Open darked89 opened 2 months ago
fq lint
does not provide an output. Its usage is meant to be either be a success or failure, signaled by the process's exit code. stdout
only contains simple log messages of the command's execution.
Are you able to provide a more concrete example of what you're trying to achieve?
Thank you for a really fast response.
I have two main goals:
fq
does output number of reads when FASTQ was validated, I want to get it.2024-07-29T20:29:08.280922Z INFO fq::commands::lint: fq-lint start
2024-07-29T20:29:08.371633Z INFO fq::commands::lint: validating single end read
2024-07-29T20:29:08.371649Z INFO fq::validators: disabled validators: []
2024-07-29T20:29:08.371659Z INFO fq::validators: enabled single read validators: ["[S003] NameValidator", "[S004] CompleteValidator", "[S002] AlphabetValidator", "[S001] PlusLineValidator", "[S005] ConsistentSeqQualValidator", "[S006] QualityStringValidator"]
2024-07-29T20:29:08.371667Z INFO fq::validators: enabled paired read validators: []
2024-07-29T20:29:08.371671Z INFO fq::commands::lint: starting validation
2024-07-29T20:39:57.031928Z INFO fq::commands::lint: read 48843609 records
2024-07-29T20:39:57.031963Z INFO fq::commands::lint: fq-lint end
Instead of playing with existing output lines the best would be to have a final line:
RESULT file_path_or_name validation_passed 48843609
For the failed one (if possible):
RESULT failed_file_path_or_name failed 0_or_num_of_reads_before_fail
In both cases columns separated by TABs (easiest to read), no special chars to beautify that RESULT line of the output. That way ingestion of the useful data would be trivial.
Many thanks for your help
Hi,
I have used
fq lint
on a bunch of files piping the output to a one text file. Two issues:fq lint
output is fine to read but bit tricky to parse. Contains some formatting chars but no file/path in each row. Getting 'file.foo 12345678or rather
file_path number_of_reads` is not obtainable by simple grepping.Hope it helps
Darek