[spctools-discuss] re: patch: Sqt2XML fixes
It doesn't look like this patch ever made it into the SVN tree. Could someone look at adding it? I think someone here's going to mention this program in a paper, but without this patch this program doesn't function correctly. Thanks! http://groups.google.com/group/spctools-discuss/browse_thread/thread/c4701a916104?fwc=1 -- You received this message because you are subscribed to the Google Groups spctools-discuss group. To post to this group, send email to spctools-disc...@googlegroups.com. To unsubscribe from this group, send email to spctools-discuss+unsubscr...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=.
[spctools-discuss] Ubuntu/Debian/RedHat TPP packages?
Has there been any thought about packaging up TPP for Ubuntu/Debian and possibly RedHat/CentOS? I went through the exercise of installing it from scratch, following the directions on the wiki page, and I can imagine that this would be quite daunting for a non-programmer. Just off the top of my head, it looks like the main problem to solve will be that TPP is tending to rely on bleeding-edge versions of the Boost libraries. Is there any chance that a change could be made to stick with versions that are merely reasonably current (and thus packaged)? (Ubuntu Jaunty has 1.37, for example.) --~--~-~--~~~---~--~~ You received this message because you are subscribed to the Google Groups spctools-discuss group. To post to this group, send email to spctools-discuss@googlegroups.com To unsubscribe from this group, send email to spctools-discuss+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en -~--~~~~--~~--~--~---
[spctools-discuss] Re: Ubuntu/Debian/RedHat TPP packages?
Version 1.39 of Boost isn't in Ubuntu currently, so there's nothing to link to that way. I assume you mean doing something like folding Boost into the TPP/extern directory and handling Boost as libexpat is handled, for example. I'm not completely unsympathetic to this idea, but on the whole I'm against this. Having your own local copy means supporting your own local copy, which translates into more work (which I don't like to do :-). As to whether it's worthwhile to package TPP for Linux, I don't know. I've been trying to help out Eliza, who would clearly benefit. I'd have probably tried out TPP sooner myself if there had been an easily installed Linux package. But are there really a lot of potential users, and does the TPP project care about reaching them? I don't even know how large the Windows user community is. As to volunteering, it's not out of the question. It'd depend on the above (whether it's really worth doing). Also, I think that in order to make this work well, we'd really want to separate TPP from its dependencies. That is, rather than including expat (for example) in the TPP source tree, instead have each version stipulate that it depends on version X of expat (or more typically, version X or later). I think this would greatly simplify the packaging task. (You could still provide an auxilliary tarball of the dependencies for Windows users, but Linux users would get them for free as part of their distribution.) That's my thought. Does it sound radical? Mike On Sep 8, 11:05 am, Matthew Chambers matthew.chamb...@vanderbilt.edu wrote: If TPP would link to boost statically it wouldn't be an issue. But IIRC there has been a thread on this topic before and it wasn't deemed worth the effort of maintaining...unless you're volunteering? ;) -Matt Mike Coleman wrote: Has there been any thought about packaging up TPP for Ubuntu/Debian and possibly RedHat/CentOS? I went through the exercise of installing it from scratch, following the directions on the wiki page, and I can imagine that this would be quite daunting for a non-programmer. Just off the top of my head, it looks like the main problem to solve will be that TPP is tending to rely on bleeding-edge versions of the Boost libraries. Is there any chance that a change could be made to stick with versions that are merely reasonably current (and thus packaged)? (Ubuntu Jaunty has 1.37, for example.) --~--~-~--~~~---~--~~ You received this message because you are subscribed to the Google Groups spctools-discuss group. To post to this group, send email to spctools-discuss@googlegroups.com To unsubscribe from this group, send email to spctools-discuss+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en -~--~~~~--~~--~--~---
[spctools-discuss] Re: Ubuntu/Debian/RedHat TPP packages?
