diff --git a/LICENSE b/LICENSE new file mode 100644 --- /dev/null +++ b/LICENSE @@ -0,0 +1,340 @@ + GNU GENERAL PUBLIC LICENSE + Version 2, June 1991 + + Copyright (C) 1989, 1991 Free Software Foundation, Inc. + 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The licenses for most software are designed to take away your +freedom to share and change it. By contrast, the GNU General Public +License is intended to guarantee your freedom to share and change free +software--to make sure the software is free for all its users. This +General Public License applies to most of the Free Software +Foundation's software and to any other program whose authors commit to +using it. (Some other Free Software Foundation software is covered by +the GNU Library General Public License instead.) You can apply it to +your programs, too. + + When we speak of free software, we are referring to freedom, not +price. Our General Public Licenses are designed to make sure that you +have the freedom to distribute copies of free software (and charge for +this service if you wish), that you receive source code or can get it +if you want it, that you can change the software or use pieces of it +in new free programs; and that you know you can do these things. + + To protect your rights, we need to make restrictions that forbid +anyone to deny you these rights or to ask you to surrender the rights. +These restrictions translate to certain responsibilities for you if you +distribute copies of the software, or if you modify it. + + For example, if you distribute copies of such a program, whether +gratis or for a fee, you must give the recipients all the rights that +you have. You must make sure that they, too, receive or can get the +source code. And you must show them these terms so they know their +rights. + + We protect your rights with two steps: (1) copyright the software, and +(2) offer you this license which gives you legal permission to copy, +distribute and/or modify the software. + + Also, for each author's protection and ours, we want to make certain +that everyone understands that there is no warranty for this free +software. If the software is modified by someone else and passed on, we +want its recipients to know that what they have is not the original, so +that any problems introduced by others will not reflect on the original +authors' reputations. + + Finally, any free program is threatened constantly by software +patents. We wish to avoid the danger that redistributors of a free +program will individually obtain patent licenses, in effect making the +program proprietary. To prevent this, we have made it clear that any +patent must be licensed for everyone's free use or not licensed at all. + + The precise terms and conditions for copying, distribution and +modification follow. + + GNU GENERAL PUBLIC LICENSE + TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION + + 0. This License applies to any program or other work which contains +a notice placed by the copyright holder saying it may be distributed +under the terms of this General Public License. The "Program", below, +refers to any such program or work, and a "work based on the Program" +means either the Program or any derivative work under copyright law: +that is to say, a work containing the Program or a portion of it, +either verbatim or with modifications and/or translated into another +language. (Hereinafter, translation is included without limitation in +the term "modification".) Each licensee is addressed as "you". + +Activities other than copying, distribution and modification are not +covered by this License; they are outside its scope. The act of +running the Program is not restricted, and the output from the Program +is covered only if its contents constitute a work based on the +Program (independent of having been made by running the Program). +Whether that is true depends on what the Program does. + + 1. You may copy and distribute verbatim copies of the Program's +source code as you receive it, in any medium, provided that you +conspicuously and appropriately publish on each copy an appropriate +copyright notice and disclaimer of warranty; keep intact all the +notices that refer to this License and to the absence of any warranty; +and give any other recipients of the Program a copy of this License +along with the Program. + +You may charge a fee for