Merge pull request #42 from moshi4/develop

Bump to v1.1.0

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "pygenomeviz"
-version = "1.0.0"
+version = "1.1.0"
 description = "A genome visualization python package for comparative genomics"
 authors = ["moshi4"]
 license = "MIT"

src/pygenomeviz/__init__.py

@@ -2,7 +2,7 @@
 
 from pygenomeviz.genomeviz import GenomeViz
 
-__version__ = "1.0.0"
+__version__ = "1.1.0"
 
 __all__ = [
     "GenomeViz",

src/pygenomeviz/align/tool/base.py

@@ -5,7 +5,6 @@
 import shlex
 import shutil
 import subprocess as sp
-import sys
 from abc import ABC, abstractmethod
 from pathlib import Path
 from typing import Sequence
@@ -121,13 +120,13 @@ def run_cmd(
             if len(stdout_lines) > 0:
                 logger.error("STDOUT:")
                 for line in stdout_lines:
-                    logger.error(line)
+                    logger.error(f"> {line}")
             stderr_lines = cmd_res.stderr.splitlines()
             if len(stderr_lines) > 0:
                 logger.error("STDERR:")
                 for line in stderr_lines:
-                    logger.error(line)
-            sys.exit(1)
+                    logger.error(f"> {line}")
+            raise RuntimeError(f"Failed to run '{self.get_tool_name()}' aligner!!")
 
     def _parse_input_gbk_seqs(
         self, seqs: Sequence[str | Path | Genbank]

src/pygenomeviz/genomeviz.py

@@ -550,6 +550,11 @@ def savefig(
             DPI
         pad_inches : float, optional
             Padding inches
+
+        Warnings
+        --------
+        To plot a figure that settings a user-defined legend, subtracks, or annotations,
+        call `fig.savefig()` instead of `gv.savefig()`.
         """
         fig = self.plotfig(dpi=dpi)
         fig.savefig(
@@ -575,7 +580,8 @@ def savefig_html(
         html_outfile : str | Path | StringIO | BytesIO
             Output HTML file (*.html)
         figure : Figure | None, optional
-            If Figure set, plot html viewer using user customized figure
+            If Figure is set, plot html viewer using user customized figure.
+            Set to output figure including user-specified legend, subtracks, etc.
         """
         # Load SVG contents
         fig = self.plotfig(fast_render=False) if figure is None else figure

src/pygenomeviz/gui/app.py

@@ -389,10 +389,10 @@
 
 with genome_info_container.form(key="form"):
     title_col, form_col = st.columns([4, 1])
-    title_col.markdown("**Genome Min-Max Range Option**")
+    title_col.markdown("**Genome Min-Max Range & Reverse Option**")
     form_col.form_submit_button(
         label="Update Figure",
-        help="Apply min-max range option changes to figure",
+        help="Apply min-max range & reverse option changes to figure",
     )
 
     name2seqid2range: dict[str, dict[str, tuple[int, int]]] = {}
@@ -401,7 +401,7 @@
         with st.expander(expander_label, expanded=False):
             seqid2range = {}
             seqid2features = gbk.get_seqid2features(None)
-            for seqid, size in gbk.get_seqid2size().items():
+            for idx, (seqid, size) in enumerate(gbk.get_seqid2size().items()):
                 range_cols = st.columns([3, 3, 1])
                 min_range = range_cols[0].number_input(
                     label=f"**{seqid}** ({size:,} bp)",
@@ -427,9 +427,19 @@
                 if min_range > max_range:
                     st.error(f"**{max_range=}** must be larger than **{min_range=}**")
                     st.stop()
-                if min_range == max_range:
-                    continue
-                seqid2range[seqid] = (min_range, max_range)
+                if min_range != max_range:
+                    seqid2range[seqid] = (min_range, max_range)
+                reverse = range_cols[2].selectbox(
+                    label="Reverse",
+                    options=[True, False],
+                    index=1,
+                    format_func=lambda b: "Yes" if b else "No",
+                    key=f"{gbk.name} {seqid} reverse",
+                )
+                if reverse is True:
+                    gbk.records[idx] = gbk.records[idx].reverse_complement(
+                        id=True, name=True, description=True
+                    )
             name2seqid2range[gbk.name] = seqid2range
 