My ideas somewhat differ on this, but you guys are doing the work, and it would hardly do for me to be disagreeable. I'm glad to hear that you're working on build scripts--this should improve the situation, and is a step towards packaging later, if you decide it's worthwhile. Mike On Sep 8, 2:06 pm, Brian Pratt brian.pr...@insilicos.com wrote: Windows actually remains the most important thing to package, if for no other reason than that's where the converters have to live. And, I think, if you look at the traffic on the list it's at least half the TPP user base (that's not very scientific though, I grant you). Again, we already do build Boost out of the extern directory, precisely because, for example, boost 1.39 isn't in any debian package yet. It's less bother in the end to just build things like boost and expat than it is to manage dependencies on external packages (and thus maintain a several different package manager configurations for several different linux distros). Like you, I'm not up for extra work, and the way we're doing it now seems to be the laziest available without simply dumping the dependency management upon the would-be builder. We do provide scripts for building on several linux distros, which hopefully will become increasingly robust as they get more use. They do have to be able to assume some baseline (like a normally functioning bash shell) but then so does a package manager. I just don't think it's broken, especially given the resources we have. Brian On Tue, Sep 8, 2009 at 10:33 AM, Mike Coleman tutu...@gmail.com wrote: Version 1.39 of Boost isn't in Ubuntu currently, so there's nothing to link to that way. I assume you mean doing something like folding Boost into the TPP/extern directory and handling Boost as libexpat is handled, for example. I'm not completely unsympathetic to this idea, but on the whole I'm against this. Having your own local copy means supporting your own local copy, which translates into more work (which I don't like to do :-). As to whether it's worthwhile to package TPP for Linux, I don't know. I've been trying to help out Eliza, who would clearly benefit. I'd have probably tried out TPP sooner myself if there had been an easily installed Linux package. But are there really a lot of potential users, and does the TPP project care about reaching them? I don't even know how large the Windows user community is. As to volunteering, it's not out of the question. It'd depend on the above (whether it's really worth doing). Also, I think that in order to make this work well, we'd really want to separate TPP from its dependencies. That is, rather than including expat (for example) in the TPP source tree, instead have each version stipulate that it depends on version X of expat (or more typically, version X or later). I think this would greatly simplify the packaging task. (You could still provide an auxilliary tarball of the dependencies for Windows users, but Linux users would get them for free as part of their distribution.) That's my thought. Does it sound radical? Mike On Sep 8, 11:05 am, Matthew Chambers matthew.chamb...@vanderbilt.edu wrote: If TPP would link to boost statically it wouldn't be an issue. But IIRC there has been a thread on this topic before and it wasn't deemed worth the effort of maintaining...unless you're volunteering? ;) -Matt Mike Coleman wrote: Has there been any thought about packaging up TPP for Ubuntu/Debian and possibly RedHat/CentOS? I went through the exercise of installing it from scratch, following the directions on the wiki page, and I can imagine that this would be quite daunting for a non-programmer. Just off the top of my head, it looks like the main problem to solve will be that TPP is tending to rely on bleeding-edge versions of the Boost libraries. Is there any chance that a change could be made to stick with versions that are merely reasonably current (and thus packaged)? (Ubuntu Jaunty has 1.37, for example.) --~--~-~--~~~---~--~~ You received this message because you are subscribed to the Google Groups spctools-discuss group. To post to this group, send email to spctools-discuss@googlegroups.com To unsubscribe from this group, send email to spctools-discuss+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en -~--~~~~--~~--~--~---
[spctools-discuss] Re: Failure with make
