From f2324623607dc59a093fabe819ff66588c0e06ef Mon Sep 17 00:00:00 2001
From: NMarthe <nina.marthe@ird.fr>
Date: Tue, 31 Oct 2023 12:52:31 +0100
Subject: [PATCH] =?UTF-8?q?corrig=C3=A9=20la=20detection=20des=20chromosom?=
=?UTF-8?q?es?=
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---
seg_coord/getSegmentsCoordinates.py | 31 ++++++++++++++++++++++++-----
1 file changed, 26 insertions(+), 5 deletions(-)
diff --git a/seg_coord/getSegmentsCoordinates.py b/seg_coord/getSegmentsCoordinates.py
index 27c5704..3eccffa 100644
--- a/seg_coord/getSegmentsCoordinates.py
+++ b/seg_coord/getSegmentsCoordinates.py
@@ -1,6 +1,27 @@
import subprocess
import sys
+def has_numbers(inputString):
+ return any(char.isdigit() for char in inputString)
+
+def getChrName(chromosome_field):
+ chromosome_id=""
+ if has_numbers(chromosome_field):
+ for char in reversed(chromosome_field): #Â take the last digits of the field
+ if not char.isdigit():
+ break
+ else:
+ chromosome_id+=char
+ chromosome_id="Chr"+chromosome_id[::-1]
+ else:
+ for char in reversed(chromosome_field): #Â take the last uppercase chars of the fied
+ if not char.isupper():
+ break
+ else:
+ chromosome_id+=char
+ chromosome_id="Chr"+chromosome_id[::-1]
+ return chromosome_id
+
if not(len(sys.argv)==2) :
print("expected input : gfa file with walks.")
print("output : bed files giving the coordinates of the segments on the genomes (or on minigraph segments).")
@@ -38,12 +59,12 @@ walks.close()
file_names=list()
for line in lines :
line=line.split()
- name=line[1]
- chr_field=line[3].split('_')
- chromosome=chr_field[len(chr_field)-1]
+ name=line[3]
path_start=int(line[4])
+ chromosome_field=line[3]
+ chromosome_id=getChrName(chromosome_field)
- file_name=name+'_'+chromosome+'.bed'
+ file_name=name+'.bed'
# if we are writing in the file for the first time, overwrite it. else, append it
# this is because chromosomes can be fragmented. the coordinates of all the fragments from the same chromosome will be written in the same bed file.
@@ -59,7 +80,7 @@ for line in lines :
for i in range(1, len(path)): # for each segment in the path, write the position of the segment in the output bed file
# coordinates calculation : start=position, stop=position+segment_size-1, then position+=segment_size
- chr='Chr'+chromosome[len(chromosome)-2:]
+ chr='Chr'+chromosome_id[len(chromosome_id)-2:]
seg_start=position
seg_name='s'+path[i][1:]
--
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