 

src/pygenomeviz/gui/plot.py

@@ -28,8 +28,10 @@ def plot_by_gui_cfg(
 
     Returns
     -------
-    gv, align_coords : tuple[GenomeViz, list[AlignCoord]]
-        GenomeViz instance, AlignCoord list
+    gv : GenomeViz
+        GenomeViz instance
+    align_coords : list[AlignCoord]
+        AlignCoord list
     """
     # Create genomeviz instance
     gv = GenomeViz(
@@ -92,8 +94,8 @@ def plot_by_gui_cfg(
     utils.remove_old_files(gui_cache_dir)
 
     # Create md5 hash unique filename to enable cache alignment result
-    md5_hash_source = "\n".join([str(gbk) for gbk in gbk_list]).encode()
-    md5_hash_value = hashlib.md5(md5_hash_source).hexdigest()
+    md5_hash_source = "\n".join([f"{gbk} {gbk.full_genome_seq}" for gbk in gbk_list])
+    md5_hash_value = hashlib.md5(md5_hash_source.encode()).hexdigest()
     aln_coords_filename = f"{md5_hash_value}_{cfg.aln.method}.tsv"
     aln_coords_file = gui_cache_dir / aln_coords_filename.replace(" ", "")
 

src/pygenomeviz/parser/genbank.py

@@ -133,8 +133,10 @@ def calc_gc_skew(
 
         Returns
         -------
-        gc_skew_result_tuple : tuple[NDArray[np.int64], NDArray[np.float64]]
-            Position list & GC skew list
+        pos_list : NDArray[np.int64]
+            Position list
+        gc_skew_list : NDArray[np.float64]
+            GC skew list
         """
         pos_list, gc_skew_list = [], []
         seq = self.genome_seq if seq is None else seq
@@ -185,8 +187,10 @@ def calc_gc_content(
 
         Returns
         -------
-        gc_content_result_tuple : tuple[NDArray[np.int64], NDArray[np.float64]]
-            Position list & GC content list
+        pos_list : NDArray[np.int64]
+            Position list
+        gc_content_list : NDArray[np.float64]
+            GC content list
         """
         pos_list, gc_content_list = [], []
         seq = self.genome_seq if seq is None else seq

src/pygenomeviz/parser/gff.py

@@ -259,8 +259,12 @@ def _parse_gff(
 
         Returns
         -------
-        gff_records, start, end : tuple[list[GffRecord], int, int]
-            GFF record list, start, end
+        gff_records : list[GffRecord]
+            GFF record list
+        start : int
+            Start position of target_seqid record
+        end : int
+            End position of target_seqid record
         """
         gff_file = Path(gff_file)
         if gff_file.suffix == ".gz":
@@ -296,8 +300,12 @@ def _parse_gff_textio(
 
         Returns
         -------
-        gff_records, start, end : tuple[list[GffRecord], int, int]
-            GFF record list, start, end
+        gff_records : list[GffRecord]
+            GFF record list
+        start : int
+            Start position of target_seqid record
+        end : int
+            End position of target_seqid record
         """
         # Parse GFF lines
         gff_all_lines = handle.read().splitlines()

src/pygenomeviz/track/feature.py

@@ -833,8 +833,10 @@ def _extract_exon_intron_locs(
 
         Returns
         -------
-        exon_locs, intron_locs : tuple[list[tuple[int, int]], list[tuple[int, int]]]
-            Exon & intron locations
+        exon_locs : list[tuple[int, int]]
+            Exon locations
+        intron_locs : list[tuple[int, int]]
+            Intron locations
         """
         exon_locs: list[tuple[int, int]] = []
         intron_locs: list[tuple[int, int]] = []

src/pygenomeviz/utils/download.py

@@ -69,7 +69,7 @@ def load_example_genbank_dataset(
 ) -> list[Path]:
     """Load pygenomeviz example genbank dataset
 
-    Load genbank datasets from https://github.com/moshi4/pygenomeviz-data-v1
+    Load genbank datasets from <https://github.com/moshi4/pygenomeviz-data-v1>
     and cache datasets in local directory (Default: `~/.cache/pygenomeviz/`).
 
     List of dataset name
@@ -137,7 +137,7 @@ def load_example_gff_file(
 ) -> Path:
     """Load pygenomeviz example GFF file
 
-    Load example GFF file from https://github.com/moshi4/pygenomeviz-data-v1/
+    Load example GFF file from <https://github.com/moshi4/pygenomeviz-data-v1/>
     and cache GFF file in local directory (Default: `~/.cache/pygenomeviz/`).
 
     List of example GFF filename