diff --git a/Functions.py b/Functions.py
index 923adebfc90eea1f5bd16c3476c2e4aaf2f2dd66..eed43ab2d32ce082c06fd6b65fd9e8e30805a611 100644
--- a/Functions.py
+++ b/Functions.py
@@ -2,9 +2,6 @@ from Graph_gff import Segments, Features, get_feature_start_on_segment, get_feat
global segments_on_target_genome
segments_on_target_genome={}
-global target_genome_name
-target_genome_name="CM020642.1_Azucena_chromosome10"
-target_genome_name="genome4_chr10"
# get the start position of the features on the linear genome, using their coordinates on the graph and the coordinantes of the segments on the genome
def get_feature_start_on_genome(start_seg,feat_id):
@@ -245,7 +242,7 @@ def compare_strand(list_1,list_2,list_1_unstrand,list_2_unstrand):
same_strand_count+=1
return [seg_common,same_strand_count]
-def get_feature_path(paths,first_seg,last_seg):
+def get_feature_path(paths,first_seg,last_seg,target_genome_name):
# find the path in azucena.
first_strand=convert_strand(segments_on_target_genome[first_seg][3])
first_seg_stranded=first_strand+first_seg
@@ -325,7 +322,7 @@ class Variation:
#def __str__(self):
# return f"id={self.id}, position on the original genome={self.chr}:{self.start}-{self.stop}, size={self.size}, features={self.features}"
-def create_var(feature_id,first_seg,last_seg,paths):
+def create_var(feature_id,first_seg,last_seg,paths,target_genome_name):
feature=Features[feature_id]
start_new_genome=get_feature_start_on_genome(first_seg,feature_id)
stop_new_genome=get_feature_stop_on_genome(last_seg,feature_id)
@@ -333,7 +330,7 @@ def create_var(feature_id,first_seg,last_seg,paths):
size_diff=str(size_new_genome-feature.size)
#Â get feature paths on the original genome and on the target genome
- list_segfeat_azu=get_feature_path(paths,first_seg,last_seg)
+ list_segfeat_azu=get_feature_path(paths,first_seg,last_seg,target_genome_name)
list_segfeat_nb=feature.segments_list
[list_segfeat_nb,list_segfeat_azu,inversion]=detect_gene_inversion(list_segfeat_nb,list_segfeat_azu)
diff --git a/Functions_output.py b/Functions_output.py
index 7fdfe540d0e1aaadbe305c41c2ee2b020823835d..82c6edcfa8d9bb498f0a99199eab26a80be23b79 100644
--- a/Functions_output.py
+++ b/Functions_output.py
@@ -51,7 +51,7 @@ def gff_one(first_seg,last_seg,feature_id,list_seg,max_diff):
# writes the gff of azucena using the gff of the graph
-def genome_gff(pos_seg, gff, gfa, out_once, out_detail, out_var):
+def genome_gff(pos_seg, gff, gfa, out_once, out_detail, out_var,target_genome_name):
print("generation of the genome's gff ")
#Â create variables and open files
@@ -112,7 +112,7 @@ def genome_gff(pos_seg, gff, gfa, out_once, out_detail, out_var):
# outputs the detail of variations of the feature :
if var:
- print_variations(first_seg,last_seg,feat,paths,seg_seq)
+ print_variations(first_seg,last_seg,feat,paths,seg_seq,target_genome_name)
write_line("",output_variations,True)
if stats==True:
@@ -141,10 +141,10 @@ def genome_gff(pos_seg, gff, gfa, out_once, out_detail, out_var):
# functions to get the detail of the variations in the features
-def print_variations(first_seg,last_seg,feat,paths,seg_seq):
+def print_variations(first_seg,last_seg,feat,paths,seg_seq,target_genome_name):
if (first_seg!=''): # if the feature is not completly absent # add the else, output absent features
- [variation,list_segfeat_nb,list_segfeat_azu]=create_var(feat,first_seg,last_seg,paths) # removes the strands in the segment lists
