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Read correctly coordinates on multiple lines for GBFF #240

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merged 6 commits into from
Jun 13, 2024
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@jpjarnoux jpjarnoux commented Jun 11, 2024

Genes coordinates can be written on multiple lines in GBFF files.
For instance:

     misc_feature    complement(order(23276..23344,23180..23233,23108..23167,
                     22982..23050,22853..22921))
                     /gene="dsbI"
                     /locus_tag="Cj0017c"
                     /inference="protein motif:TMHMM:2.0"
     misc_feature    complement(order(25348..25416,24661..24729))
                     /locus_tag="Cj0019c"
                     /inference="protein motif:TMHMM:2.0"
     misc_feature    complement(order(33433..33492,33331..33399,33205..33273,
                     33076..33144,32908..32976,32779..32847,32653..32721,
                     32548..32616,32437..32505,32332..32400,32251..32319))
                     /locus_tag="Cj0025c"
                     /inference="protein motif:TMHMM:2.0"

This PR changes the GBFF parsing to read the coordinates correctly and should (maybe) fix this issue #195

@jpjarnoux jpjarnoux marked this pull request as ready for review June 12, 2024 12:23
@jpjarnoux jpjarnoux requested a review from JeanMainguy June 12, 2024 12:23
@jpjarnoux jpjarnoux merged commit b25455d into dev Jun 13, 2024
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@jpjarnoux jpjarnoux deleted the issue195 branch June 13, 2024 12:37
@jpjarnoux jpjarnoux mentioned this pull request Jun 13, 2024
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2 participants