Hi, everyone .
I have a dataset like this .
1st column has protein Ids of different organisms and 2nd column has domain names.
Protein Ids domain
Abiotrophia_defectiva_peg_0144 wzz
Abiotrophia_defectiva_peg_0198 wxy
Abiotrophia_defectiva_peg_0200 wzz
Abiotrophia_defectiva_peg_0215 wca
Abyssicoccus_albus_123_peg_1185 wzz
Abyssicoccus_albus_123_peg_1189 wzx
Abyssicoccus_albus_123_peg_1200 wza
Abyssicoccus_albus_123_peg_1322 wca
Abyssicoccus_albus_123_peg_1324 wbb
Bradyrhizobium_elkanii_peg_6717 wac
Bradyrhizobium_elkanii_peg_6718 wzx
Bradyrhizobium_elkanii_peg_6721 waa
Bradyrhizobium_elkanii_peg_6752 wca
Bradyrhizobium_elkanii_peg_6780 wvx
I want to know which proteins are near by . means according to "peg" numbers if I say protein numbers coming under +/- 5 they are near by and they form cluster.
output should look like :
Abiotrophia_defectiva_peg_0198 wxy
Abiotrophia_defectiva_peg_0200 wzz
----------------------------------------
Abyssicoccus_albus_123_peg_1185 wzz
Abyssicoccus_albus_123_peg_1189 wzx
Abyssicoccus_albus_123_peg_1322 wca
Abyssicoccus_albus_123_peg_1324 wbb
-----------------------------------------
Bradyrhizobium_elkanii_peg_6717 wac
Bradyrhizobium_elkanii_peg_6718 wzx
Bradyrhizobium_elkanii_peg_6721 waa
-------------------------------------------
there should be a separate inf partition line between each cluster.
Is there any way I can do this task for my data . I can do manually in excel sheet but my dataset is very large. So I need some script for this .
Please do let me know . Thanks
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Confused_human •
1 answer
You can do this with python pretty easily.
1) loop through the file line by line
2) Split the line by the first column by "_" and select the last "item" which in this case will be the numbers after "peg_". Python syntax for this is:
peg_number = line.split("_")[-1]. This will grab the numbers you want (0144, 0200, etc.)
3) You would now want to store this number in a list (append), or dictionary and then check to see any of the following peg_numbers are within +/- 5 of the value.
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you already asked this. Cluster of neighboring genes by index (Looking for linux shell Script)