+ [variation,list_segfeat_nb,list_segfeat_azu]=create_var(feat,first_seg,last_seg,paths,target_genome_name) # removes the strands in the segment lists
feature=Features[feat]
feat_start=feature.start
# loop to go through both paths with i and j
diff --git a/main.py b/main.py
index 64ee9b29a3f8990ded5325e37d7cfabd81997723..4f1f88eeba424aa85f69f60c8e8c5f0eaae01daf 100755
--- a/main.py
+++ b/main.py
@@ -7,7 +7,53 @@ from Graph_gff import *
from Functions_output import *
#from inference import *
-run="test"
+run="command_line"
+
+if run=="command_line":
+
+ import sys
+ if not(len(sys.argv)>=4) :# intersect, gfa, pos_seg
+ print("expected input : intersect, gfa file with walks, bed file with positions of the segments on the target genome")
+ #print("output : graph gff, graph gaf, target genome gff*2+variations")
+ sys.exit(1)
+ elif (sys.argv[1]=="-h") :
+ print("expected input : intersect, gfa file with walks, bed file with positions of the segments on the target genome")
+ print("output : graph gff, graph gaf, target genome gff*2+variations")
+ sys.exit(1)
+
+ intersect=sys.argv[1]
+ gfa=sys.argv[2]
+ pos_seg=sys.argv[3]
+
+ out_gff=gfa.split("/")[-1].split(".")[0:-1][0]+".gff"
+ out_gaf=gfa.split("/")[-1].split(".")[0:-1][0]+".gaf"
+ out_once=pos_seg.split("/")[-1].split(".")[0:-1][0]+".gff"
+ out_detail=pos_seg.split("/")[-1].split(".")[0:-1][0]+"_detail.gff"
+ out_var=pos_seg.split("/")[-1].split(".")[0:-1][0]+"_variations.txt"
+ if len(sys.argv)==5:
+ target_genome_name=sys.argv[5]
+ else:
+ target_genome_name=pos_seg.split("/")[-1].split(".")[0:-1][0]
+ print(target_genome_name)
+
+
+ # input : intersect, gfa, pos_seg.
+ # out_gff, out_gaf, out_once, out_var, out_detail.
+ #Â out_gf/af = "graph.gf/af"
+ # out_once/detail: récupérer pos_seg, enlever le .bed, ajouter _detail au besoin. pareil pour var, le renommer azu_var_chr10.txt ?
+ # pos_seg.split("/")[-1].split(".")[0:-1][0]+".gff"
+
+ load_intersect(intersect)
+
+ # outputs the gff and gaf of the graph for chr10
+ graph_gff(out_gff)
+ graph_gaf(out_gaf,gfa)
+
+ # outputs the gff of a genome for the chr10
+ genome_gff(pos_seg,out_gff,gfa,out_once,out_detail,out_var,target_genome_name)
+
+
+
if run=="test":
intersect_path='/home/nina/annotpangenome/test_data/input_data_inf/intersect.bed'
@@ -27,29 +73,10 @@ if run=="test":
gff="test_data/graph.gff"
- # outputs the gff of a genome for the chr10
- genome_gff(pos_seg,gff,gfa,out_once,out_detail,out_var)
-
-
-if run=="chr3":
- intersect_path='/home/nina/annotpangenome/chr3/intersect_segments_genes_irgsp_chr3.bed'
- load_intersect(intersect_path)
-
- # outputs the gff of the graph for chr10
- output_gff='graph_chr3.gff'
- gfa="test_graph"
- graph_gff(output_gff)
-
- pos_seg="seg_coord/AzucenaRS1_chromosome3_corrected.bed"
- out_once="azucena_chr3.gff"
- out_var="variations_chr3.txt"
- out_detail="azucena_detail_chr3.gff"
-
-
- gff="graph_chr3.gff"
+ target_genome_name="genome4_chr10"
# outputs the gff of a genome for the chr10
- genome_gff(pos_seg,gff,gfa,out_once,out_detail,out_var)
+ genome_gff(pos_seg,gff,gfa,out_once,out_detail,out_var,target_genome_name)
if run=="reel":
@@ -79,8 +106,9 @@ if run=="reel":
out_var="variations_chr10.gff"
gff="graph_chr10.gff"
+ target_genome_name="CM020642.1_Azucena_chromosome10"
# outputs the gff of a genome for the chr10
- genome_gff(pos_seg,gff,gfa,out_once,out_detail,out_var)
+ genome_gff(pos_seg,gff,gfa,out_once,out_detail,out_var,target_genome_name)