use xopen

zhangrengang · Mar 12, 2022 · 8afe8ce · 8afe8ce
1 parent 87c66f0
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diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -26,7 +26,7 @@ jobs:
         conda-channels: bioconda
     # install dependencies
     - run: conda install biopython
-    - run: conda install pp
+    - run: conda install xopen
     - run: conda install hmmer
     - run: conda install blast
 

diff --git a/README.md b/README.md
@@ -216,7 +216,7 @@ mafft --auto rice6.9.5.liban.rexdb.cls.pep.INT_TPase.faa > rice6.9.5.liban.rexdb
 ```
 Note: the domain names between rexdb and gydb are different: PROT (rexdb) = AP (gydb), RH (rexdb) = RNaseH (gydb). You should use the actual domain name.
 
-Here, a R script (depending on [ggtree](https://yulab-smu.top/treedata-book/)) is provided to fast visualize the LTR tree. An example in `example_data/`:
+Here, an R script (depending on [ggtree](https://yulab-smu.top/treedata-book/)) is provided to fast visualize the LTR tree. An example in `example_data/`:
 ```
 ../scripts/LTR_tree.R rice6.9.5.liban.rexdb.cls.pep_RT_RH_INT.aln.treefile rice6.9.5.liban.rexdb.cls.tsv rice6.9.5.liban.rexdb.cls.pep_RT_RH_INT.aln.treefile.png
 ```

diff --git a/TEsorter/app.py b/TEsorter/app.py
@@ -14,7 +14,6 @@
 import itertools
 from collections import Counter, OrderedDict
 from Bio import SeqIO
-from xopen import xopen as open
 import logging
 logging.basicConfig(level = logging.INFO,format = '%(asctime)s -%(levelname)s- %(message)s')
 logger = logging.getLogger(__name__)
@@ -30,6 +29,9 @@
 # for multi-processing HMMScan
 from .modules.RunCmdsMP import run_cmd, pp_run, pool_func
 from .modules.split_records import split_fastx_by_chunk_num, cut_seqs
+#from .modules.small_tools import open_file as open
+from xopen import xopen as open
+
 # for pass-2 blast classifying
 from .modules.get_record import get_records
 from TEsorter.version import __version__
@@ -122,10 +124,10 @@ def Args():
 					default=False,
 					help="input is genome sequences [default=%(default)s]")
 	group_genome.add_argument("-win_size",  action="store",
-					default=int(1e6), type=int,
+					default=int(270e3), type=int,
 					help="window size of chunking genome sequences [default=%(default)s]")
 	group_genome.add_argument("-win_ovl",  action="store",
-					default=int(1e5), type=int,
+					default=int(30e3), type=int,
