Hi,
I'm trying to add some test to fastx-toolkit,
I pulled a fresh copy, tries "sh run_functional_tests.sh -list"
and got the following output:
...
...
===========================================================================================================================================
id name section::FASTA_manipulation-fasta_manipulation
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
fasta_compute_length Compute sequence length
fasta_filter_by_length Filter sequences by length
fasta_concatenate0 Concatenate
fasta2tab FASTA-to-Tabular
tab2fasta Tabular-to-FASTA
FASTA Width
_name= RNA/DNA
cshl_fastx_collapser Collapse
===========================================================================================================================================
id name section::NGS:_QC_and_manipulation-cshl_library_information
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
fastq_gen_conv FASTQ Groomer
cshl_fastq_quality_converter Quality format converter
cshl_fastx_quality_statistics Compute quality statistics
cshl_fastq_quality_boxplot Draw quality score boxplot
Draw nucleotides distribution chart
split_paired_reads Split paired end reads
quality_score_distribution Build base quality distribution
trim_reads Select high quality segments
_name= SOLiD-to-FASTQ
_name= Compute quality statistics
_name= Draw quality score boxplot
===========================================================================================================================================
...
...
Some of the tools (e.g. "FASTA width", or even "SOLiD-to-FASTQ" which isn't my tool) shows invalid 'id'.
Is this normal? and how do I run test for these tools?
thanks,
-gordon
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