Allow special characters in file names OR quoting thereof

Feature requests
1

Hi,

I’m using mothur in batch mode, and just found out that some commands (e.g. align.seqs) don’t like dashes in the file name. E.g:

mothur > align.seqs(fasta=Project123-456.trim.contigs.good.unique.fasta, reference=/Sequences/Silva/silva.bacteria/silva.bacteria.fasta)

crashes with

Unable to open Project123. Trying default /illumina/Projects/Project123

I can’t use " or ’ to quote the entire filename - but found out that I could escape the dash with . However, other commands/arguments (e.g. summary.seqs) wouldn’t accept escaped dashes (uses the raw string and complains there is no “Project123-456.trim.contigs.good.unique.fasta” file).

I couldn’t find any documentation on this - could you either tell me which special characters and which commands/arguments need escapes for special characters or could you introduce a generic scheme for quoting command arguments (then I could make sure that all filenames are always quoted)? I process some data where I would like to name the mothur files like the other project files (which sometimes contain dashes). Right now I have to find out which commands/arguments need the escapes by trial and error, which is rather time consuming… Or am I missing something obvious?

Thanks,
Samuel

2

Same problem encountered this problem when using SSUsearch.

SSUsearch’s pipeline sends commands to mothur in the following manner

mothur “#classify.seqs(fasta=$Tag.ssu.out/$Tag.qc.$Gene.align.filter.fa, template=$Gene_db_cc, taxonomy=$Gene_tax_cc, cutoff=50, processors=$Cpu)”

does this mean we should escape all special characters or only the dash character?

however my $Tag bash variable has a dash character within it.

Guo, J., Cole, J. R., Zhang, Q., Brown, C. T., & Tiedje, J. M. (2016). Microbial Community Analysis with Ribosomal Gene Fragments from Shotgun Metagenomes, 82(1), 157–166. http://doi.org/10.1128/AEM.02772-15.Editor

3

Only the ones with dashes in them.

Pat