 					help="overlap size of windows [default=%(default)s]")
 
 	args = parser.parse_args()
@@ -178,6 +180,8 @@ def pipeline(args):
 
 	if args.genome:
 		logger.info( 'Start identifying pipeline (GENOME mode)' )
+		#print(open(args.sequence))
+		#print([(rc.id, len(rc.seq)) for rc in SeqIO.parse(open(args.sequence), 'fasta')])
 		seq_type = 'nucl'
 		genomeAnn(genome=args.sequence, 
 			window_size=args.win_size, window_ovl=args.win_ovl, 
@@ -1055,7 +1059,7 @@ def hmmscan_pp(inSeq, hmmdb='rexdb.hmm', hmmout=None, tmpdir='./tmp', processors
 		hmmout = prefix + '.domtbl'
 	overwrite = not (os.path.exists(hmmout) and os.path.getsize(hmmout) >0) or force_write_hmmscan
 
-	chunk_prefix = '{}/{}'.format(tmpdir, 'chunk_aaseq')
+	chunk_prefix = '{}/{}'.format(tmpdir, 'chunk')
 	if processors > 1:
 		chunk_num = processors*2
 		_, _, _, chunk_files = split_fastx_by_chunk_num(

diff --git a/TEsorter/modules/split_records.py b/TEsorter/modules/split_records.py
@@ -6,7 +6,9 @@
 from io import IOBase
 from Bio import SeqIO
 
-from TEsorter.modules.small_tools import open_file as open
+#from TEsorter.modules.small_tools import open_file as open
+#from .small_tools import open_file as open
+from xopen import xopen as open
 
 __version__ = '1.0'
 def split_sam_by_chunk_size(inSam, prefix, chunk_size):
@@ -205,8 +207,9 @@ def split_fastx_by_chunk_num(inFastx, prefix, chunk_num, seqfmt, suffix):
 	return (i, chunk_num, i/chunk_num, outfiles)
 def cut_seqs(inSeq, outSeq, window_size=500000, window_ovl=100000, seqfmt='fasta'):
 	window_size, window_ovl = int(window_size) ,int(window_ovl)
-	for rc in SeqIO.parse(inSeq, seqfmt):
+	for rc in SeqIO.parse(open(inSeq), seqfmt):
 		seq_len = len(rc.seq)
+	#	print(rc.id, seq_len)
 		for s in range(0, seq_len+1, window_size):
 			e = s + window_size + window_ovl
 			if e > seq_len:

diff --git a/TEsorter/modules/translate_seq.py b/TEsorter/modules/translate_seq.py
@@ -3,7 +3,6 @@
 from collections import OrderedDict
 from Bio import SeqIO
 from Bio.Data import CodonTable
-from xopen import xopen as open
 
 def six_frame_translate(inFa, fout=sys.stdout, seqfmt='fasta', transl_table=1):
 	d_length = OrderedDict()

diff --git a/TEsorter/test/rice6.9.5.liban.rexdb.cls.lib b/TEsorter/test/rice6.9.5.liban.rexdb.cls.lib
diff --git a/TEsorter/test/rice6.9.5.liban.rexdb.cls.pep b/TEsorter/test/rice6.9.5.liban.rexdb.cls.pep
