p3-feature-upstream¶
Find Upstream DNA Regions¶
p3-feature-upstream.pl [options] parms
This script takes as input a file of feature IDs. For each feature, it appends the upstream region on the input record.
Use the --downstream
) option to get the downstream regions instead.
Parameters¶
There are no positional parameters.
The standard input can be overridden using the options in Input Options.
Additional command-line options are those given in Column Options plus the following.
downstream
Display downstream instead of upstream regions.
length
Specifies the length to display upstream. The default is
100
.
in
Specifies the length to display inside the feature. The default is
0
, indicating none.
verbose
Show data API trace messages on STDERR.
Example¶
This command is shown in the tutorial p3_common_tasks.html
p3-echo -t genome_id 1313.7001 | p3-get-genome-features –eq feature_type,CDS –attr patric_id –attr product | p3-feature-upstream –col=feature.patric_id
genome_id feature.patric_id feature.product upstream 1313.7001 fig|1313.7001.peg.1182 beta-glycosyl hydrolase ttgtcatctcctcttgactctcgttaatataagaaataaaataagggcgttgatttatataatcgctatcaatataacaatgcaatcaggaggttttgca 1313.7001 fig|1313.7001.peg.1189 IMP cyclohydrolase (EC 3.5.4.10) / Phosphoribosylaminoimidazolecarboxamide formyltransferase (EC 2.1.2.3) gatcaatatcttaggtatgcttagccttggttttgcttatcttgttttactgttactgcatttaattggtgtttaactaatgattaaaaaggagaatata …