the physical act of transferring a copy, and +you may at your option offer warranty protection in exchange for a fee. + + 2. You may modify your copy or copies of the Program or any portion +of it, thus forming a work based on the Program, and copy and +distribute such modifications or work under the terms of Section 1 +above, provided that you also meet all of these conditions: + + a) You must cause the modified files to carry prominent notices + stating that you changed the files and the date of any change. + + b) You must cause any work that you distribute or publish, that in + whole or in part contains or is derived from the Program or any + part thereof, to be licensed as a whole at no charge to all third + parties under the terms of this License. + + c) If the modified program normally reads commands interactively + when run, you must cause it, when started running for such + interactive use in the most ordinary way, to print or display an + announcement including an appropriate copyright notice and a + notice that there is no warranty (or else, saying that you provide + a warranty) and that users may redistribute the program under + these conditions, and telling the user how to view a copy of this + License. (Exception: if the Program itself is interactive but + does not normally print such an announcement, your work based on + the Program is not required to print an announcement.) + +These requirements apply to the modified work as a whole. If +identifiable sections of that work are not derived from the Program, +and can be reasonably considered independent and separate works in +themselves, then this License, and its terms, do not apply to those +sections when you distribute them as separate works. But when you +distribute the same sections as part of a whole which is a work based +on the Program, the distribution of the whole must be on the terms of +this License, whose permissions for other licensees extend to the +entire whole, and thus to each and every part regardless of who wrote it. + +Thus, it is not the intent of this section to claim rights or contest +your rights to work written entirely by you; rather, the intent is to +exercise the right to control the distribution of derivative or +collective works based on the Program. + +In addition, mere aggregation of another work not based on the Program +with the Program (or with a work based on the Program) on a volume of +a storage or distribution medium does not bring the other work under +the scope of this License. + + 3. You may copy and distribute the Program (or a work based on it, +under Section 2) in object code or executable form under the terms of +Sections 1 and 2 above provided that you also do one of the following: + + a) Accompany it with the complete corresponding machine-readable + source code, which must be distributed under the terms of Sections + 1 and 2 above on a medium customarily used for software interchange; or, + + b) Accompany it with a written offer, valid for at least three + years, to give any third party, for a charge no more than your + cost of physically performing source distribution, a complete + machine-readable copy of the corresponding source code, to be + distributed under the terms of Sections 1 and 2 above on a medium + customarily used for software interchange; or, + + c) Accompany it with the information you received as to the offer + to distribute corresponding source code. (This alternative is + allowed only for noncommercial distribution and only if you + received the program in object code or executable form with such + an offer, in accord with Subsection b above.) + +The source code for a work means the preferred form of the work for +making modifications to it. For an executable work, complete source +code means all the source code for all modules it contains, plus any +associated interface definition files, plus the scripts used to +control compilation and installation of the executable. However, as a +special exception, the source code distributed need not include +anything that is normally distributed (in either source or binary +form) with the major components (compiler, kernel, and so on) of the +operating system on which the executable runs, unless that component +itself accompanies the executable. + +If distribution of executable or object code is made by offering +access to copy from a