diff --git a/README.md b/README.md index ac7b155..c31499e 100644 --- a/README.md +++ b/README.md @@ -352,7 +352,7 @@ Multiple distinct variant sequences and reference contexts can generate the same * [IsovarResult](https://github.com/openvax/isovar/blob/master/isovar/isovar_result.py): Since a single variant locus might have reads which assemble into multiple incompatible coding sequences, an `IsovarResult` represents a variant and one or more `ProteinSequence` objects which are associated with it. We typically don't want to deal with *every* possible translation of *every* distinct sequence detected around a variant, so the protein sequences are sorted by their number of supporting fragments and the best protein sequence is made easy to access. The `IsovarResult` object also has many informative properties such `num_alt_fragments`, `fraction_ref_reads`, &c. - +![](isovar_design.png) ## Other Isovar Commandline Tools diff --git a/isovar/protein_sequence_helpers.py b/isovar/protein_sequence_helpers.py index c71bc2d..104370c 100644 --- a/isovar/protein_sequence_helpers.py +++ b/isovar/protein_sequence_helpers.py @@ -43,8 +43,7 @@ def sort_protein_sequences(protein_sequences): def group_equivalent_translations(translations): """ Convert a list of Translation objects into a (potentially smaller) list - of ProteinSequence objects by grouping the - equivalent amino acid sequences. + of ProteinSequence objects by grouping the equivalent amino acid sequences. Parameters ---------- diff --git a/isovar/read_collector.py b/isovar/read_collector.py index d4fec35..afb8bad 100644 --- a/isovar/read_collector.py +++ b/isovar/read_collector.py @@ -33,7 +33,7 @@ class ReadCollector(object): """ - ReadCreator holds options related to extracting reads from SAM/BAM alignment files + ReadCollector holds options related to extracting reads from SAM/BAM alignment files and provides methods for different ways to create LocusRead objects. """ def __init__( diff --git a/isovar_design.png b/isovar_design.png new file mode 100644 index 0000000..f4ec98b Binary files /dev/null and b/isovar_design.png differ