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Fix loader on PHAF files not working as expected #83

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manulera opened this issue Jul 31, 2023 · 1 comment
Open

Fix loader on PHAF files not working as expected #83

manulera opened this issue Jul 31, 2023 · 1 comment
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@kimrutherford @manulera

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@manulera
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Hi @kimrutherford, I am working on the allele fixes that you mentioned on the other issue, and I noticed that the fixes do not work as expected on the PHAF files. For example, from the lines below:

allele_qc/change_log/allele_manual_changes_formatted_2_19042023.tsv

Lines 232 to 234 in 0e344f7

SPNCRNA.98 srp7-D4E-1 GC inserted after nt 158,GC inserted after nt 164 PMID:8390662 T158-GC,C164-GC nucleotide_insertion
SPNCRNA.98 srp7-D4E-2 G160C,GC inserted after nt 158,GC inserted after nt 164 PMID:8390662 T158-GC,G160C,C164-GC nucleotide_insertion_and_mutation
SPNCRNA.98 srp7-D4E-3 GC inserted after nt 164 PMID:8390662 C164-GC nucleotide_insertion

These were the changes. Note how the descriptions of the two alleles did not change (only the allele type).

Index: trunk/external_data/phaf_files/chado_load/ltp_phafs/PMID_8390662_phaf.tsv
===================================================================
--- trunk/external_data/phaf_files/chado_load/ltp_phafs/PMID_8390662_phaf.tsv	(revision 8870)
+++ trunk/external_data/phaf_files/chado_load/ltp_phafs/PMID_8390662_phaf.tsv	(revision 8871)
@@ -9,8 +9,8 @@
 SPNCRNA.98	FYPO:0002061	GAAA-160-CTTC	Not specified	972 h-		ura4-D18 leu1-32 ade6-704		srp7-PTL1-2		nucleotide mutation	Cell growth assay	FYECO:0000005,FYECO:0000137				PMID:8390662	4896	2014-06-10	
 SPNCRNA.98	FYPO:0002061	GAAAC-160-CTTCA	Not specified	972 h-		ura4-D18 leu1-32 ade6-704		srp7-PTL2C		nucleotide mutation	Cell growth assay	FYECO:0000005,FYECO:0000137				PMID:8390662	4896	2014-06-10	
 SPNCRNA.98	FYPO:0002061	GAAAC-160-TTTCA	Not specified	972 h-		ura4-D18 leu1-32 ade6-704		srp7-PTL2U		nucleotide mutation	Cell growth assay	FYECO:0000005,FYECO:0000137				PMID:8390662	4896	2014-06-10	
-SPNCRNA.98	FYPO:0002061	GC inserted after nt 158, GC inserted after nt 164	Not specified	972 h-		ura4-D18 leu1-32 ade6-704		srp7-D4E-1		other	Cell growth assay	FYECO:0000005,FYECO:0000137				PMID:8390662	4896	2014-06-10	
-SPNCRNA.98	FYPO:0002061	G160C, GC inserted after nt 158, GC inserted after nt 164	Not specified	972 h-		ura4-D18 leu1-32 ade6-704		srp7-D4E-2		other	Cell growth assay	FYECO:0000005,FYECO:0000137				PMID:8390662	4896	2014-06-10	
+SPNCRNA.98	FYPO:0002061	GC inserted after nt 158, GC inserted after nt 164	Not specified	972 h-		ura4-D18 leu1-32 ade6-704		srp7-D4E-1		nucleotide_insertion	Cell growth assay	FYECO:0000005,FYECO:0000137				PMID:8390662	4896	2014-06-10	
+SPNCRNA.98	FYPO:0002061	G160C, GC inserted after nt 158, GC inserted after nt 164	Not specified	972 h-		ura4-D18 leu1-32 ade6-704		srp7-D4E-2		nucleotide_insertion_and_mutation	Cell growth assay	FYECO:0000005,FYECO:0000137				PMID:8390662	4896	2014-06-10	
 SPNCRNA.98	FYPO:0002061	G159C,C164A	Not specified	972 h-		ura4-D18 leu1-32 ade6-704		srp7-G159C,C164A		nucleotide mutation	Cell growth assay	FYECO:0000005,FYECO:0000137				PMID:8390662	4896	2014-06-10	
 SPNCRNA.98	FYPO:0002061	T158C,A166C	Not specified	972 h-		ura4-D18 leu1-32 ade6-704		srp7-U158C,A166C		nucleotide mutation	Cell growth assay	FYECO:0000005,FYECO:0000137				PMID:8390662	4896	2014-06-10	
 SPNCRNA.98	FYPO:0000080	G159A,C164T	Not specified	972 h-		ura4-D18 leu1-32 ade6-704		srp7-G159A,C164U		nucleotide mutation	Cell growth assay	FYECO:0000005,FYECO:0000137				PMID:8390662	4896	2014-06-10	
@@ -30,7 +30,7 @@
 SPNCRNA.98	FYPO:0002060	A162C,C164G	Not specified	972 h-		ura4-D18 leu1-32 ade6-704		srp7-A162C,C164G		nucleotide mutation	Cell growth assay	FYECO:0000005,FYECO:0000137				PMID:8390662	4896	2014-06-10	
 SPNCRNA.98	FYPO:0002060	GGAAAC-159-CTTCGG	Not specified	972 h-		ura4-D18 leu1-32 ade6-704		srp7-STL2-1		nucleotide mutation	Cell growth assay	FYECO:0000005,FYECO:0000137				PMID:8390662	4896	2014-06-10	
 SPNCRNA.98	FYPO:0002060	GAAA-160-TTTC	Not specified	972 h-		ura4-D18 leu1-32 ade6-704		srp7-PTL1-1		nucleotide mutation	Cell growth assay	FYECO:0000005,FYECO:0000137				PMID:8390662	4896	2014-06-10	
-SPNCRNA.98	FYPO:0002060	GC inserted after nt 164	Not specified	972 h-		ura4-D18 leu1-32 ade6-704		srp7-D4E-3		other	Cell growth assay	FYECO:0000005,FYECO:0000137				PMID:8390662	4896	2014-06-10	
+SPNCRNA.98	FYPO:0002060	C164-GC	Not specified	972 h-		ura4-D18 leu1-32 ade6-704		srp7-D4E-3		nucleotide_insertion	Cell growth assay	FYECO:0000005,FYECO:0000137				PMID:8390662	4896	2014-06-10	
 SPNCRNA.98	FYPO:0002060	G159A	Not specified	972 h-		ura4-D18 leu1-32 ade6-704		srp7-G159A		nucleotide mutation	Cell growth assay	FYECO:0000005,FYECO:0000137				PMID:8390662	4896	2014-06-10	
 SPNCRNA.98	FYPO:0002060	G159T	Not specified	972 h-		ura4-D18 leu1-32 ade6-704		srp7-G159U		nucleotide mutation	Cell growth assay	FYECO:0000005,FYECO:0000137				PMID:8390662	4896	2014-06-10	
 SPNCRNA.98	FYPO:0002060	C164A	Not specified	972 h-		ura4-D18 leu1-32 ade6-704		srp7-C164A		nucleotide mutation	Cell growth assay	FYECO:0000005,FYECO:0000137				PMID:8390662	4896	2014-06-10
@manulera
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I have fixed the description in the file manually now.

@manulera manulera mentioned this issue Jul 31, 2023
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@manulera manulera mentioned this issue Aug 15, 2023
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