Allow testing of karyotype and synteny (#661)

* remove set_usage()

* Allow testing of graphics.karyotype

* Add missing testdata files

* Test synteny as well

jcvi/apps/base.py

@@ -12,6 +12,7 @@
 import sys
 import time
 
+from argparse import ArgumentParser, SUPPRESS
 from collections.abc import Iterable
 from configparser import (
     ConfigParser,
@@ -20,14 +21,13 @@
     NoSectionError,
     ParsingError,
 )
-
-from argparse import ArgumentParser, SUPPRESS
 from http.client import HTTPSConnection
 from socket import gethostname
 from subprocess import CalledProcessError, PIPE, call, check_output
 from time import ctime
 from typing import Any, Collection, List, Optional, Tuple, Union
 from urllib.parse import urlencode
+
 from natsort import natsorted
 from rich.console import Console
 from rich.logging import RichHandler
@@ -277,7 +277,7 @@ def set_outfile(self, outfile: Optional[str] = "stdout"):
         """
         self.add_argument("-o", "--outfile", default=outfile, help="Outfile name")
 
-    def set_outdir(self, outdir="."):
+    def set_outdir(self, outdir: Optional[str] = "."):
         self.add_argument("--outdir", default=outdir, help="Specify output directory")
 
     def set_email(self):
@@ -735,7 +735,7 @@ def set_pairs(self):
         part, e.g. /1, /2, or .f, .r, default behavior is to truncate until last
         char.
         """
-        self.set_usage(self.set_pairs.__doc__)
+        self.usage = self.set_pairs.__doc__
 
         self.add_argument(
             "--pairsfile", default=None, help="Write valid pairs to pairsfile"
@@ -2225,7 +2225,7 @@ def inspect(object):
         print("{}: {}".format(k, details), file=sys.stderr)
 
 
-def sample_N(a: Collection[Any], N: int, seed: Optional[int] = None) -> List[Any]:
+def sample_N(a: Collection, N: int, seed: Optional[int] = None) -> List:
     """
     When size of N is > size of a, random.sample() will emit an error:
     ValueError: sample larger than population

jcvi/apps/fetch.py

@@ -158,7 +158,7 @@ def ensembl(args):
 
     valid_species = [x for x in ls_ftp(fasta_url) if "." not in x]
     doc = "\n".join((ensembl.__doc__, tile(valid_species)))
-    p.set_usage(doc)
+    p.usage = doc
 
     if len(args) != 1:
         sys.exit(not p.print_help())
@@ -273,15 +273,15 @@ def phytozome(args):
             downloader=downloader,
         )
         g = GlobusXMLParser(directory_listing)
-    except:
+    except Exception as _:
         logger.error("Error downloading directory listing ... cleaning up")
         cleanup(directory_listing, cookies)
         sys.exit(1)
 
     genomes = g.get_genomes()
     valid_species = genomes.keys()
     species_tile = tile(valid_species)
-    p.set_usage("\n".join((phytozome.__doc__, species_tile)))
+    p.usage = "\n".join((phytozome.__doc__, species_tile))
 
     if len(args) != 1:
         sys.exit(not p.print_help())
@@ -383,7 +383,7 @@ def phytozome9(args):
     valid_species = [x for x in ls_ftp(url) if "." not in x]
 
     doc = "\n".join((phytozome9.__doc__, tile(valid_species)))
-    p.set_usage(doc)
+    p.usage = doc
 
     if len(args) != 1:
         sys.exit(not p.print_help())

jcvi/graphics/karyotype.py

@@ -22,7 +22,7 @@
 
 import sys
 
-from typing import Optional
+from typing import List, Optional
 
 from ..apps.base import OptionParser, logger
 from ..compara.synteny import SimpleFile
@@ -408,7 +408,7 @@ def __init__(
         self.layout = layout
 
 
-def main():
+def main(args: List[str]):
     p = OptionParser(__doc__)
     p.add_argument(
         "--basepair",
@@ -441,7 +441,7 @@ def main():
         help="Style of chromosome labels",
     )
     p.set_outfile("karyotype.pdf")
-    opts, args, iopts = p.set_image_options(figsize="8x7")
+    opts, args, iopts = p.set_image_options(args, figsize="8x7")
 
     if len(args) != 2:
         sys.exit(not p.print_help())
@@ -467,6 +467,8 @@ def main():
     image_name = update_figname(opts.outfile, iopts.format)
     savefig(image_name, dpi=iopts.dpi, iopts=iopts)
 
