I don't want to be accused of passing effort out to the list, but I would like to know, from the experts, the fastest way to execute some code..
I have a file of tab delimited items like so...16,000 lines long read into a single variable. (The right bracket is part of the file, not a quote mark) >DAPA_ECO57 MFTGSIVAIVTPMDEKGNVCR 2267.1049 1 >DAPA_ECOL6 MFTGSIVAIVTPMDEKGNVCR 2267.1049 1 >DAPA_ECOLI MFTGSIVAIVTPMDEKGNVCR 2267.1049 1 >(-M)YEGS_ECOLI AEFPASLLILNGKSTDNLPLR 2268.2398 1 >GLTS_ECOLI MFHLDTLATLVAATLTLLLGR 2269.28372 0 >(-M)YDIV_ECOLI KIFLENLYHSDCYFLPIR 2270.1462 1 >YBAA_ECO57 MKYVDGFVVAVPADKKDAYR 2271.16256 3 >YBAA_ECOL6 MKYVDGFVVAVPADKKDAYR 2271.16256 3 >YBAA_ECOLI MKYVDGFVVAVPADKKDAYR 2271.16256 3 I now want to search each line, and match an input number (obsMass) against the third item of each line (pepMass) If it matches, within a certain tolerance (expressed in parts per million (ppm) - the tolerance changes with the magnitude of the number) I want to do something with that line. Ties (or multiple hits to the same obsMass) are OK. I then want to repeat that process for several thousand different values of obsMass. In other words, I will evaluate the mass matching loop tens of millions of times. Some questions - is there advantage in sorting the list by mass first? Would I gain speed by using integer arithmetic (is that even possible?) or by matching the numbers as strings? And most importantly.. Is there an elegant rev way of handling this that I don't even know about?! Thanks Rob ________________________________ Prof R J Beynon[h] Proteomics and Functional Genomics Group Faculty of Veterinary Science University of Liverpool Crown Street, Liverpool L69 7ZJ ________________________________ Phone: +44 151 794 4312 Fax: +44 151 794 4243 Email: [EMAIL PROTECTED] http://www.liv.ac.uk/pfg ________________________________ _______________________________________________ use-revolution mailing list [email protected] Please visit this url to subscribe, unsubscribe and manage your subscription preferences: http://lists.runrev.com/mailman/listinfo/use-revolution