There may be multiple problems. Please upload a new 'strace' log... On Sep 4, 3:05 am, Eliza blond...@googlemail.com wrote: Mike - having an empty Makefile.config.incl didn't fix anything. I am still getting the error: make: *** No rule to make target `/ Makefile.pwiz.incl'. Stop. On Sep 1, 10:21 pm, Mike Coleman tutu...@gmail.com wrote: Okay, this turned out to be useful. It appears that the contents of your file 'Makefile.config.incl' is including itself (it appears to be a copy of 'Makefile.incl'). This recurses about 1000 times, at which point you hit the file handle limit. The resulting error is apparently ignored due to the '-include'. So, either make 'Makefile.config.incl' an empty file, or otherwise I think it should be just a short file including a few variable definitions. Also, verify that neither of these files is a symbolic or hard link to the other. Probably this will fix things, or at least move things forward. Mike On Aug 31, 2:34 am, Eliza blond...@googlemail.com wrote: OK I have added make.strace.gz to the file uploads. On Aug 28, 6:34 pm, Mike Coleman tutu...@gmail.com wrote: Okay, if you really want to bring out the big guns, do something like this $ strace -f -s 1024 -v -o make.strace make and put the resulting 'make.strace' log somewhere where we can look at it. I think this is erroring out pretty quickly, so hopefully that log won't be too huge. No promises, but this may very well clarify what's going wrong. You'll have to install the strace package if it's not already present. Mike On Aug 28, 4:59 am, Eliza blond...@googlemail.com wrote: That doesn't make any difference. On Aug 27, 8:12 pm, Brian Pratt brian.pr...@insilicos.com wrote: Yeah, that's what we use here too. Perhaps you could try it as a different, newly created user? It sounds like there is something peculiar about your shell setup. -Original Message- From: spctools-discuss@googlegroups.com [mailto:spctools-disc...@googlegroups.com] On Behalf Of Eliza Sent: Thursday, August 27, 2009 12:13 AM To: spctools-discuss Subject: [spctools-discuss] Re: Failure with make Bash On Aug 20, 11:55 pm, Brian Pratt brian.pr...@insilicos.com wrote: We basically tried that already: Eliza says the suggested export PWD=/opt/trans_proteomic_pipeline/src ; make all install did not work. She also tried the SRC_ROOT= $(shell pwd) change to the makefile. There's something deeper going on. Eliza, what shell do you use? I do see from googling that $PWD might be bash-specific, possibly there are other unintended bash dependencies. Brian -Original Message- From: spctools-discuss@googlegroups.com [mailto:spctools-disc...@googlegroups.com] On Behalf Of Mike Coleman Sent: Thursday, August 20, 2009 1:26 PM To: spctools-discuss Subject: [spctools-discuss] Re: Failure with make Eliza, I'm still suspicious about the $PWD thing. If you're running 'make' normally, you might try something like $ PWD=$(pwd) make ... instead of just $ make ... to see whether that improves your situation. Alternatively, for the 'root' steps, you could do something like $ sudo PWD=$(pwd) make ... Mike --~--~-~--~~~---~--~~ You received this message because you are subscribed to the Google Groups spctools-discuss group. To post to this group, send email to spctools-discuss@googlegroups.com To unsubscribe from this group, send email to spctools-discuss+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en -~--~~~~--~~--~--~---
[spctools-discuss] Re: Failure with make
Okay, this turned out to be useful. It appears that the contents of your file 'Makefile.config.incl' is including itself (it appears to be a copy of 'Makefile.incl'). This recurses about 1000 times, at which point you hit the file handle limit. The resulting error is apparently ignored due to the '-include'. So, either make 'Makefile.config.incl' an empty file, or otherwise I think it should be just a short file including a few variable definitions. Also, verify that neither of these files is a symbolic or hard link to the other. Probably this will fix things, or at least move things forward. Mike On Aug 31, 2:34 am, Eliza blond...@googlemail.com wrote: OK I have added make.strace.gz to the file uploads. On Aug 28, 6:34 pm, Mike Coleman tutu...@gmail.com wrote: Okay, if you really want to bring out the big guns, do something like this $ strace -f -s 1024 -v -o make.strace make and put the resulting 'make.strace' log somewhere where we can look at it. I think this is erroring out pretty quickly, so hopefully that log won't be too huge. No promises, but this may very well clarify what's going wrong. You'll have to install the strace package if it's not already present. Mike On Aug 28, 4:59 am, Eliza blond...@googlemail.com wrote: That doesn't make any difference. On Aug 27, 8:12 pm, Brian Pratt brian.pr...