Download cds region coordinates
1
Hello everyone,
I want to download only cds region coordinates from given input file in genbank format through some script or bioperl modules.
Can anyone suggest me a module of bioperl or biopython which will do the above mentioned job. And if there are no such modules available, how should i approach this problem.
bioperl
biopython
exon
coding regions
• 2.1k views
using a simple xslt stylesheet ?
<?xml version="1.0" encoding="UTF-8"?>
<xsl:stylesheet xmlns:xsl= "http://www.w3.org/1999/XSL/Transform " version= "1.0" >
<xsl:output method= "text" />
<xsl:template match= "/" >
<xsl:apply-templates select= "//GBFeature[GBFeature_key='CDS']/GBFeature_intervals/GBInterval" />
</xsl:template>
<xsl:template match= "GBInterval" >
<xsl:value-of select= "GBInterval_from" />
<xsl:text> </xsl:text>
<xsl:value-of select= "GBInterval_to" />
<xsl:text> </xsl:text>
<xsl:apply-templates select= "../../GBFeature_quals/GBQualifier" />
<xsl:text>
</xsl:text>
</xsl:template>
<xsl:template match= "GBQualifier" >
<xsl:value-of select= "GBQualifier_name" />
<xsl:text> :</xsl:text>
<xsl:value-of select= "GBQualifier_value" />
<xsl:text> </xsl:text>
</xsl:template>
</xsl:stylesheet>
e.g:
curl -s "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id=U00096&retmode=xml " |\
xsltproc --novalid transform.xsl - | cut -c 1-100 | tail
4633745 4633233 gene:yjjX locus_tag:b4394 gene_synonym:ECK4386; JW5801 codon_start:1 transl_table:11
4633797 4634444 gene:ytjC locus_tag:b4395 gene_synonym:ECK4387; gpmB; JW4358 function :enzyme; Not cl
4635310 4634441 gene:rob locus_tag:b4396 gene_synonym:cbpB; ECK4388; JW4359; robA function :factor; D
4635521 4635994 gene:creA locus_tag:b4397 gene_synonym:ECK4389; JW4360; yjjD codon_start:1 transl_ta
4636007 4636696 gene:creB locus_tag:b4398 gene_synonym:ECK4390; JW4361; ORF2; yjjE function :regulato
4636696 4638120 gene:creC locus_tag:b4399 gene_synonym:ECK4391; JW4362; phoM function :enzyme; Global
4638178 4639530 gene:creD locus_tag:b4400 gene_synonym:cet; ECK4392; JW4363; refII function :putative
4640306 4639590 gene:arcA locus_tag:b4401 gene_synonym:cpxC; dye; ECK4393; fexA; JW4364; msp; seg; s
4640402 4640542 gene:yjjY locus_tag:b4402 gene_synonym:ECK4394; JW4365 codon_start:1 transl_table:11
4640942 4641628 gene:yjtD locus_tag:b4403 gene_synonym:ECK4395; JW4366; lasT GO_process:GO:0009451 -
Login before adding your answer.
Traffic: 2550 users visited in the last hour
Thank you for answering my query. I got the desired result.