+    return image_name
+
 
 if __name__ == "__main__":
-    main()
+    main(sys.argv[1:])

jcvi/graphics/synteny.py

@@ -18,9 +18,11 @@
 """
 
 import sys
-from typing import Optional
+
+from typing import List, Optional
 
 import numpy as np
+
 from matplotlib import transforms
 from matplotlib.path import Path
 
@@ -626,7 +628,7 @@ def draw_gene_legend(
         ax.text(xr, ytop + d / 2, "repeat", ha="center")
 
 
-def main():
+def main(args: List[str]):
     p = OptionParser(__doc__)
     p.add_argument("--switch", help="Rename the seqid with two-column file")
     p.add_argument("--tree", help="Display trees on the bottom of the figure")
@@ -684,7 +686,7 @@ def main():
         action="store_true",
         help="If set, do not exclude small features from annotation track (<1%% of region)",
     )
-    opts, args, iopts = p.set_image_options(figsize="8x7")
+    opts, args, iopts = p.set_image_options(args, figsize="8x7")
 
     if len(args) != 3:
         sys.exit(not p.print_help())
@@ -728,6 +730,8 @@ def main():
     image_name = pf + "." + iopts.format
     savefig(image_name, dpi=iopts.dpi, iopts=iopts)
 
+    return image_name
+
 
 if __name__ == "__main__":
-    main()
+    main(sys.argv[1:])

tests/graphics/__init__.py

@@ -0,0 +1 @@
+

tests/graphics/data/blocks

@@ -0,0 +1,50 @@
+GSVIVT01012261001	.
+GSVIVT01012259001	.
+GSVIVT01012258001	.
+GSVIVT01012257001	.
+GSVIVT01012255001	Prupe.1G290900.1
+GSVIVT01012253001	Prupe.1G290800.2
+GSVIVT01012252001	Prupe.1G290700.1
+GSVIVT01012250001	Prupe.1G290600.1
+GSVIVT01012249001	Prupe.1G290500.1
+GSVIVT01012248001	Prupe.1G290400.1
+GSVIVT01012247001	Prupe.1G290200.2
+GSVIVT01012246001	Prupe.1G290100.3
+GSVIVT01012245001	Prupe.1G290000.1
+GSVIVT01012244001	Prupe.1G289800.1
+GSVIVT01012243001	.
+GSVIVT01012242001	.
+GSVIVT01012241001	.
+GSVIVT01012240001	.
+GSVIVT01012239001	Prupe.1G289700.1
+GSVIVT01012238001	.
+GSVIVT01012237001	Prupe.1G289300.1
+GSVIVT01012236001	Prupe.1G289200.2
+GSVIVT01012235001	.
+GSVIVT01012234001	Prupe.1G289100.1
+GSVIVT01012233001	Prupe.1G289000.1
+GSVIVT01012232001	.
+GSVIVT01012231001	Prupe.1G288900.1
+GSVIVT01012230001	Prupe.1G288700.1
+GSVIVT01012229001	.
+GSVIVT01012228001	Prupe.1G288300.1
+GSVIVT01012227001	Prupe.1G288100.3
+GSVIVT01012226001	.
+GSVIVT01012225001	Prupe.1G288000.1
+GSVIVT01012224001	Prupe.1G287800.1
+GSVIVT01012223001	Prupe.1G287500.1
+GSVIVT01012222001	Prupe.1G287300.2
+GSVIVT01012221001	Prupe.1G287300.1
+GSVIVT01012220001	Prupe.1G287200.1
+GSVIVT01012219001	Prupe.1G286800.1
+GSVIVT01012218001	Prupe.1G286700.2
+GSVIVT01012217001	.
+GSVIVT01012216001	Prupe.1G285700.1
+GSVIVT01012215001	Prupe.1G286600.2
+GSVIVT01012214001	Prupe.1G286500.1
+GSVIVT01012213001	Prupe.1G286400.1
+GSVIVT01012212001	Prupe.1G286200.1
+GSVIVT01012211001	Prupe.1G286100.1
+GSVIVT01012210001	Prupe.1G286000.1
+GSVIVT01012209001	Prupe.1G286000.1
+GSVIVT01012208001	Prupe.1G285900.1

tests/graphics/data/blocks.layout

@@ -0,0 +1,5 @@
+# x,   y, rotation,   ha,     va,   color, ratio,            label
+0.5, 0.6,        0, left, center,       m,     1,       grape Chr1
+0.5, 0.4,        0, left, center, #fc8d62,     1, peach scaffold_1
+# edges
+e, 0, 1