@insilicos.com wrote: Yeah, that's what we use here too. Perhaps you could try it as a different, newly created user? It sounds like there is something peculiar about your shell setup. -Original Message- From: spctools-discuss@googlegroups.com [mailto:spctools-disc...@googlegroups.com] On Behalf Of Eliza Sent: Thursday, August 27, 2009 12:13 AM To: spctools-discuss Subject: [spctools-discuss] Re: Failure with make Bash On Aug 20, 11:55 pm, Brian Pratt brian.pr...@insilicos.com wrote: We basically tried that already: Eliza says the suggested export PWD=/opt/trans_proteomic_pipeline/src ; make all install did not work. She also tried the SRC_ROOT= $(shell pwd) change to the makefile. There's something deeper going on. Eliza, what shell do you use? I do see from googling that $PWD might be bash-specific, possibly there are other unintended bash dependencies. Brian -Original Message- From: spctools-discuss@googlegroups.com [mailto:spctools-disc...@googlegroups.com] On Behalf Of Mike Coleman Sent: Thursday, August 20, 2009 1:26 PM To: spctools-discuss Subject: [spctools-discuss] Re: Failure with make Eliza, I'm still suspicious about the $PWD thing. If you're running 'make' normally, you might try something like $ PWD=$(pwd) make ... instead of just $ make ... to see whether that improves your situation. Alternatively, for the 'root' steps, you could do something like $ sudo PWD=$(pwd) make ... Mike --~--~-~--~~~---~--~~ You received this message because you are subscribed to the Google Groups spctools-discuss group. To post to this group, send email to spctools-discuss@googlegroups.com To unsubscribe from this group, send email to spctools-discuss+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en -~--~~~~--~~--~--~---
[spctools-discuss] Re: Failure with make
Eliza, I'm still suspicious about the $PWD thing. If you're running 'make' normally, you might try something like $ PWD=$(pwd) make ... instead of just $ make ... to see whether that improves your situation. Alternatively, for the 'root' steps, you could do something like $ sudo PWD=$(pwd) make ... Mike --~--~-~--~~~---~--~~ You received this message because you are subscribed to the Google Groups spctools-discuss group. To post to this group, send email to spctools-discuss@googlegroups.com To unsubscribe from this group, send email to spctools-discuss+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en -~--~~~~--~~--~--~---
[spctools-discuss] Re: Failure with make
I can speak to that, having just bumped into it. SRC_ROOT is defined as $(PWD)/ in the Makefile, but $PWD may not exist in the environment, leading to a definition of SRC_ROOT=/. In particular, on the latest version of Ubuntu, 'sudo printenv' shows no definition of PWD. I'm not that crazy about them having left it out, but there it is, and there's really no standard that says it has to be defined. For GNU make, you could use one of On Aug 13, 11:51 am, Brian Pratt brian.pr...@insilicos.com wrote: Natalie is correct, the issue is around SRC_ROOT=/ . As she says, your current working directory needs to be the one that contains the main TPP makefile (and the Makefile.pwiz.incl file). -Original Message- From: spctools-discuss@googlegroups.com [mailto:spctools-disc...@googlegroups.com] On Behalf Of Eliza Sent: Thursday, August 13, 2009 7:46 AM To: spctools-discuss Subject: [spctools-discuss] Re: Failure with make I got the latest version of TPP (4.3.0) and this time when trying to make I am getting the following error: Makefile.incl:431: /Makefile.pwiz.incl: No such file or directory make: *** No rule to make target `/Makefile.pwiz.incl'. Stop. On Aug 5, 10:25 pm, Natalie Tasman natalie.tas...@insilicos.com wrote: Hi Eliza, It sounds like something strange is going on. Maybe you should re- load the sourcecode. Also, I've never seen SRC_ROOT=/ come up before. Are you starting the build from /, rather than the actual TPP/ src directory? You want to cd there first. It does sound like a corrupted checkout (missing files, etc), too, possibly. Natalie On Aug 5, 2009, at 1:29 AM, Eliza wrote: Hi Natalie, I have tried your suggestion and 'make distclean; make fails at: make -C ../extern/xtandem/src SRC_ROOT=/ ARCH=linux BUILD_DIR=/../ build/linux clean make[1]: Entering directory `/usr/local/src/tpp-4.2.1/extern/xtandem/ src' make[1]: *** No rule to make target `clean'. Stop. Thanks, Eliza. On Jul 31, 8:19 pm, Natalie Tasman natalie.tas...