Fixes #385 by modifying the tutorial.

EI-CoreBioinformatics · Mar 15, 2021 · 8b63828 · 8b63828
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diff --git a/docs/Library/Mikado.daijin.rst b/docs/Library/Mikado.daijin.rst
@@ -1,6 +1,15 @@
 Mikado.daijin package
 =====================
 
+Submodules
+----------
+
+.. toctree::
+   :maxdepth: 4
+
+   Mikado.daijin.assemble
+   Mikado.daijin.mikado
+
 Module contents
 ---------------
 

diff --git a/docs/Library/Mikado.parsers.rst b/docs/Library/Mikado.parsers.rst
@@ -13,6 +13,7 @@ Submodules
    Mikado.parsers.bed12
    Mikado.parsers.blast_utils
    Mikado.parsers.gfannotation
+   Mikado.parsers.parser
 
 Module contents
 ---------------

diff --git a/docs/Library/Mikado.scales.rst b/docs/Library/Mikado.scales.rst
@@ -22,6 +22,7 @@ Submodules
    Mikado.scales.class_codes
    Mikado.scales.compare
    Mikado.scales.contrast
+   Mikado.scales.contrast
    Mikado.scales.resultstorer
 
 Module contents

diff --git a/docs/Library/Mikado.serializers.blast_serializer.rst b/docs/Library/Mikado.serializers.blast_serializer.rst
@@ -7,9 +7,11 @@ Submodules
 .. toctree::
    :maxdepth: 4
 
+   Mikado.serializers.blast_serializer.aln_string_parser
    Mikado.serializers.blast_serializer.aln_string_parser
    Mikado.serializers.blast_serializer.blast_serialiser
    Mikado.serializers.blast_serializer.btop_parser
+   Mikado.serializers.blast_serializer.btop_parser
    Mikado.serializers.blast_serializer.hit
    Mikado.serializers.blast_serializer.hsp
    Mikado.serializers.blast_serializer.query

diff --git a/docs/Library/Mikado.subprograms.util.rst b/docs/Library/Mikado.subprograms.util.rst
@@ -9,6 +9,7 @@ Submodules
 
    Mikado.subprograms.util.awk_gtf
    Mikado.subprograms.util.class_codes
+   Mikado.subprograms.util.collapse_compare_stats
    Mikado.subprograms.util.convert
    Mikado.subprograms.util.grep
    Mikado.subprograms.util.metrics

diff --git a/docs/Library/Mikado.transcripts.rst b/docs/Library/Mikado.transcripts.rst
@@ -15,6 +15,7 @@ Submodules
 .. toctree::
    :maxdepth: 4
 
+   Mikado.transcripts.pad
    Mikado.transcripts.reference_gene
    Mikado.transcripts.transcript
    Mikado.transcripts.transcriptchecker

diff --git a/docs/Library/Mikado.utilities.rst b/docs/Library/Mikado.utilities.rst
@@ -9,11 +9,14 @@ Submodules
 
    Mikado.utilities.dbutils
    Mikado.utilities.f1
+   Mikado.utilities.f1
    Mikado.utilities.file_type
    Mikado.utilities.intervaltree
+   Mikado.utilities.intervaltree
    Mikado.utilities.log_utils
    Mikado.utilities.namespace
    Mikado.utilities.overlap
+   Mikado.utilities.overlap
 
 Module contents
 ---------------

diff --git a/docs/References.rst b/docs/References.rst
@@ -45,4 +45,7 @@ References
 .. [BXPython]  https://bitbucket.org/james_taylor/bx-python/overview
 .. [Snakeviz]  https://jiffyclub.github.io/snakeviz/
 .. [PASA]  **Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies** Haas, B.J., Delcher, A.L., Mount, S.M., Wortman, J.R., Smith Jr, R.K., Jr., Hannick, L.I., Maiti, R., Ronning, C.M., Rusch, D.B., Town, C.D. et al. *Nucleic Acids Res*, 2003, 31, 5654-5666. doi:10.1093/nar/gkg770
-.. [GffRead] **GFF Utilities: GffRead and GffCompare** Pertea, G. and Pertea, M. *F1000*, 2020, 9, ISCB Comm J-304. doi:10.12688/f1000research.23297.2
+.. [GffRead] **GFF Utilities: GffRead and GffCompare** Pertea, G. and Pertea, M. *F1000*, 2020, 9, ISCB Comm J-304. doi:10.12688/f1000research.23297.2
+.. [Prodigal] **Prodigal: prokaryotic gene recognition and translation initiation site identification.** Hyatt, D.,
+   Chen, GL., LoCascio, P.F. et al. BMC Bioinformatics 11, 119 (2010). doi:10.1186/1471-2105-11-119
+.. [TransDecoder] https://github.com/TransDecoder/TransDecoder/wiki
diff --git a/docs/Tutorial/index.rst b/docs/Tutorial/index.rst