I'm using genefuse JSON output to handle fusions information in order to prioritize them, so I'm using a Python script to read the JSON file. Sometimes the JSON output is corrupted because in the "qual" value of each read it could be used the double-quotes symbol. For example:
"reads":[ { "break":33, "strand":"reversed", "seq":"TTTTTTATAGGATTTGGGAAGGTAATGGAAAATTCCAGTCAAAGGGGGTTGTTCTCTGGTGGGCAGGGGCGGGGGTCACAAGGTGCTCAGTGGGGGAG", "qual":"9.B>?<5:=B94ACABA;BA@79B>B?6@A?@BB"@=<@:A=9@ABB>BB>B>?B.@A6BB?@>?@@B?7AAB>=<B=AA@A7B@:?<A9AA@@?=??" },
When genefuse writes the JSON file the double-quotes is not escaped, so trying to read the JSON file cause an error.
At the moment I'm avoiding the problem using a regex pattern to manipulate the JSON file and make it correct. I hope there's a way to update the construction of the JSON output in order to add the escape slash before double-quotes in "qual" value.
I'm using genefuse JSON output to handle fusions information in order to prioritize them, so I'm using a Python script to read the JSON file. Sometimes the JSON output is corrupted because in the "qual" value of each read it could be used the double-quotes symbol. For example:
"reads":[ { "break":33, "strand":"reversed", "seq":"TTTTTTATAGGATTTGGGAAGGTAATGGAAAATTCCAGTCAAAGGGGGTTGTTCTCTGGTGGGCAGGGGCGGGGGTCACAAGGTGCTCAGTGGGGGAG", "qual":"9.B>?<5:=B94ACABA;BA@79B>B?6@A?@BB"@=<@:A=9@ABB>BB>B>?B.@A6BB?@>?@@B?7AAB>=<B=AA@A7B@:?<A9AA@@?=??" },When genefuse writes the JSON file the double-quotes is not escaped, so trying to read the JSON file cause an error.
At the moment I'm avoiding the problem using a regex pattern to manipulate the JSON file and make it correct. I hope there's a way to update the construction of the JSON output in order to add the escape slash before double-quotes in "qual" value.