diff --git a/TEsorter/test/rice6.9.5.liban.rexdb.cls.tsv b/TEsorter/test/rice6.9.5.liban.rexdb.cls.tsv
@@ -12,7 +12,7 @@ Os0035#DNAauto/MULE	TIR	MuDR_Mutator	unknown	unknown	+	TPase|MuDR_Mutator
 Os0039_INT_RIRE3#LTR/Gypsy	LTR	Gypsy	Tekay	yes	+	GAG|Tekay PROT|Tekay RT|Tekay RH|Tekay INT|Tekay CHD|Tekay
 Os0040_INT#LTR/Gypsy	LTR	Gypsy	Retand	no	+	GAG|Retand PROT|Retand RH|Retand INT|Retand
 Os0041_INT#LTR/Copia	LTR	Copia	Ale	no	+	INT|Ale RT|Ale RH|Ale
-Os0044#LINE/unknown	LINE	unknown	unknown	unknown	+	ENDO|LINE RT|LINE
+Os0044#LINE/unknown	LINE	unknown	unknown	unknown	+	RT|LINE
 Os0052#DNAauto/CACTA	TIR	EnSpm_CACTA	unknown	unknown	+	TPase|EnSpm_CACTA
 Os0057_INT#LTR/Copia	LTR	Copia	SIRE	yes	+	GAG|SIRE PROT|SIRE INT|SIRE RT|SIRE RH|SIRE
 Os0058_INT#LTR/Gypsy	LTR	Gypsy	Reina	yes	+	GAG|Reina PROT|Reina RT|Reina RH|Reina INT|Reina CHD|Reina
@@ -48,7 +48,7 @@ Os0157_INT#LTR/Gypsy	LTR	Gypsy	Tekay	yes	+	GAG|Tekay PROT|Tekay RT|Tekay RH|Teka
 Os0158_INT#LTR/Gypsy	LTR	Gypsy	Retand	no	+	GAG|Retand
 Os0159_INT#LTR/Gypsy	LTR	Gypsy	Reina	no	+	GAG|Reina PROT|Reina CHD|Reina
 Os0160_INT#LTR/Copia	LTR	Copia	Ivana	yes	+	GAG|Ivana PROT|Ivana INT|Ivana RT|Ivana RH|Ivana
-Os0162_INT#LTR/Gypsy	LTR	Gypsy	Athila	no	+	GAG|Athila RT|Athila RH|Athila INT|Athila
+Os0162_INT#LTR/Gypsy	LTR	Gypsy	Athila	yes	+	GAG|Athila PROT|Athila RT|Athila RH|Athila INT|Athila
 Os0168_INT#LTR/Copia	LTR	Copia	Ale	yes	+	GAG|Ale PROT|Ale INT|Ale RT|Ale RH|Ale
 Os0170_INT#LTR/Gypsy	LTR	Gypsy	Reina	yes	+	GAG|Reina PROT|Reina RT|Reina RH|Reina INT|Reina CHD|Reina
 Os0171_INT#LTR/Copia	LTR	Copia	SIRE	no	+	GAG|SIRE
@@ -88,6 +88,7 @@ Os0267_INT#LTR/Gypsy	LTR	Gypsy	Reina	yes	+	GAG|Reina PROT|Reina RT|Reina RH|Rein
 Os0268_INT#LTR/Gypsy	LTR	Gypsy	Retand	no	+	GAG|Retand
 Os0272_INT#LTR/Gypsy	LTR	Gypsy	Reina	yes	+	GAG|Reina PROT|Reina RT|Reina RH|Reina INT|Reina CHD|Reina
 Os0272_LTR#LTR/Gypsy	LTR	Gypsy	chromo-unclass	no	-	CHD|chromo-unclass
+Os0273_INT#LTR/Copia	LTR	Copia	Ale	no	+	GAG|Ale
 Os0274_INT#LTR/Gypsy	LTR	Gypsy	CRM	no	+	GAG|CRM
 Os0278_INT#LTR/Gypsy	LTR	Gypsy	CRM	yes	+	GAG|CRM PROT|CRM RT|CRM RH|CRM INT|CRM
 Os0278_LTR#LTR/Gypsy	LTR	Gypsy	CRM	no	+	CHDCR|CRM
@@ -101,6 +102,7 @@ Os0294#DNAauto/CACTG	TIR	EnSpm_CACTA	unknown	unknown	+	TPase|EnSpm_CACTA
 Os0295_INT#LTR/Gypsy	LTR	Gypsy	Reina	yes	+	GAG|Reina PROT|Reina RT|Reina RH|Reina INT|Reina CHD|Reina
