Thank you very much for the explanations, I am trying to process it and think it makes sense and will be very helpful later on. I appreciate it .
The awk using the entire one line of index.html returns the above output (which is very close). In each Alignments there is the portion in bold IonXpress_004_R_2016_09_01_10_24_52_user_S5-00580-4-Medexome_Auto_user_S5-00580-4-Medexome_65 that will match the portion in bold in path, /results/analysis/output/Home/Auto_user_S5-00580-4-Medexome_65_028/plugin_out/FileExporter_out.52. Thus grouping all the matching strings together in the same order aalready outputting. That way any duplicates can be identified (like line 1 and the last line) and removed. If there is no match found then the next line is processed (nothing needs to happen). I am not sure why there in the index.html, but it looks like the API used to retrieve that file has duplicates in it. In the --Alignments from index.html only the portion up to the second _ is needed. So in IonXpress_004_R_2016_09_01_10_24_52_user_S5-00580-4-Medexome_Auto_user_S5-00580-4-Medexome_65 only IonXpress_004. I will write something as well, but I'm sure it will need work.
Thank you very much for all of your help .
So using the above as an example:
IonXpress_004_R_2016_09_01_10_24_52_user_S5-00580-4-Medexome_Auto_user_S5-00580-4-Medexome_65 -- Alignments from index.html portion in bold matches portion in bold from
/results/analysis/output/Home/Auto_user_S5-00580-4-Medexome_65_028/plugin_out/FileExporter_out.52 -- path from index.html so all the user_S5-00580-4-Medexome are grouped together.
awk attempt
1 bold marking removes duplicates in Aligned Reads
2 bold marking parses Alignments using the second _ removing everything after
3 bold marking groups all _user in Alignments with path (I don't think this will work as I just removed the _user from Alignments
Last edited by cmccabe; 09-23-2016 at 04:17 PM..
Reason: added details, added awk
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