Question
Using ubuntu program (on Windows) nano command line, please answer the questions about shell scripts 1) Merging two files for a flexible lookup program OMIM
Using ubuntu program (on Windows) nano command line, please answer the questions about shell scripts
1) Merging two files for a flexible lookup program OMIM (Online Mendelian Inheritance in Man; https://www.omim.org/) contains information about genetic disorders, and the genes and genomic regions that are associated with these disorders.
genemap2.txt file (https://www2.unb.ca/~rmalenf1/BIOL3933/genemap2.txt) and morbidmap.txt (https://www2.unb.ca/~rmalenf1/BIOL3933/morbidmap.txt) respectively, they contain the locations of genes and genomic locations associated with genetic disorders of the OMIM database.
You would like to write a simple script to check if a mutation at a particular nucleotide is located somewhere in the range of a gene, and you would also like to check if the mutation is located in a region that is associated with a genetic disorder.
-Download the 2 URL (by the curl command) and use command-line arguments to specify the location of interest. (write it so it's not hard coded (your command can be used for any data) For example, to check if position 4,671,231 on chromosome 3 is in the range of any genes or associated with any genetic conditions, I would run my script as follows, and get the following result:
Erene]% ./Malenfant-Rene-Part2.sh chr3 4671231 This SNP is in the range of these genes: ARHI2 ITPR1, SCA15, SCA16, SCA29 These genes are associated with the following conditions: ARHI2 Age-related hearing impairment 2 (2) ITPR1, SCA15, SCA16, SCA29Gillespie syndrome, 206700 (3) ITPR1, SCA15, SCA16, SCA29 Spinocerebellar ataxia 15, 606658 (3) ITPR1, SCA15, SCA16, SCA29 Spinocerebellar ataxia 29, congenital nonprogressive, 117360 (3) Erene]% ./Malenfant-Rene-Part2.sh chr3 4671231 This SNP is in the range of these genes: ARHI2 ITPR1, SCA15, SCA16, SCA29 These genes are associated with the following conditions: ARHI2 Age-related hearing impairment 2 (2) ITPR1, SCA15, SCA16, SCA29Gillespie syndrome, 206700 (3) ITPR1, SCA15, SCA16, SCA29 Spinocerebellar ataxia 15, 606658 (3) ITPR1, SCA15, SCA16, SCA29 Spinocerebellar ataxia 29, congenital nonprogressive, 117360 (3)Step by Step Solution
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