designated place, then offering equivalent +access to copy the source code from the same place counts as +distribution of the source code, even though third parties are not +compelled to copy the source along with the object code. + + 4. You may not copy, modify, sublicense, or distribute the Program +except as expressly provided under this License. Any attempt +otherwise to copy, modify, sublicense or distribute the Program is +void, and will automatically terminate your rights under this License. +However, parties who have received copies, or rights, from you under +this License will not have their licenses terminated so long as such +parties remain in full compliance. + + 5. You are not required to accept this License, since you have not +signed it. However, nothing else grants you permission to modify or +distribute the Program or its derivative works. These actions are +prohibited by law if you do not accept this License. Therefore, by +modifying or distributing the Program (or any work based on the +Program), you indicate your acceptance of this License to do so, and +all its terms and conditions for copying, distributing or modifying +the Program or works based on it. + + 6. Each time you redistribute the Program (or any work based on the +Program), the recipient automatically receives a license from the +original licensor to copy, distribute or modify the Program subject to +these terms and conditions. You may not impose any further +restrictions on the recipients' exercise of the rights granted herein. +You are not responsible for enforcing compliance by third parties to +this License. + + 7. If, as a consequence of a court judgment or allegation of patent +infringement or for any other reason (not limited to patent issues), +conditions are imposed on you (whether by court order, agreement or +otherwise) that contradict the conditions of this License, they do not +excuse you from the conditions of this License. If you cannot +distribute so as to satisfy simultaneously your obligations under this +License and any other pertinent obligations, then as a consequence you +may not distribute the Program at all. For example, if a patent +license would not permit royalty-free redistribution of the Program by +all those who receive copies directly or indirectly through you, then +the only way you could satisfy both it and this License would be to +refrain entirely from distribution of the Program. + +If any portion of this section is held invalid or unenforceable under +any particular circumstance, the balance of the section is intended to +apply and the section as a whole is intended to apply in other +circumstances. + +It is not the purpose of this section to induce you to infringe any +patents or other property right claims or to contest validity of any +such claims; this section has the sole purpose of protecting the +integrity of the free software distribution system, which is +implemented by public license practices. Many people have made +generous contributions to the wide range of software distributed +through that system in reliance on consistent application of that +system; it is up to the author/donor to decide if he or she is willing +to distribute software through any other system and a licensee cannot +impose that choice. + +This section is intended to make thoroughly clear what is believed to +be a consequence of the rest of this License. + + 8. If the distribution and/or use of the Program is restricted in +certain countries either by patents or by copyrighted interfaces, the +original copyright holder who places the Program under this License +may add an explicit geographical distribution limitation excluding +those countries, so that distribution is permitted only in or among +countries not thus excluded. In such case, this License incorporates +the limitation as if written in the body of this License. + + 9. The Free Software Foundation may publish revised and/or new versions +of the General Public License from time to time. Such new versions will +be similar in spirit to the present version, but may differ in detail to +address new problems or concerns. + +Each version is given a distinguishing version number. If the Program +specifies a version number of this License which applies to it and "any +later version", you have the option of following the terms and conditions +either of that