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 …