 Os0305_INT#LTR/Gypsy	LTR	Gypsy	Reina	yes	+	GAG|Reina PROT|Reina RT|Reina RH|Reina INT|Reina CHD|Reina
 Os0311_INT#LTR/Gypsy	LTR	Gypsy	CRM	yes	+	GAG|CRM PROT|CRM RT|CRM RH|CRM INT|CRM
+Os0311_LTR#LTR/Gypsy	LTR	Gypsy	CRM	no	+	CHDCR|CRM
 Os0316_INT#LTR/Gypsy	LTR	Gypsy	Reina	yes	+	GAG|Reina PROT|Reina RT|Reina RH|Reina INT|Reina CHD|Reina
 Os0321_INT#LTR/Copia	LTR	Copia	Ale	yes	+	GAG|Ale PROT|Ale INT|Ale RT|Ale RH|Ale
 Os0322_INT#LTR/Gypsy	LTR	Gypsy	Retand	no	+	GAG|Retand RT|Retand aRH|Retand INT|Retand
@@ -145,7 +147,8 @@ Os0592_INT#LTR/Copia	LTR	Copia	TAR	yes	+	GAG|TAR PROT|TAR INT|TAR RT|TAR RH|TAR
 Os0618#LINE/unknown	LINE	unknown	unknown	unknown	+	ENDO|LINE RT|LINE RH|LINE
 Os0632_INT#LTR/Gypsy	LTR	Gypsy	Retand	yes	+	GAG|Retand PROT|Retand RT|Retand RH|Retand INT|Retand
 Os0651#LINE/unknown	LINE	unknown	unknown	unknown	+	ENDO|LINE RT|LINE
-Os0656_INT#LTR/Copia	LTR	Copia	SIRE	no	+	GAG|SIRE
+Os0652#LINE/unknown	LINE	unknown	unknown	unknown	+	RT|LINE
+Os0656_INT#LTR/Copia	LTR	Copia	Ale	no	+	GAG|Ale
 Os0678#DNAauto/POLE	TIR	PIF_Harbinger	unknown	unknown	+	TPase|PIF_Harbinger
 Os0681#DNAauto/CACTA	TIR	EnSpm_CACTA	unknown	unknown	+	TPase|EnSpm_CACTA
 Os0699_INT#LTR/Copia	LTR	Copia	Ale	yes	+	GAG|Ale PROT|Ale INT|Ale RT|Ale RH|Ale
@@ -226,6 +229,7 @@ Os1300_INT#LTR/Gypsy	LTR	Gypsy	Reina	yes	+	GAG|Reina PROT|Reina RT|Reina RH|Rein
 Os1309#DNAauto/MULE	TIR	MuDR_Mutator	unknown	unknown	+	TPase|MuDR_Mutator
 Os1322#DNAnona/MULE	TIR	MuDR_Mutator	unknown	unknown	+	TPase|MuDR_Mutator
 Os1335_INT#LTR/Gypsy	LTR	Gypsy	Retand	yes	+	GAG|Retand PROT|Retand RT|Retand RH|Retand INT|Retand
+Os1337_LTR#LTR/Gypsy	LTR	Gypsy	CRM	no	+	CHDCR|CRM
 Os1347_IC#DNAauto/Helitron	Helitron	unknown	unknown	unknown	+	HEL2|Helitron
 Os1353_INT#LTR/Gypsy	LTR	Gypsy	Retand	yes	+	GAG|Retand PROT|Retand RT|Retand RH|Retand INT|Retand
 Os1396#DNAnona/MULE	TIR	MuDR_Mutator	unknown	unknown	+	TPase|MuDR_Mutator
@@ -304,10 +308,10 @@ Os2253_INT#LTR/Gypsy	LTR	Gypsy	Reina	yes	+	GAG|Reina PROT|Reina RT|Reina RH|Rein
 Os2256_INT#LTR/Copia	LTR	Copia	Ale	no	+	PROT|Ale INT|Ale RT|Ale RH|Ale
 Os2270#DNAauto/MULE	TIR	MuDR_Mutator	unknown	unknown	+	TPase|MuDR_Mutator
 Os2274#DNAauto/MULE	TIR	MuDR_Mutator	unknown	unknown	-	TPase|MuDR_Mutator
-Os2280_INT#LTR/Gypsy	LTR	Gypsy	Retand	no	+	GAG|Retand PROT|Retand RT|Retand INT|Retand
+Os2280_INT#LTR/Gypsy	LTR	Gypsy	Retand	yes	+	GAG|Retand PROT|Retand RT|Retand RH|Retand INT|Retand