version or of any later version published by the Free +Software Foundation. If the Program does not specify a version number of +this License, you may choose any version ever published by the Free Software +Foundation. + + 10. If you wish to incorporate parts of the Program into other free +programs whose distribution conditions are different, write to the author +to ask for permission. For software which is copyrighted by the Free +Software Foundation, write to the Free Software Foundation; we sometimes +make exceptions for this. Our decision will be guided by the two goals +of preserving the free status of all derivatives of our free software and +of promoting the sharing and reuse of software generally. + + NO WARRANTY + + 11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY +FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN +OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES +PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED +OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS +TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE +PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, +REPAIR OR CORRECTION. + + 12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING +WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR +REDISTRIBUTE THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, +INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING +OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED +TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY +YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER +PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE +POSSIBILITY OF SUCH DAMAGES. + + END OF TERMS AND CONDITIONS + + How to Apply These Terms to Your New Programs + + If you develop a new program, and you want it to be of the greatest +possible use to the public, the best way to achieve this is to make it +free software which everyone can redistribute and change under these terms. + + To do so, attach the following notices to the program. It is safest +to attach them to the start of each source file to most effectively +convey the exclusion of warranty; and each file should have at least +the "copyright" line and a pointer to where the full notice is found. + + + Copyright (C) + + This program is free software; you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation; either version 2 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with this program; if not, write to the Free Software + Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA + + +Also add information on how to contact you by electronic and paper mail. + +If the program is interactive, make it output a short notice like this +when it starts in an interactive mode: + + Gnomovision version 69, Copyright (C) year name of author + Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'. + This is free software, and you are welcome to redistribute it + under certain conditions; type `show c' for details. + +The hypothetical commands `show w' and `show c' should show the appropriate +parts of the General Public License. Of course, the commands you use may +be called something other than `show w' and `show c'; they could even be +mouse-clicks or menu items--whatever suits your program. + +You should also get your employer (if you work as a programmer) or your +school, if any, to sign a "copyright disclaimer" for the program, if +necessary. Here is a sample; alter the names: + + Yoyodyne, Inc., hereby disclaims all copyright interest in the program + `Gnomovision' (which makes passes at compilers) written by James Hacker. + + , 1 April 1989 + Ty Coon, President of Vice + +This General Public License does not permit incorporating your program into +proprietary programs. If your program is a subroutine library, you may +consider it more useful to permit linking proprietary applications with the +library. If this is what you want to do, use the GNU Library General +Public License instead of this License. diff --git a/README b/README new file mode 100644 --- /dev/null +++ b/README @@ -0,0 +1,47 @@ + +SYNOPSIS + + xml2x - convert blast output in XML format, either to a (csv) + table suitable for e.g. importing into Excel or OOCalc, or + to HTML. Optionally annotating the output with GO terms. + +INSTALLATION + + The usual cabal routine, should also be possible to compile via + the