fix bug for sep '|'

soi/OrthoFinder.py

@@ -1758,7 +1758,7 @@ def species_specific_genes(OFdir, sp, outTsv, ex_sps=[]):
 	print('\t'.join(['gene', 'group']), file=outTsv)
 	d_genes = result.get_species_specific2(sp, ex_sps)
 	for gene, group in sorted(d_genes.items()):
-		print('\t'.join([gene.split('|')[1], str(group)]), file=outTsv)
+		print('\t'.join([gene.split('|', 1)[1], str(group)]), file=outTsv)
 
 def bootstrap_species_tree(OFdir, outdir, bootstrap=1000, iqtree_options='-mset JTT'):
 	'''重新用iqtree建树'''
@@ -1878,7 +1878,7 @@ def gene_format_common(gene):
 	if not '|' in gene:
 		sp, g = None, gene
 		return (sp, g)
-	sp, g = gene.split('|')
+	sp, g = gene.split('|', 1)
 	sp1 = sp[:len(sp)/2]
 	sp2 = sp[len(sp)/2+1:]
 	if sp1 == sp2:
@@ -2123,7 +2123,7 @@ def og2gene(OFdir, oglist, outsv, species=None):
 		if not og in oglist:
 			continue
 		for gene in group.get_group(sps=species):
-			gene = gene.split('|')[-1]
+			gene = gene.split('|', 1)[-1]
 			line = [gene, og] #+ group.raw_genes
 			print('\t'.join(line), file=outsv)
 def classify_genes(OFdir, outsv=sys.stdout, species=None):
@@ -2135,7 +2135,7 @@ def add_og(OFdir, richfile, outrichfile):
 	for group in OrthoFinder(OFdir).orthogroups:
 		og = group.ogid
 		for gene in group.get_group():
-			gene = gene.split('|')[-1]
+			gene = gene.split('|', 1)[-1]
 			d_genes[gene] = og
 
 	for i, line in enumerate(open(richfile)):

soi/mcscan.py

@@ -576,7 +576,7 @@ def gene_pairs(self):
 	def gene_genes(self):
 		return [list(map(self.gene2geneid, genes)) for genes in self.genes]
 	def gene2geneid(self, gene):
-		return gene.split('|')[1]
+		return gene.split('|', 1)[1]
 	def parse_genes(self, genes1,genes2):
 		self.pairs = list(zip(genes1,genes2))
 		self.ks = []
@@ -768,7 +768,7 @@ def anchors2bed(collinearity, gff, chrmap, left_anchors, right_anchors, outbed=s
 		g2_range = '{}-{}'.format(left_g2.raw_gene, right_g2.raw_gene)
 		g1_range = '{}-{}'.format(left_g1.raw_gene, right_g1.raw_gene)
 		id = '{}:{}:{}'.format(sp2, g2_range, g1_range)
-		line = [chr2.split('|')[-1], g2_start-1, g2_end, id, sp2, ]
+		line = [chr2.split('|', 1)[-1], g2_start-1, g2_end, id, sp2, ]
 		line = list(map(str, line))
 		print('\t'.join(line), file=outbed)
 		left_gs.add(left_g1)
@@ -778,7 +778,7 @@ def anchors2bed(collinearity, gff, chrmap, left_anchors, right_anchors, outbed=s
 	left_g1, left_g2 = min(left_gs, key=lambda x:x.start), max(right_gs, key=lambda x:x.end)
 	g1_chr, g1_start, g1_end = left_g1.chr, left_g1.start, right_g1.end
 	id = '{}:{}'.format(anchor_sp, g1_range)
-	line = [anchor_chr.split('|')[-1], g1_start-1, g1_end, id, anchor_sp, ]
+	line = [anchor_chr.split('|', 1)[-1], g1_start-1, g1_end, id, anchor_sp, ]
 	line = list(map(str, line))
 	print('\t'.join(line), file=outbed)