 Os2298_INT#LTR/Gypsy	LTR	Gypsy	Reina	yes	+	GAG|Reina PROT|Reina RT|Reina RH|Reina INT|Reina CHD|Reina
 Os2307#DNAauto/MULE	TIR	MuDR_Mutator	unknown	unknown	+	TPase|MuDR_Mutator
-Os2312#DNAauto/Helitron	Helitron	unknown	unknown	unknown	-	HEL2|Helitron
+Os2312#DNAauto/Helitron	Helitron	unknown	unknown	unknown	-	HEL1|Helitron HEL2|Helitron
 Os2326_INT#LTR/Copia	LTR	Copia	Ivana	no	+	GAG|Ivana
 Os2344_LTR#LTR/Gypsy	LTR	Gypsy	CRM	no	+	CHDCR|CRM
 Os2371_INT#LTR/Copia	LTR	Copia	Ale	yes	+	GAG|Ale PROT|Ale INT|Ale RT|Ale RH|Ale
@@ -316,7 +320,6 @@ Os2453#DNAauto/MULE	TIR	MuDR_Mutator	unknown	unknown	+	TPase|MuDR_Mutator
 Os2475_INT#LTR/Gypsy	LTR	Gypsy	Tekay	no	+	GAG|Tekay
 Os2480#DNAauto/CACTA	TIR	EnSpm_CACTA	unknown	unknown	-	TPase|EnSpm_CACTA
 Os2530#DNAnona/hAT	TIR	hAT	unknown	unknown	+	TPase|hAT
-Os2577_INT#LTR/Gypsy	LTR	Gypsy	Ogre	no	+	aRH|Ogre
 Os2585#DNAauto/MULE	TIR	MuDR_Mutator	unknown	unknown	+	TPase|MuDR_Mutator
 Os2618_INT#LTR/Copia	LTR	Copia	Ivana	no	+	GAG|Ivana
 Os2623#DNAauto/MULE	TIR	MuDR_Mutator	unknown	unknown	-	TPase|MuDR_Mutator
@@ -331,6 +334,7 @@ Os2830_INT#LTR/Gypsy	LTR	Gypsy	Athila	no	+	GAG|Athila
 Os2835#DNAauto/MULE	TIR	MuDR_Mutator	unknown	unknown	-	TPase|MuDR_Mutator
 Os2840_INT#LTR/Copia	LTR	Copia	TAR	yes	+	GAG|TAR PROT|TAR INT|TAR RT|TAR RH|TAR
 Os2911_INT#LTR/Copia	LTR	Copia	Bianca	no	+	GAG|Bianca INT|Bianca RT|Bianca RH|Bianca
+Os2941#DNAauto/MULE	TIR	MuDR_Mutator	unknown	unknown	+	TPase|MuDR_Mutator
 Os2947_ICL#DNAnona/hAT	TIR	hAT	unknown	unknown	+	TPase|hAT
 Os2997#LINE/unknown	LINE	unknown	unknown	unknown	+	ENDO|LINE RT|LINE
 Os3087_INT#LTR/Gypsy	LTR	Gypsy	CRM	no	+	GAG|CRM
@@ -361,6 +365,7 @@ Os3265#DNAauto/MLE	TIR	Tc1_Mariner	unknown	unknown	+	TPase|Tc1_Mariner
 Os3267#DNAauto/MLE	TIR	Tc1_Mariner	unknown	unknown	+	TPase|Tc1_Mariner
 Os3268#DNAauto/MLE	TIR	Tc1_Mariner	unknown	unknown	+	TPase|Tc1_Mariner
 Os3280#DNAauto/CACTA	TIR	EnSpm_CACTA	unknown	unknown	+	TPase|EnSpm_CACTA
+Os3281#DNAauto/hAT	TIR	hAT	unknown	unknown	+	TPase|hAT
 Os3285#DNAauto/CACTA	TIR	EnSpm_CACTA	unknown	unknown	-	TPase|EnSpm_CACTA
 Os3287#DNAauto/hAT	TIR	hAT	unknown	unknown	+	TPase|hAT
 Os3290_INT#LTR/Gypsy	LTR	Gypsy	Reina	yes	+	GAG|Reina PROT|Reina RT|Reina RH|Reina INT|Reina CHD|Reina
@@ -389,7 +394,7 @@ Os3312_INT#LTR/Gypsy	LTR	Gypsy	CRM	yes	+	GAG|CRM PROT|CRM RT|CRM RH|CRM INT|CRM
