update ete run scripts + misc

Author: psathyrella

bin/plot-lb-tree.py

@@ -381,7 +381,7 @@ def plot_trees(args):
 parser.add_argument('--label-root-node', action='store_true')
 parser.add_argument('--node-label-regex', help='portion of node label to keep (rest is discarded if regex is found, if no regex label is left unchanged). E.g. \'ig.\' reduces them all to the locus')
 parser.add_argument('--tree-style', default='rectangular', choices=['rectangular', 'circular'])
-parser.add_argument('--partis-dir', default=str(Path(__file__)).parent.parent), help='path to main partis install dir')
+parser.add_argument('--partis-dir', default=str(Path(__file__).parent.parent), help='path to main partis install dir')
 parser.add_argument('--log-lbr', action='store_true')
 parser.add_argument('--seq-len', type=int)
 parser.add_argument('--uid-translations', help='colon-separated list of comma-separated pairs of uid:translated-id pairs')
@@ -398,16 +398,11 @@ def plot_trees(args):
 if args.meta_info_key_to_color is None and not args.meta_info_to_emphasize:  # it'd be nice to move this stuff, but whatevs
     print('  note: if neither --meta-info-key-to-color or --meta-info-to-emphasize are set, other style attributes may not be set')
 
-sys.path.insert(1, args.partis_dir) # + '/python')
-try:
-    import partis.utils as utils
-    import partis.treeutils as treeutils
-    import partis.glutils as glutils
-    import partis.plotting as plotting
-    import partis.lbplotting as lbplotting
-except ImportError as e:
-    print(e)
-    raise Exception('couldn\'t import from main partis dir \'%s\' (set with --partis-dir)' % args.partis_dir)
+import partis.utils as utils
+import partis.treeutils as treeutils
+import partis.glutils as glutils
+import partis.plotting as plotting
+import partis.lbplotting as lbplotting
 args.meta_info_to_emphasize = utils.get_arg_list(args.meta_info_to_emphasize, key_val_pairs=True)
 args.meta_emph_formats = utils.get_arg_list(args.meta_emph_formats, key_val_pairs=True)
 utils.meta_emph_arg_process(args)

bin/test-germline-inference.py

@@ -38,7 +38,7 @@ def get_outfname(args, method, annotation_performance_plots=False, return_parent
 def simulate(args):
     if utils.output_exists(args, args.simfname):
         return
-    cmd_str = args.partis_path + ' simulate --n-sim-events ' + str(args.n_sim_events) + ' --outfname ' + args.simfname + ' --n-leaves ' + str(args.n_leaves) + ' --rearrange-from-scratch --force-dont-generate-germline-set --shm-parameter-dir ' + partis_dir + '/data/recombinator/scratch-parameters'
+    cmd_str = args.partis_path + ' simulate --n-sim-events ' + str(args.n_sim_events) + ' --outfname ' + args.simfname + ' --n-leaves ' + str(args.n_leaves) + ' --rearrange-from-scratch --force-dont-generate-germline-set --shm-parameter-dir ' + utils.get_partis_dir() + '/data/recombinator/scratch-parameters'
     cmd_str += ' --allow-nonfunctional-scratch-seqs'
     if args.n_leaf_distribution is None:
         cmd_str += ' --constant-number-of-leaves'
@@ -105,7 +105,7 @@ def run_other_method(args, method):
         cmd += ' --overwrite'
     if args.gls_gen:
         cmd += ' --gls-gen'
-        cmd += ' --glfo-dir ' + partis_dir + '/' + args.default_germline_dir  # the partis mehods have this as the default internally, but we want/have to set it explicitly here
+        cmd += ' --glfo-dir ' + utils.get_partis_dir() + '/' + args.default_germline_dir  # the partis mehods have this as the default internally, but we want/have to set it explicitly here
     else:
         cmd += ' --glfo-dir ' + args.inf_glfo_dir
     cmd += ' --simulation-germline-dir ' + args.outdir + '/germlines/simulation'  # alleleclusterer is the only one that really uses this, but for now I want its dbg output to have the sim info

partis/partitionplotter.py

@@ -2,6 +2,7 @@
 from __future__ import print_function
 import csv
 import os
+import shutil
 import math
 import numpy
 import itertools
@@ -954,7 +955,7 @@ def vmuts(vclass_muts, mutfo, uid):
             skstrs = ',  '.join('%d (%s)'%(n_skipped[k], skip_dbg_strs.get(k, k)) for k in [k for k in sorted(n_skipped) if n_skipped[k]>0])
             print('      skipped %d / %d trees (ran %d): %s' % (sum(n_skipped.values()), len(self.sclusts), len(cmdfos), skstrs))
 
-        clean_up = False
+        clean_up = True
         if len(cmdfos) > 0:
 # TODO keep all i/o files, save command line
             # sys.exit()

partis/utils.py

@@ -5278,8 +5278,8 @@ def mamba_cmds(env, only_prep=False):
 # ----------------------------------------------------------------------------------------
 def run_ete_script(sub_cmd, return_for_cmdfos=False, dryrun=False, extra_str='', debug=True):
     prof_cmds = '' #' -m cProfile -s tottime -o prof.out'
-    # xvfb_err_str = '' # '-e %s' % XXX outdir + '/xvfb-err'  # tell xvfb-run to write its error to this file (rather than its default of /dev/null). This is only errors actually from xvfb-run, e.g. xauth stuff is broken
-    cmd = '%s/bin/xvfb-run -a python3%s %s' % (get_partis_dir(), prof_cmds, sub_cmd)
+    # Use QT_QPA_PLATFORM=offscreen for PyQt5 headless rendering (no need for xvfb-run)
+    cmd = 'QT_QPA_PLATFORM=offscreen python3%s %s' % (prof_cmds, sub_cmd)
     if debug or dryrun:
         print('%s%s %s' % (extra_str, color('red', 'run'), cmd))
     if return_for_cmdfos:

setup.py

@@ -139,6 +139,7 @@ def has_ext_modules(self):
         'plotting': [
             'circlify',
             'ete3',
+            'PyQt5',
             'joypy',
             'levenshtein',
         ],

test/mobille-igblast-run.py

@@ -107,7 +107,7 @@ def convert_file(ifnfcn, ofnfcn, airr_input=False, igbl_gldir=False, plot_perfor
         if airr_input:
             cmd += ' --airr-input'
         if igbl_gldir:
-            cmd += ' --glfo-dir %s/igbl-db/fasta/partis-format-parsed --locus %s' % (args.igbdir, locus)  #  --template-glfo-dir %s/data/germlines/%s, partis_dir, args.species)  # just ran with the template set once so i could write the parsed glfo dirs
+            cmd += ' --glfo-dir %s/igbl-db/fasta/partis-format-parsed --locus %s' % (args.igbdir, locus)  #  --template-glfo-dir %s/data/germlines/%s, utils.get_partis_dir(), args.species)  # just ran with the template set once so i could write the parsed glfo dirs
         if plot_performance:
             cmd += ' --simfname %s --plotdir %s --only-csv-plots --only-plot-performance' % (simfn(locus), antn_plotdir(locus))
         cmdfos += [{