@insilicos.com wrote: Hi Eliza, I haven't run into this before, but you may want to try a make distclean; make sequence. I would also look at the compiler output earlier in the stream and see if there were any uncaught errors building the AminoAcid that might provide a clue. Please let us know how it goes, and good luck, Natalie On Jul 31, 2009, at 4:25 AM, Eliza wrote: Hi, I am receiving the following error when trying to issue 'make' in the src directory: make[1]: *** No rule to make target `/../build/linux/AminoAcid.o', needed by `/../build/linux/libpwiz.a'. Stop. make[1]: Leaving directory `/usr/local/src/tpp-4.2.1/src' make: *** [default] Error 2 TPP version 4.2.1 Debian Etch kernel 2.6.15.4 Compiler version 4.3.2 Thanks, Eliza. --~--~-~--~~~---~--~~ You received this message because you are subscribed to the Google Groups spctools-discuss group. To post to this group, send email to spctools-discuss@googlegroups.com To unsubscribe from this group, send email to spctools-discuss+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en -~--~~~~--~~--~--~---
[spctools-discuss] Re: Failure with make
[sorry about the previous half-finished post] I can speak to that, having just bumped into it. SRC_ROOT is defined as $(PWD)/ in the Makefile, but $PWD may not exist in the environment, leading to a definition of SRC_ROOT=/. In particular, on the latest version of Ubuntu, 'sudo printenv' shows no definition of PWD. I'm not that crazy about them having left it out, but there it is, and there's really no standard that says it has to be defined. For GNU make, you could use one of $(realpath .) $(abspath .) $(shell pwd) The best solution, though, would be to get rid of SRC_ROOT altogether and use relative paths, if possible. Mike On Aug 13, 11:51 am, Brian Pratt brian.pr...@insilicos.com wrote: Natalie is correct, the issue is around SRC_ROOT=/ . As she says, your current working directory needs to be the one that contains the main TPP makefile (and the Makefile.pwiz.incl file). -Original Message- From: spctools-discuss@googlegroups.com [mailto:spctools-disc...@googlegroups.com] On Behalf Of Eliza Sent: Thursday, August 13, 2009 7:46 AM To: spctools-discuss Subject: [spctools-discuss] Re: Failure with make I got the latest version of TPP (4.3.0) and this time when trying to make I am getting the following error: Makefile.incl:431: /Makefile.pwiz.incl: No such file or directory make: *** No rule to make target `/Makefile.pwiz.incl'. Stop. On Aug 5, 10:25 pm, Natalie Tasman natalie.tas...@insilicos.com wrote: Hi Eliza, It sounds like something strange is going on. Maybe you should re- load the sourcecode. Also, I've never seen SRC_ROOT=/ come up before. Are you starting the build from /, rather than the actual TPP/ src directory? You want to cd there first. It does sound like a corrupted checkout (missing files, etc), too, possibly. Natalie On Aug 5, 2009, at 1:29 AM, Eliza wrote: Hi Natalie, I have tried your suggestion and 'make distclean; make fails at: make -C ../extern/xtandem/src SRC_ROOT=/ ARCH=linux BUILD_DIR=/../ build/linux clean make[1]: Entering directory `/usr/local/src/tpp-4.2.1/extern/xtandem/ src' make[1]: *** No rule to make target `clean'. Stop. Thanks, Eliza. On Jul 31, 8:19 pm, Natalie Tasman natalie.tas...@insilicos.com wrote: Hi Eliza, I haven't run into this before, but you may want to try a make distclean; make sequence. I would also look at the compiler output earlier in the stream and see if there were any uncaught errors building the AminoAcid that might provide a clue. Please let us know how it goes, and good luck, Natalie On Jul 31, 2009, at 4:25 AM, Eliza wrote: Hi, I am receiving the following error when trying to issue 'make' in the src directory: make[1]: *** No rule to make target `/../build/linux/AminoAcid.o', needed by `/../build/linux/libpwiz.a'. Stop. make[1]: Leaving directory `/usr/local/src/tpp-4.2.1/src' make: *** [default] Error 2 TPP version 4.2.1 Debian Etch kernel 2.6.15.4 Compiler version 4.3.2 Thanks, Eliza. --~--~-~--~~~---~--~~ You received this message because you are subscribed to the Google Groups spctools-discuss group. To post to this group, send email to spctools-discuss@googlegroups.com To unsubscribe from this group, send email to spctools-discuss+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en -~--~~~~--~~--~--~---
[spctools-discuss] Re: Failure with make
