Download cds region coordinates

Question

[ankittanwar12]

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.

Answer 1

[Pierre Lindenbaum]

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 -

[ankittanwar12]

Thank you for answering my query. I got the desired result.