added a check that the sourge and target genome names are found in the walks/paths of the graph

GrAnnoT/argparser.py

@@ -87,6 +87,23 @@ def read_args(args):
         sys.exit(f"grannot: error: one of the following options is required for the option -id/--identity : -ann/--annotation, -aln/--alignment, -var/--variation")
     # todo : adapt pav to have the same requirements as cov and id, or no requirement at all. change in grannot_help.md
 
+    # convert input files in Path objects
+    args.outdir=Path(args.outdir).resolve() # resolve() finds the absolute path, and adds the '/' if needed
+    seg_coord_path=Path(args.segment_coordinates_path).resolve()
+    args.graph=Path(args.graph.name).resolve()
+    args.gff=Path(args.gff.name).resolve()
+
+    # check if source and target genomes are in the graph
+    walks_list = os.popen(f"grep ^W {args.graph.as_posix()} | cut -f 2 | grep -v 'MINIGRAPH'").read().split('\n')
+    paths_list = os.popen(f"grep ^P {args.graph.as_posix()} | cut -f 2").read().split('\n')
+    if len(paths_list)!=0:
+        genome_list_path=set([elem.split('#')[0] for elem in paths_list] + walks_list)
+    if args.source_genome not in genome_list_path:
+        sys.exit(f"grannot: error: the source genome given was not found in the graph")
+    for target_genome in args.target[:]:
+        if target_genome not in genome_list_path:
+            sys.exit(f"grannot: error: a target genome given was not found in the graph")
+
     # check bedtools installation
     bedtools_test=subprocess.run("bedtools --version",shell=True,check=False,stdout=subprocess.DEVNULL,stderr=sys.stderr)
     if int(bedtools_test.returncode)>0:
@@ -102,12 +119,6 @@ def read_args(args):
     if args.coverage==None:
         args.coverage=80
 
-    # convert input files in Path objects
-    args.outdir=Path(args.outdir).resolve() # resolve() finds the absolute path, and adds the '/' if needed
-    seg_coord_path=Path(args.segment_coordinates_path).resolve()
-    args.graph=Path(args.graph.name).resolve()
-    args.gff=Path(args.gff.name).resolve()
-
     # run getSegCoord on the target genomes + the source genome if needed
     if not(args.annotation or args.variation or args.alignment or args.pav_matrix): # if we only need the graph annotation, no need to get SegCoord for all the genomes
         path_list=[]
@@ -147,7 +158,7 @@ def run_intersect(args,seg_coord_path):
             first_source_haplo=min(source_haplotypes)
             args.source_haplotype=first_source_haplo
             haplo=f"#{first_source_haplo}#"
-            print('\033[35m'+f'Warning : No source haplotype was given with \'-sh\'. Haplotype {first_source_haplo} will be used.''\033[0m')
+            print('\033[35m'+f'Warning : No source haplotype was given with \'-sh\'. Haplotype {first_source_haplo} will be used.'+'\033[0m')
             files=list(seg_coord_path.glob(f"*{args.source_genome}*{haplo}*.bed")) # get all bed files from the source genome haplotype in seg_coord
             message=f'No bed files corresponding to the source genome haplotype {first_source_haplo} found in {seg_coord_path}'
         else:
@@ -160,7 +171,7 @@ def run_intersect(args,seg_coord_path):
             print(f'     Found {len(files)} paths corresponding to the source genome haplotype {args.source_haplotype}')
     else:
         files=list(seg_coord_path.glob(f"*{args.source_genome}*.bed")) # get all bed files from the source genome in seg_coord
-        message=f'No bed files corresponding to the source genome found in {seg_coord_path}'
+        message='\33[31m'+f'Error : No bed files corresponding to the source genome found in {seg_coord_path}. Please check that the source genome name is right.'+'\033[0m'
         if len(files)==0:
             sys.exit(message)
         if args.verbose: