST_GENDER :: F' PASSAGE :: M1/C1 (2009-04-24) LOCATION :: United States / California' COLLECT_DATE :: 09-Apr-2009 Lineage :: A(H1N1)pdm09 RESIST_TO_ADAMANTANES :: Resistant' RESIST_TO_OSELTAMIVIR :: Sensitive' RESIST_TO_ZANAMVIR :: Sensitive' SPECIMEN_ID :: H13596 SENDER_LAB :: Naval Health Research Center' SEQLAB_SAMPLE_ID :: 2009712111 EPI_SEQUENCE_ID :: EPI273604 ##FluData-END##<br class=""><br class="">Are there any objections to me putting in a pull request with this change? I made this same fix in BioPerl. Of course, if the comment is a “normal” one, it will be treated the same as it is treated now. Another words, the vast majority of comments stay the same.<br class=""><br class="">I’ll also add tests.<br class=""><br class="">Thanks again,<br class=""><br class="">Brian O.</body></html>