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 …