 Os3312_LTR#LTR/Gypsy	LTR	Gypsy	CRM	no	+	CHDCR|CRM
 Os3313_INT#LTR/Gypsy	LTR	Gypsy	Reina	yes	+	GAG|Reina PROT|Reina RT|Reina RH|Reina INT|Reina CHD|Reina
 Os3314_INT#LTR/Gypsy	LTR	Gypsy	Reina	yes	+	GAG|Reina PROT|Reina RT|Reina RH|Reina INT|Reina CHD|Reina
-Os3315_INT#LTR/Gypsy	LTR	Gypsy	Reina	no	+	GAG|Reina PROT|Reina RT|Reina RH|Reina CHD|Reina
+Os3315_INT#LTR/Gypsy	LTR	Gypsy	Reina	yes	+	GAG|Reina PROT|Reina RT|Reina RH|Reina INT|Reina CHD|Reina
 Os3316_INT#LTR/Gypsy	LTR	Gypsy	Reina	yes	+	GAG|Reina PROT|Reina RT|Reina RH|Reina INT|Reina CHD|Reina
 Os3317_INT#LTR/Gypsy	LTR	Gypsy	Reina	yes	+	GAG|Reina PROT|Reina RT|Reina RH|Reina INT|Reina CHD|Reina
 Os3318_INT#LTR/Copia	LTR	Copia	Ale	yes	+	GAG|Ale PROT|Ale INT|Ale RT|Ale RH|Ale
@@ -435,7 +440,7 @@ Os3383#DNAauto/MULE	TIR	MuDR_Mutator	unknown	unknown	+	TPase|MuDR_Mutator
 Os3384#DNAauto/MULE	TIR	MuDR_Mutator	unknown	unknown	-	TPase|MuDR_Mutator
 Os3385#DNAauto/MULE	TIR	MuDR_Mutator	unknown	unknown	+	TPase|MuDR_Mutator
 Os3386#DNAauto/MULE	TIR	MuDR_Mutator	unknown	unknown	-	TPase|MuDR_Mutator
-Os3387#DNAauto/MULE	mixture	mixture	unknown	unknown	-	TPase|MuDR_Mutator CHDCR|CRM
+Os3387#DNAauto/MULE	TIR	MuDR_Mutator	unknown	unknown	-	TPase|MuDR_Mutator
 Os3388#DNAauto/MULE	TIR	MuDR_Mutator	unknown	unknown	+	TPase|MuDR_Mutator
 Os3389#DNAauto/MULE	TIR	MuDR_Mutator	unknown	unknown	+	TPase|MuDR_Mutator
 Os3390#DNAauto/MULE	TIR	MuDR_Mutator	unknown	unknown	+	TPase|MuDR_Mutator
@@ -467,7 +472,7 @@ Os3449_INT#LTR/Gypsy	LTR	Gypsy	Reina	yes	+	GAG|Reina PROT|Reina RT|Reina RH|Rein
 Os3450_INT#LTR/Copia	LTR	Copia	Ale	yes	+	GAG|Ale PROT|Ale INT|Ale RT|Ale RH|Ale
 Os3451_INT#LTR/Copia	LTR	Copia	Ale	no	+	GAG|Ale PROT|Ale RT|Ale RH|Ale
 Os3452_INT#LTR/Gypsy	LTR	Gypsy	Reina	yes	+	GAG|Reina PROT|Reina RT|Reina RH|Reina INT|Reina CHD|Reina
-Os3453_INT#LTR/Gypsy	LTR	Gypsy	Reina	no	+	GAG|Reina PROT|Reina RT|Reina RH|Reina CHD|Reina
+Os3453_INT#LTR/Gypsy	LTR	Gypsy	Reina	yes	+	GAG|Reina PROT|Reina RT|Reina RH|Reina INT|Reina CHD|Reina
 Os3454_INT#LTR/Copia	LTR	Copia	Ivana	no	+	GAG|Ivana RT|Ivana RH|Ivana
 Os3455_INT#LTR/Gypsy	LTR	Gypsy	Reina	yes	+	GAG|Reina PROT|Reina RT|Reina RH|Reina INT|Reina CHD|Reina
 Os3456_INT#LTR/Gypsy	LTR	Gypsy	Reina	yes	+	GAG|Reina PROT|Reina RT|Reina RH|Reina INT|Reina CHD|Reina
@@ -477,7 +482,7 @@ Os3459_INT#LTR/Copia	LTR	Copia	Ale	yes	+	GAG|Ale PROT|Ale INT|Ale RT|Ale RH|Ale
