Specify Input Files

Commands that accept input files as positional arguments support three ways to list them, which you can combine freely.

List files explicitly

The simplest method: name each file directly:

seismic {command} out/sample-1/idmut/ref-1 out/sample-2/idmut/ref-1

Use glob patterns

Use shell wildcards to match many files at once:

seismic {command} out/*/idmut/ref-1

The shell expands the pattern before passing the list to SEISMIC-RNA. See glob patterns for the full syntax (* matches any text, ? matches one character, [12] matches either 1 or 2).

Pass a directory

Passing a directory causes SEISMIC-RNA to search it recursively for all matching files:

seismic {command} out/

This is useful when you want to process every output file from a previous step.

Combine methods

You can mix all three methods in one command:

seismic {command} out/sample-[123] out/sample-26 out/sample-7/filter/ref-1

Glob patterns in options that accept multiple paths

Several options that accept more than one file or directory can also expand glob patterns. The options that support this are:

  • -x / --fastqx, -y / --fastqy, -z / --fastqz (FASTQ inputs)

  • -X / --dmfastqx, -Y / --dmfastqy, -Z / --dmfastqz (demultiplexed FASTQ inputs)

  • -d / --param-dir (simulation parameter directories)

  • --ct-file, --ct-pos-5 (connectivity table files)

  • --struct-file (reference structure files)

  • --mask-pos-file, --drop-read-file (filter input lists)

Important

You must prefix every wildcard character with a backslash (\) when the pattern is the value of an option flag. Without the backslash, the shell expands the pattern into separate arguments before SEISMIC-RNA sees them: only the first matched file becomes the value of the option, and the rest are left over as stray arguments, which causes the command to fail.

For example, to pass both mates of a paired-end sample as -x, escape the brackets so SEISMIC-RNA (not the shell) does the expansion:

seismic align refs.fa -x samples/sample1_R\[12\].fastq

The same rule applies to * and ?:

seismic align refs.fa -x samples/sample1_R\*.fastq

You can repeat the option to combine literal paths and escaped patterns:

seismic align refs.fa -x sample1_R1.fastq -x sample1_R2.fastq \
                     -x extras/\*.fastq

A pattern that matches no files raises an error, so typos in patterns are surfaced immediately rather than silently ignored.

Options that accept only a single file (for example --regions-file, --samples-meta, --refs-meta) do not expand glob patterns; give them an exact path.