Dealing with rows in tabular data

Question: Dealing with rows in tabular data

2.7 years ago by

United Kingdom

d.angra • 50 wrote:

Hello Experts

I am using use galaxy for genome wide SNP discovery. I have discovered about 770,000 SNPs. After performing operations in galaxy I have been able to get sequences for each of them.I obviously have a pool of several genotypes. At this point I have 2 questions 1) How should annotate my vcf file so that I know in the end from where does each SNP come from? 2) Are there any tools for dealing with rows in galaxy. The tools in text manipulations mostly involve columns, or I cant get hold of tools working with rows. I need to delete alternate rows which I do not require. I am certain somebody must have done it in the past. Hope to hear from you soon, I am struggling with this for few days.

Dips

tabular data manipulation • 839 views

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modified 2.7 years ago • written 2.7 years ago by d.angra • 50

2.7 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

For annotation, see the tools in the group NGS: Variant Analysis. From there, VCF Tools or others may be helpful, search by the term VCF to review the options.

General tools to slice data files by line are in the group Text Manipulation. For alternate rows one could add in line numbers (Add column with option: iterate) to create a tabular dataset with actual line numbers included. Then use the tool Filter or Select to pick certain rows of interest (odd, even, specific line numbers). At the end, don't forget to remove the counting column and reset the file format to VCF.

Hopefully this helps, Jen, Galaxy team

ADD COMMENT • link written 2.7 years ago by Jennifer Hillman Jackson ♦ 25k

2.7 years ago by

d.angra • 50

United Kingdom

d.angra • 50 wrote:

Hello Jen Thankyou. This has been extremely helpful. Dips

ADD COMMENT • link written 2.7 years ago by d.angra • 50

2.7 years ago by

d.angra • 50

United Kingdom

d.angra • 50 wrote:

Hi Jen I thought I would achieve some success with your reply. However I am caught at few places. First I need to know how to iterate columns if I need to give only two numbers 1 and 2 . Second are there any short functions known to select only even number rows. I had a good look over filter and sort functions with limited understanding.Could you please direct me in the direction where I could get more help on this.

Thanks in advance Dips

ADD COMMENT • link written 2.7 years ago by d.angra • 50

For the line numbers, start with just "1" (no quotes).

Try a regular expression to filter on this column using the select tool. Many resources for regular expressions are on the internet. You'll have to test them out to suit your exact data. Rearrange columns if that helps (put the new column first, using the tool Cut).

ADD REPLY • link written 2.7 years ago by Jennifer Hillman Jackson ♦ 25k

Hi To accomplish this I used AWK programming. Thanks

ADD REPLY • link written 2.7 years ago by d.angra • 50

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