 Os3460_INT#LTR/Copia	LTR	Copia	Ale	yes	+	GAG|Ale PROT|Ale INT|Ale RT|Ale RH|Ale
 Os3461_INT#LTR/Gypsy	LTR	Gypsy	Reina	yes	+	GAG|Reina PROT|Reina RT|Reina RH|Reina INT|Reina CHD|Reina
 Os3462_INT#LTR/Copia	LTR	Copia	Ale	yes	+	GAG|Ale PROT|Ale INT|Ale RT|Ale RH|Ale
-Os3463_INT#LTR/Gypsy	LTR	Gypsy	Reina	yes	+	GAG|Reina PROT|Reina RT|Reina RH|Reina INT|Reina CHD|Reina
+Os3463_INT#LTR/Gypsy	LTR	Gypsy	Reina	no	+	GAG|Reina RT|Reina RH|Reina INT|Reina CHD|Reina
 Os3465_INT#LTR/Gypsy	LTR	Gypsy	Ogre	yes	+	GAG|Ogre PROT|Ogre RT|Ogre RH|Ogre INT|Ogre
 Os3466_INT#LTR/Gypsy	LTR	Gypsy	Reina	yes	+	GAG|Reina PROT|Reina RT|Reina RH|Reina INT|Reina CHD|Reina
 Os3467_INT#LTR/Gypsy	LTR	Gypsy	Reina	yes	+	GAG|Reina PROT|Reina RT|Reina RH|Reina INT|Reina CHD|Reina
@@ -513,14 +518,14 @@ Os3499_INT#LTR/Gypsy	LTR	Gypsy	Ogre	yes	+	GAG|Ogre PROT|Ogre RT|Ogre RH|Ogre INT
 Os3500_INT#LTR/Gypsy	LTR	Gypsy	Reina	yes	+	GAG|Reina PROT|Reina RT|Reina RH|Reina INT|Reina CHD|Reina
 Os3501_INT#LTR/Copia	LTR	Copia	Ivana	yes	+	GAG|Ivana PROT|Ivana INT|Ivana RT|Ivana RH|Ivana
 Os3502_INT#LTR/Copia	LTR	Copia	Ale	yes	+	GAG|Ale PROT|Ale INT|Ale RT|Ale RH|Ale
-Os3503_INT#LTR/Gypsy	LTR	Gypsy	Reina	no	+	GAG|Reina PROT|Reina RT|Reina RH|Reina CHD|Reina
+Os3503_INT#LTR/Gypsy	LTR	Gypsy	Reina	no	+	GAG|Reina PROT|Reina RT|Reina RH|Reina
 Os3504_INT#LTR/Gypsy	LTR	Gypsy	Reina	yes	+	GAG|Reina PROT|Reina RT|Reina RH|Reina INT|Reina CHD|Reina
 Os3505_INT#LTR/Copia	LTR	Copia	Ale	yes	+	GAG|Ale PROT|Ale INT|Ale RT|Ale RH|Ale
 Os3506_INT#LTR/Gypsy	LTR	Gypsy	Reina	yes	+	GAG|Reina PROT|Reina RT|Reina RH|Reina INT|Reina CHD|Reina
 Os3507_INT#LTR/Gypsy	LTR	Gypsy	Reina	yes	+	GAG|Reina PROT|Reina RT|Reina RH|Reina INT|Reina CHD|Reina
 Os3509_INT#LTR/Gypsy	LTR	Gypsy	Reina	yes	+	GAG|Reina PROT|Reina RT|Reina RH|Reina INT|Reina CHD|Reina
 Os3510_INT#LTR/Gypsy	LTR	Gypsy	Reina	yes	+	GAG|Reina PROT|Reina RT|Reina RH|Reina INT|Reina CHD|Reina
-Os3511_INT#LTR/Gypsy	LTR	Gypsy	Reina	no	+	GAG|Reina PROT|Reina RH|Reina INT|Reina CHD|Reina
+Os3511_INT#LTR/Gypsy	LTR	Gypsy	Reina	yes	+	GAG|Reina PROT|Reina RT|Reina RH|Reina INT|Reina CHD|Reina
 Os3513_INT#LTR/Copia	LTR	Copia	Ale	yes	+	GAG|Ale PROT|Ale INT|Ale RT|Ale RH|Ale
 Os3514_INT#LTR/Copia	LTR	Copia	Ale	yes	+	GAG|Ale PROT|Ale INT|Ale RT|Ale RH|Ale
 Os3515_INT#LTR/Gypsy	LTR	Gypsy	Reina	yes	+	GAG|Reina PROT|Reina RT|Reina RH|Reina INT|Reina CHD|Reina