It may have, I'm not sure. I'd never seen this behavior previously. And actually, I filed a bug on it, as I think $PWD shouldn't be gratuitously removed. So far I'm not getting much traction convincing anyone else of that, though. Mike On Aug 13, 3:24 pm, Natalie Tasman natalie.tas...@insilicos.com wrote: Hi Mike, That's a strange report about Ubuntu. I'm routinely building on 8.04 and 9.04. Did something change in 9.10? -Natalie On Aug 13, 2009, at 1:09 PM, Mike Coleman wrote: [sorry about the previous half-finished post] I can speak to that, having just bumped into it. SRC_ROOT is defined as $(PWD)/ in the Makefile, but $PWD may not exist in the environment, leading to a definition of SRC_ROOT=/. In particular, on the latest version of Ubuntu, 'sudo printenv' shows no definition of PWD. I'm not that crazy about them having left it out, but there it is, and there's really no standard that says it has to be defined. For GNU make, you could use one of $(realpath .) $(abspath .) $(shell pwd) The best solution, though, would be to get rid of SRC_ROOT altogether and use relative paths, if possible. Mike On Aug 13, 11:51 am, Brian Pratt brian.pr...@insilicos.com wrote: Natalie is correct, the issue is around SRC_ROOT=/ . As she says, your current working directory needs to be the one that contains the main TPP makefile (and the Makefile.pwiz.incl file). -Original Message- From: spctools-discuss@googlegroups.com [mailto:spctools-disc...@googlegroups.com] On Behalf Of Eliza Sent: Thursday, August 13, 2009 7:46 AM To: spctools-discuss Subject: [spctools-discuss] Re: Failure with make I got the latest version of TPP (4.3.0) and this time when trying to make I am getting the following error: Makefile.incl:431: /Makefile.pwiz.incl: No such file or directory make: *** No rule to make target `/Makefile.pwiz.incl'. Stop. On Aug 5, 10:25 pm, Natalie Tasman natalie.tas...@insilicos.com wrote: Hi Eliza, It sounds like something strange is going on. Maybe you should re- load the sourcecode. Also, I've never seen SRC_ROOT=/ come up before. Are you starting the build from /, rather than the actual TPP/ src directory? You want to cd there first. It does sound like a corrupted checkout (missing files, etc), too, possibly. Natalie On Aug 5, 2009, at 1:29 AM, Eliza wrote: Hi Natalie, I have tried your suggestion and 'make distclean; make fails at: make -C ../extern/xtandem/src SRC_ROOT=/ ARCH=linux BUILD_DIR=/../ build/linux clean make[1]: Entering directory `/usr/local/src/tpp-4.2.1/extern/ xtandem/ src' make[1]: *** No rule to make target `clean'. Stop. Thanks, Eliza. On Jul 31, 8:19 pm, Natalie Tasman natalie.tas...@insilicos.com wrote: Hi Eliza, I haven't run into this before, but you may want to try a make distclean; make sequence. I would also look at the compiler output earlier in the stream and see if there were any uncaught errors building the AminoAcid that might provide a clue. Please let us know how it goes, and good luck, Natalie On Jul 31, 2009, at 4:25 AM, Eliza wrote: Hi, I am receiving the following error when trying to issue 'make' in the src directory: make[1]: *** No rule to make target `/../build/linux/ AminoAcid.o', needed by `/../build/linux/libpwiz.a'. Stop. make[1]: Leaving directory `/usr/local/src/tpp-4.2.1/src' make: *** [default] Error 2 TPP version 4.2.1 Debian Etch kernel 2.6.15.4 Compiler version 4.3.2 Thanks, Eliza. --~--~-~--~~~---~--~~ You received this message because you are subscribed to the Google Groups spctools-discuss group. To post to this group, send email to spctools-discuss@googlegroups.com To unsubscribe from this group, send email to spctools-discuss+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en -~--~~~~--~~--~--~---
[spctools-discuss] patch: Sqt2XML fixes
Here are some fixes for Sqt2XML. I can separate this into smaller
parts if needed, or provide it in another form.
Mike
commit af141a678622bed5074775b94b427dfa29f4126b
Author: Mike Coleman m...@delta.(none)
Date: Fri Aug 7 16:03:24 2009 -0500
fix typo
commit c6b12aac98e802bd134d92ee17ce8c92504b8841
Author: Mike Coleman m...@delta.(none)
Date: Thu Aug 6 13:08:49 2009 -0500
fix: define proton mass using double-precision constant, to avoid
losing precision
commit e74c7f634b1947be3b33e9a90b9f429f21be64d4
Author: Mike Coleman m...@delta.(none)
Date: Thu Aug 6 12:29:40 2009 -0500
fix: trim whitespace from SEQUEST output to give correct peptide
also trim locus, defensively
commit fc6067ae1644f975501a587db27d904bcd7ee32f
Author: Mike Coleman m...@delta.(none)
Date: Thu Aug 6 11:57:51 2009 -0500
fix: default DeltaCn is 0 (not 1)
commit bc0f748e4dc1e613dccd97c0bf4be095015f0438
Author: Mike Coleman m...@delta.(none)
Date: Thu Aug 6 11:43:36 2009 -0500
fix: require only one argument
diff --git a/README.txt b/README.txt
index a4b9ed9..f0eb92c 100644
--- a/README.txt
+++ b/README.txt
@@ -248,7 +248,7 @@ You need to start with a converter to write out
search results as 'summary.xml'
You can view the search results by opening the 'summary.xml' file in
your browser.
