Fastaheader reading, Memory reduction and speedup #7
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Add new extractMummer function to reduce memory foodprint and speed up! As it does the necessary steps during reading the line!
Calls the new function in alignerRobot
Takes only the first header information of the for each fasta header as mummer does.
peterjc
reviewed
Sep 24, 2018
| @@ -18,7 +18,8 @@ def obtainLength(folderName, fileName): | |||
| if tmplen != 0: | |||
| lenDic[tmpName] = tmplen | |||
| tmplen = 0 | |||
| tmpName = tmp[1:] | |||
| headerList = tmp.split(); | |||
| tmpName = headerList[0][1:] | |||
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How about this:
tmpName = tmp.split(None, 1)[1:]There is often more than one space in the FASTA header lines, so splitting at the first space may well be quicker overall.
Also there is no reason to create the extra temp variable headerList here, is there?
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:) thats indeed looks better, at that time it was just a quick and dirty fix.
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It is a shame the tool owner has not been active here recently...
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Changed some part of the code for the first Step. Reduced the memory footprint in our case from 300GB to 2GB. Additionally it will create a speedup as no unnecessary copies are produced.