Hi Pierre, you are right.Thank you very much!
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Chuangye •
Filtering Micrornas Data With Awk
chr17 10558721 10558801 ssc-mir-486-1 + 0.475 chr17 10558763 10558830 ssc-mir-486 +
chr17 33406488 33406568 ssc-mir-103-2 - 1.7375 chr17 33406491 33406569 ssc-mir-103a-2 -
chr17 33406488 33406568 ssc-mir-103-2 - 1.7375 chr17 33406499 33406561 ssc-mir-103b-2 +
chr17 40405261 40405341 ssc-mir-499 - 1.9125 chr17 40405237 40405359 ssc-mir-499a -
chr17 40405261 40405341 ssc-mir-499 - 1.9125 chr17 40405262 40405335 ssc-mir-499b +
chr17 61587157 61587234 ssc-mir-296 - 0.987012987012987 chr17 61587158 61587236 ssc-mir-296 -
chrX 58683649 58683729 ssc-mir-374b + 1.725 chrX 58683647 58683717 ssc-mir-374c -
chrX 58683649 58683729 ssc-mir-374b + 1.725 chrX 58683647 58683719 ssc-mir-374b +
The result should be:
chr17 33406488 33406568 ssc-mir-103-2 - 1.7375 chr17 33406499 33406561 ssc-mir-103b-2 +
chr17 40405261 40405341 ssc-mir-499 - 1.9125 chr17 40405262 40405335 ssc-mir-499b +
chrX 58683649 58683729 ssc-mir-374b + 1.725 chrX 58683647 58683717 ssc-mir-374c -
My scripts:
awk 'BEGIN{OFS="\t"}(!($5==$11)&&($6>1))' intersect.txt
Or
awk 'BEGIN{OFS="\t"}($5!=$11 && $6>1)' intersect.txt
And the answer is:
chr17 33406488 33406568 ssc-mir-103-2 - 1.7375 chr17 33406499 33406561 ssc-mir-103b-2 +
chr17 40405261 40405341 ssc-mir-499 - 1.9125 chr17 40405262 40405335 ssc-mir-499b +
chrX 58683649 58683729 ssc-mir-374b + 1.725 chrX 58683647 58683717 ssc-mir-374c -
chrX 58683649 58683729 ssc-mir-374b + 1.725 chrX 58683647 58683719 ssc-mir-374b +
So why the scripts couldn't get the right answer ? And how to cope it with unix or python scripts?
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W Langdon •
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Chuangye •
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Chuangye •
2 answers
If you want the get the lines have where the strands are not the same and where the value in the 6th column is greater than 1.0:
$ awk -F ' ' '($5!=$11 && $6>1.0)' input.txt
chr17 33406488 33406568 ssc-mir-103-2 - 1.7375 chr17 33406499 33406561 ssc-mir-103b-2 +
chr17 40405261 40405341 ssc-mir-499 - 1.9125 chr17 40405262 40405335 ssc-mir-499b +
chrX 58683649 58683729 ssc-mir-374b + 1.725 chrX 58683647 58683717 ssc-mir-374c -
I don't know why your script doesn't work.
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Pierre Lindenbaum
Using the scripts as awk 'BEGIN{OFS="\t"}($6!=$14 && $8>1)'
or
awk -F ' ' '($6!=$14 && $8>1.0)' could not effective to get the lines their strands are not the same and in which the value in the 6th column is greater than 1.0. such as the data "intersect",which temporarily deposited at http://www.rayfile.com/zh-cn/files/0a846566-1954-11e1-95c1-0015c55db73d/cbbffc68/.
I don't kwnow where is the problem.
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Chuangye •
It appears there may be a problem with assigning OFS inside BEGIN. http://lists.gnu.org/archive/html/bug-gnu-utils/2011-03/msg00006.html
However, why do you want to set OFS to tab? By default gawk will split input lines on white space (which includes tabs).
I have had problems with tabs before. its often safer to either works with defaults or find some other way to parse the input (eg comma separated data).
Bill
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Ram
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W Langdon •
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W Langdon •
Nice catch on the tabs, I am very surprised by it as well. Letting awk split on any whitespace can actually lead to very surprising outcomes. In general the default split in most programming languages (perl, python) will collapse consecutive whitespaces and treat them as a single separator. Therefore empty, tab separated columns will shift subsequent columns. Once you are bitten by one of the devious tab shifting default you never rely on them again.
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Istvan Albert
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What are you trying to produce? The script right now check to see if the strands are the same and if the 6th column is greater than 1. Why are you expecting only chr17 to be produced?
Thank you! I have corrected the error.