Next, you can run xinteract to apply all or some parts of the
pipeline. Type 'xinteract' with no arguments for usage instructions.
-You can also convert and run the pipeline in one step. See xinterct
instructions for details.
+You can also convert and run the pipeline in one step. See xinteract
instructions for details.
To run the pipeline manually, starting with file1.xml and file2.xml:
diff --git a/src/Parsers/Algorithm2XML/Sqt2XML/Sqt2XML.cxx b/src/
Parsers/Algorithm2XML/Sqt2XML/Sqt2XML.cxx
index b569402..8dcd2e8 100644
--- a/src/Parsers/Algorithm2XML/Sqt2XML/Sqt2XML.cxx
+++ b/src/Parsers/Algorithm2XML/Sqt2XML/Sqt2XML.cxx
@@ -18,7 +18,15 @@
#endif
#endif
-static double fProtonMass = 1.007276f;
+static const double protonMass = 1.007276;
+
+
+string trim(string s, const string dropChars = \t\f\r\n)
+{
+ string r = s.erase(s.find_last_not_of(dropChars) + 1);
+ return r.erase(0, r.find_first_not_of(dropChars));
+}
+
void writeTagArray( SimpleXMLWriter writer, ArrayTag** tagArray )
{
@@ -61,7 +69,7 @@ int main(int argc, char** argv) {
string paramsFilepath = sequest.params;
char* sample_enzyme = new char[128];
- int minArgs = 2;
+ int minArgs = 1;
int flagArgs = 0;
strcpy(sample_enzyme, trypsin);
@@ -306,6 +314,8 @@ int main(int argc, char** argv) {
tokenStart = tokenEnd+1; tokenEnd = inputLine.find(
'\t',
tokenStart+1 );
//cout \ inputLine.substr( tokenStart,
tokenEnd-
tokenStart ) \\n;
m.sequence = inputLine.substr( tokenStart,
tokenEnd-tokenStart );
+ // SEQUEST output includes extra whitespace, so must
trim here!
+ m.sequence = trim( m.sequence );
//m.sequence = m.sequence.substr( 2,
m.sequence.length() - 4 ); //
trim flanking residue notation
//m.sequence = ConvertSqtPtmToFreiPtm( r.sequence,
fileResidueMap );
//cout m.sequence endl;
@@ -319,7 +329,9 @@ int main(int argc, char** argv) {
tokenStart = 2; // skip L and \t
tokenEnd = inputLine.find_first_of( \r\n\t ,
tokenStart+1 );
//cout \ inputLine.substr( tokenStart,
tokenEnd-
tokenStart ) \\n;
- m.loci.push_back( L_entry( inputLine.substr(
tokenStart, tokenEnd-
tokenStart ) ) );
+ string locus = inputLine.substr( tokenStart,
tokenEnd-
tokenStart );
+ locus = trim( locus );
+ m.loci.push_back( L_entry( locus ) );
getline( sqtFile, inputLine );
}
@@ -338,7 +350,7 @@ int main(int argc, char** argv) {
writer.attr( spectrum, spectrumId.str() );
writer.attr( start_scan, s.firstScan );
writer.attr( end_scan, s.lastScan );
- float precursorNeutralMass = s.observedMassPlus1 - fProtonMass;
+ float precursorNeutralMass = s.observedMassPlus1 - protonMass;
writer.attr( precursor_neutral_mass, precursorNeutralMass );
writer.attr( assumed_charge, s.chargeState );
writer.attr( index, index++ );
@@ -390,7 +402,7 @@ int main(int argc, char** argv) {
writer.attr( num_tot_proteins, (int)
m.loci.size() );
writer.attr( num_matched_ions, m.matchedIons
);
writer.attr( tot_num_ions, m.predictedIons
