primer-trim
ΒΆ
primer-trim
trims an alignment to a region defined by a set of forward and
reverse primers. Usage is as follows:
usage: seqmagick primer-trim [-h] [--reverse-is-revcomp]
[--source-format SOURCE_FORMAT]
[--output-format OUTPUT_FORMAT]
[--include-primers]
[--max-hamming-distance MAX_HAMMING_DISTANCE]
[--prune-action {trim,isolate}]
source_file output_file forward_primer
reverse_primer
Find a primer sequence in a gapped alignment, trim to amplicon
positional arguments:
source_file Source alignment file
output_file Destination trimmed file
forward_primer The forward primer used
reverse_primer The reverse primer used. By default the reverse primer
is assumed to be a subsequence of the top strand (that
is, the reverse complement of an actual downstream PCR
primer). Use --reverse-is-revcomp if this is not the
case.
optional arguments:
-h, --help show this help message and exit
--reverse-is-revcomp Reverse primer is written as the reverse complement of
the top strand (default: False)
--source-format SOURCE_FORMAT
Alignment format (default: detect from extension
--output-format OUTPUT_FORMAT
Alignment format (default: detect from extension
--include-primers Include the primers in the output (default: False)
--max-hamming-distance MAX_HAMMING_DISTANCE
Maximum Hamming distance between primer and alignment
site (default: 1). IUPAC ambiguous bases in the primer
matching unambiguous bases in the alignment are not
penalized
--prune-action {trim,isolate}
Action to take. Options are trim (trim to the region
defined by the two primers, decreasing the width of
the alignment), or isolate (convert all characters
outside the primer-defined area to gaps). default:
trim