Makefile. + +USAGE + + xml2x [options] xmlfile1 xmlfile2... + + Options include --annotations to specify the mapping between + UniProt accessions and GO terms. This file is usually called + "gene_association.goa_uniprot", and is available from the GO + consortium. The file is several GB, you may want to consider + trimming it down a bit by filtering out the automatic (IEA) + annotations. + + Additionally, you can use --go-defs to specify the description of + the GO terms, and the output will then be somewhat more + meaningful. The file is usually called "GO.terms_and_ids", + similarly available. + + Output format is specified with -C or -H, with -C being the default. + + For CSV output, the following modes are supported + + --all - output all blast matches (HSPs), one per line + --top - output only the top hit for each input sequence + --region - output top hit for regions that overlap <50% + + Use -v on an interactive terminal to keep track of progress. + +BUGS + + HTML isn't implemented yet. + + XML parsing is slow, but ndm said he'd look into it. + + Must be compiled with -smp to avoid huge memory requirements, but + the plus side is that with -smp, we use a lot less RAM than + AutoFact. diff --git a/Setup.hs b/Setup.hs new file mode 100644 --- /dev/null +++ b/Setup.hs @@ -0,0 +1,5 @@ +#!/usr/bin/env runhaskell + +import Distribution.Simple +main = defaultMain + diff --git a/src/Html.hs b/src/Html.hs new file mode 100644 --- /dev/null +++ b/src/Html.hs @@ -0,0 +1,111 @@ +{- Xml2Html + + Read BLAST Output in XML format, and output as a set of + HTML files. In contrast to almost everything else out there, + we generate HTML tables, rather than a GIF or similar for the + graphical output. + +-} + +module Html where + +import Tabulate + +import Bio.Alignment.BlastData + +import Data.ByteString.Lazy.Char8 (unpack,ByteString) +import Text.XHtml +import System.Directory +import System.IO +import Text.Printf +import Debug.Trace (trace) + +import Options (htmldir) + +instance HTML ByteString where + toHtml = toHtml . unpack + +makeDirectory :: FilePath -> IO () +makeDirectory f = do + createDirectory f `catch` (\e -> fail ("Couldn't create directory: '" ++ f++ "'\n"++show e)) + +doctype, htmlfooter, default_bg :: String + +-- manual open tags +doctype = "\n" + +htmlheader :: BlastResult -> [String] -> String +htmlheader b hs = doctype ++ "" ++ renderHtmlFragment (header << thetitle << "Blast") + ++ "" ++ renderHtmlFragment pagehdr ++ "\n\n" + ++ renderHtmlFragment (tr << map (th <<) hs) + where pagehdr = (h1 << "Blast results") + +++ p ((toHtml ("Program: "++unpack (blastversion b))) + +++ br +++ toHtml ("Database: "++ unpack (database b))) + +htmlfooter = "
\n \n" + +-- xs = writeFile "index.html" $ renderHtmlFragment document +-- mklink x = anchor ! [href (mkdirname x)] << x +++ br + +mkdirname :: FilePath -> FilePath +mkdirname x = htmldir++"/"++x++".html" + +type Link = String + +-- generate a result file, and return a link to it +mkHtml :: Handle -> (BlastRecord -> [[String]]) -> BlastRecord -> IO () +mkHtml h writer br1 = + do let ls@((q:_):_) = writer br1 + writeRow (x:xs) = hPutStr h $ renderHtmlFragment (tr << (td << mklink x : (map (td <<) xs))) + mklink x = anchor ! [href (mkdirname x)] << x + mapM writeRow ls + genBrfile q br1 + +genBrfile :: FilePath -> BlastRecord -> IO () +genBrfile fn x = writeFile (mkdirname fn) $ renderHtml $ record $ tabulate x + +record :: Table -> Html +record (t,w,rs) = table -- ! [ border 1 ] + << (tr << (th << t +++ th << ruler w + +++ map hit rs)) + where ruler i = table ! [ border 1, cellspacing 0 ] << tr << go i + go i | i > 100 = td ! [ width "97" ] + << font ! [ size "-2" ] << "|" +++ go (i-100) + | otherwise = td ! [ width (show i)] << font ! [ size "-2" ] << "" + +default_bg = "#d0e0ff" + +-- | Format a BlastHit as a +hit :: Row -> Html +hit (h_name,ms) = tr ! [bgcolor default_bg] << + (td << anchor ! [ href (unpack h_name++".html") {-, title (unwords "h_desc") -} ] << h_name + +++ td << (line ms)) + +-- | Format a set of BlastMatches from one BlastHit +-- Total length in pixels(? +line :: [Cell] -> Html +line bs = table ! [ cellspacing 0 ] << tr << map mycell bs +++ mycomment + where + mycomment = comment $ show bs +-- $ map (\b -> let (f,t) = (q_from b,q_to b) +-- in (f,t,bits b/fromIntegral (t-f),aux b)) $ bs + + mycell (Cell w c fr) = td ! [width (show w), bgcolor (makeColor c)] + << font ! [size "-2"] << (maybe "" showFrame fr) + + showFrame (Frame Plus n) = "+"++show n + showFrame (Frame Minus n) = "-"++show n + showFrame (Strands a b) = if a==b then "->" else "<-" + +-- blastn and tblastn report bits > 2/position +-- Currently we just report it and truncate to 2 (i.e. 100%). +makeColor :: Int -> String +makeColor c | c == 0 = default_bg + | c > 100 = trace (" - makeColor: value >100 ("++show c++") - truncating!") + $ makeColor 100 + | otherwise = printf "#%2x8080" ((0x80::Int)+0x79*c`div`100) + +comment :: String -> Html +comment xs = primHtml $ "" + + diff --git a/src/Options.hs b/src/Options.hs new file mode 100644 --- /dev/null +++ b/src/Options.hs @@ -0,0 +1,84 @@ +{-# LANGUAGE Rank2Types #-} + +module Options where + +import System.Environment (getArgs) +import System.Console.GetOpt +import Control.Monad + +import Bio.Util (countIO) + +htmldir :: String +htmldir = "blast.d" + +getOptions :: IO Options +getOptions = do as <- getArgs + let (optf,non,err) = getOpt Permute options as + when (not (null err)) $ error ("Usage: "++usage err) + if (null non && null as) + then error $ usageInfo ("Usage: "++usagemsg++synopsis) options + else do opt <- parseargs optf + return opt { inputs = non } + +usage :: [String] -> String +usage errs = usageInfo (concat errs ++ usagemsg) options + +usagemsg, synopsis :: String +usagemsg = "xml2x [options] blast.xml\n" +synopsis = "Convert BLASTX XML files to CSV or HTML\n" + ++ "optionally adding GO annotations.\n" + +data Options = Opts { godef, goann :: Maybe FilePath + , format :: Format + , output :: String -> IO () + , inputs :: [FilePath] + + -- verbosity/progress reporting + , verb :: Bool + , count :: forall a . Int -> String -> [a] -> IO [a] + + -- output filtering + , select :: Select + } + +data Format = Csv | Html deriving Eq +data Select = All | Top | Reg deriving Eq + +options :: [OptDescr (Options -> IO Options)] +options = [Option [] ["go-defs"] (ReqArg (\arg opt -> return opt { godef = Just arg }) "File") + "Go ids and defs" + ,Option [] ["annotations"] (ReqArg (\arg opt -> return opt { goann = Just arg }) "File") + "GOA associations" + + -- Verbosity + ,Option ['v'] ["verbose"] + (NoArg (\opt -> return opt {verb = True, count = \n msg -> countIO msg " ..done!\n" n })) + "Display progress" + ,Option ['q'] ["quiet"] (NoArg (\opt -> return opt {verb = False, count = \_ _ -> return . id})) + "Don't display progress" + + -- Output formats + ,Option ['H'] ["html-output"] (NoArg (\opt -> return opt { format = Html })) + "Output HTML" + ,Option ['C'] ["csv-output"] (NoArg (\opt -> return opt { format = Csv })) + "Output comma-separated values" + ,Option ['o'] ["output-file"] (ReqArg (\arg opt -> return opt { output = writeFile arg }) "File") + "Output file" + ,Option ['1'] ["top"] (NoArg (\opt -> return opt { select = Top })) + "Output only best BLAST hit" + ,Option [] ["all"] (NoArg (\opt -> return opt { select = All })) + "Output all BLAST hits" + ,Option [] ["regions"] (NoArg (\opt -> return opt { select = Reg })) + "Output distinct BLAST hit regions" + ] + +defaultopts :: Options +defaultopts = Opts { godef = Nothing, goann = Nothing, format = Csv + , output = putStr, verb = False, inputs = [] + , count = \_ _ -> return . id, select = All } + +parseargs :: [Options -> IO Options] -> IO Options +parseargs args = foldl (>>=) (return defaultopts) args >>= verify + where verify = return . id -- todo: check that files are correctly specified, + -- godef only makes sense with goann + diff --git a/src/Tabulate.hs b/src/Tabulate.hs new file mode 100644 --- /dev/null +++ b/src/Tabulate.hs @@ -0,0 +1,35 @@ +-- | Tabulate +-- Data structure for tables consisting of cells with various alignments. +-- For building more generic rendering of alignments + +module Tabulate where + +import Prelude hiding (words) +import Bio.Alignment.BlastData +import Data.ByteString.Lazy.Char8 (ByteString,words) +import Data.List (sortBy) + +type Table = (ByteString,Int,[Row]) +type Row = (ByteString,[Cell]) +data Cell = Cell { wd :: Int, color :: Int, frame :: Maybe Aux } deriving Show + +tabulate :: BlastRecord -> Table +tabulate b = (head $ words $ query b, qlength b, map (row (qlength b)) (hits b)) + +row :: Int -> BlastHit -> Row +row wtot h = (head $ words $ subject h, go 0 $ sort_matches $ matches h) + where + sort_matches = sortBy (\m1 m2 -> compare (min (q_from m1) (q_to m1)) (min (q_from m2) (q_to m2))) + + go :: Int -> [BlastMatch] -> [Cell] + go p [] = [Cell (wtot-p) 0 Nothing] + go p (b:bs') = + let (f',t') = (q_from b,q_to b) + (f,t) = if f'>= annotate -- >>= tabulate + +-- a sequence name and a list of annotation and bit? scores +type AnnotatedSequence = (ByteString, [(Annotation,Int)]) + +{- | Read files and return list of annotated sequences + 1. build a map of GO terms to description (25K lines - tiny) + 2. collect all proteins names from the XML file (1 pass over .xml) + 3. build a map of proteins to GO terms (1 pass over gene_assoc..), and add GO term desc + 4. revisit .xml, output: sequence, hits?, go terms/summary,...whatever +-} +annotate :: Options -> IO () -- [AnnotatedSequence] +annotate opts = do -- (Opts (Just go) (Just goa),[xml],[]) + let readXMLs fs = return . concat =<< mapM readXML fs + when (null (inputs opts)) $ fail "No input files specified!" + + -- goterms are not necessary when we don't also use goanns + (goterms,goanns) <- case goann opts of + Nothing -> return (M.empty,M.empty) + Just goa -> do + ts <- case godef opts of + Nothing -> return M.empty + Just godb -> do + t <- return . goTerms =<< (count opts) 1000 "reading GO terms: " + =<< readGO godb + when (isNothing $ M.lookup (GO 0) t) $ return () -- strictness hack + return t + + proteins <- getProts opts + when (S.member (B.empty) proteins == False) $ return () -- strictness + mt <- readGOA goa >>= (count opts) 1000 "reading GO annotations: " + >>= return . protTerms proteins + when (isNothing $ M.lookup B.empty mt) $ return () -- strictness, again + return (ts,mt) + + let tabulator = tabulate opts goterms goanns + case format opts of + Csv -> readXMLs (inputs opts) >>= csvize opts tabulator . concatMap results + Html -> readXMLs (inputs opts) >>= htmlize opts tabulator + +-- ---------------------------------------------------------------------- +-- Build tables of annotation information +-- ---------------------------------------------------------------------- + +-- | Parse GO.terms_and_ids into a map +goTerms :: [GoDef] -> Map GoTerm GoDef +goTerms = M.fromList . map go2keyval + where go2keyval gd@(GoDef gt _ _) = (gt,gd) + +-- | Read blast xml output and collect UniProt hits +getProts :: Options -> IO (Set UniProtAcc) +getProts opts = do + hs <- mapM (\f -> (count opts) 100 ("reading accessions from '"++f++"': ") + . concatMap BD.hits . concatMap BD.results =<< readXML f) (inputs opts) + return . S.fromList . map (chop . BD.subject) $ concat hs + +-- | Convert "UniProt_ABCDEF Blah blah blah" to "ABCDEF" +-- Warning: only tested on this format, may break! +chop :: ByteString -> ByteString +chop = B.drop 1 . B.dropWhile (/='_') . head . B.words + +-- | Using GO definitions and the set of uniprot terms, scan the associations file and +-- snarf all relevant data. Requires the annotations to be grouped by protein. +protTerms :: (Set UniProtAcc) -> [Annotation] -> Map UniProtAcc (UArray Int Word16) +protTerms ps as = M.fromAscList . map toArray . partitions . filter isMember $ as + where toArray (Ann up (GO gt1) _:xs) = let gs = nub (gt1:[ gt | Ann _ (GO gt) _ <- xs ]) + a = listArray (0,length gs-1) $ map fromIntegral gs + in a `seq` (pack . unpack $ up,a) + toArray [] = error "cannot read an empty list of annotations!" + isMember (Ann up _ _) = up `S.member` ps + partitions xs@(Ann x _ _:_) = let (p1,pps) = span (\(Ann y _ _) -> y==x) xs + in p1:partitions pps + partitions [] = [] + +-- --------------------------------------------------------------------- +-- | Implement CSV output +-- --------------------------------------------------------------------- + +csvize :: Options -> ([String], BlastRecord -> [[String]]) -> [BlastRecord] -> IO () +htmlize :: Options -> ([String], BlastRecord -> [[String]]) -> [BlastResult] -> IO () +csvize opts (header,writer) brs = + do hs <- count opts 10 "Generating output: " brs + let csvFormat = unlines . map (concat . intersperse "," . map maybeQuote) + maybeQuote = filter (/=',') + output opts $ csvFormat (header : concatMap writer hs) + +htmlize opts (header,writer) brs = + do doesDirectoryExist htmldir >>= \d -> if d + then when (verb opts) $ hPutStrLn stderr "Warning: reusing exisiting directory 'blast.d'" + else createDirectory htmldir + brs' <- count opts 10 "Generating output: " $ concatMap results brs + withFile "index.html" WriteMode $ \h -> do + hPutStr h (htmlheader (head brs) header) + mapM (mkHtml h writer) brs' + hPutStr h htmlfooter + +-- | read file and return a header, and a function for generating output +tabulate :: Options -> Map GoTerm GoDef -> Map UniProtAcc (UArray Int Word16) + -> ([String], BlastRecord -> [[String]]) +tabulate opts gds pts = + let header = ["Query","from","to","Target","Description","from","to","ident","bitscore","E-value","direction"] + ++ if isJust (goann opts) then ["GO terms"] + ++ case select opts of All -> [] + _ -> ["indirect GO"] + else [] + wr = case format opts of Html -> showTop + Csv -> case select opts of All -> showAll + Top -> showTop + Reg -> showReg + in (header, wr (isJust (goann opts)) gds pts) + +-- a writer generates one or more output records from a BlastRecord +type Writer = Bool -> Map GoTerm GoDef -> Map UniProtAcc (UArray Int Word16) -> (BlastRecord -> [[String]]) + +showAll, showTop, showReg :: Writer + +-- nb: the returns are due to the type of flatten :: [BlastRecord] -> .. +showAll go gds pts = map show1 . flatten . return + where show1 bf = showFlat bf ++ if go then [showGo gds pts [subject bf]] else [] + +showTop go g p = showTop' go g p . flatten . return + +showTop' :: Bool -> Map GoTerm GoDef -> Map UniProtAcc (UArray Int Word16) -> [BlastFlat] + -> [[String]] +showTop' go gds pts = map show1 . select_first + where + show1 (bf,go1,go2) = showFlat bf ++ if go then [go1,go2] else [] + select_first [] = [] + -- take all hits for this query + select_first (x:xs) = let (as,zs) = span (\y -> query x == query y) xs + (bs,ys) = span (\y -> subject x == subject y) as + ysubs = map head $ group $ map subject ys + in (merge (x:bs), showGo gds pts [subject x],showGo gds pts ysubs) + : select_first zs + +-- merge all hits against the same subject +merge :: [BlastFlat] -> BlastFlat +merge (x:xs) = let (rest,_) = partition (\y -> e_val y == e_val x) xs + q1 = minimum (map q_from (x:rest)) + q2 = maximum (map q_to (x:rest)) + s1 = minimum (map h_from (x:rest)) + s2 = maximum (map h_to (x:rest)) + in x { q_from = q1, q_to = q2, h_from = s1, h_to = s2 } +merge [] = error "needs at least one blast hit to generate output" + +showReg go gds pts = concatMap (showTop' go gds pts) . select_region . flatten . return + where + select_region [] = [] + select_region (x:xs) = let (this' ,next) = span ((query x==).query) xs + (this'',next') = partition ((dir x==).dir) this' + x' = merge (x:takeWhile ((subject x==).subject) this'') + this = sortBy (compare `on` q_from) $ this'' + in regions [x'] (q_from x', q_to x') this ++ select_region (next'++next) + + regions :: [BlastFlat] -> (Int,Int) -> [BlastFlat] -> [[BlastFlat]] + regions x (a,b) (y:ys) = if overlap (a,b) y then regions (y:x) (min a (q_from y), max b (q_to y)) ys + else reverse x : regions [y] (q_from y, q_to y) ys + regions x (_,_) [] = [reverse x] + + overlap (a,b) s = q_from s < (a+b) `div` 2 || q_to s < b + (a+b) `div` 2 + f `on` g = \x y -> f (g x) (g y) + +-- | generate one record (i.e. line of output) +showFlat :: BlastFlat -> [String] +showFlat bf = [ head $ words $ unpack $ query bf + , show $ q_from bf, show $ q_to bf + , head $ words $ unpack $ subject bf + , unpack $ B.dropWhile (==' ') $ B.dropWhile (/=' ') $ subject bf + , show $ h_from bf, show $ h_to bf + , show (fst . identity $ bf), show (bits bf), show (e_val bf) + , dir bf + ] + +dir :: BlastFlat -> String +dir bf = case aux bf of Strands p p' -> if p==p' then "Fwd" else "Rev" + Frame d _ -> if d==Minus then "Rev" else "Fwd" + +showGo :: Map GoTerm GoDef -> Map UniProtAcc (UArray Int Word16) -> [UniProtAcc] -> String +showGo gds pts gs = showGD . unions . map fromJust . filter isJust + . map (flip M.lookup pts) . map chop $ gs + where + showGD = concatMap (\gd -> show (GO $ fromIntegral gd) ++ showGT (M.lookup (GO $ fromIntegral gd) gds)) + showGT (Just (GoDef _ str cls)) = " ("++show cls++": "++unpack str++") " + showGT Nothing = " " + unions = nub . concatMap elems diff --git a/xml2x.cabal b/xml2x.cabal new file mode 100644 --- /dev/null +++ b/xml2x.cabal @@ -0,0 +1,30 @@ +Name: xml2x +Version: 0.2 +License: GPL +License-File: LICENSE + +Author: Ketil Malde +Maintainer: Ketil Malde + +Stability: Beta +Category: Bioinformatics +Synopsis: Convert BLAST output in XML format to CSV or HTML +Description: xml2x - convert blast output in XML format, either to a (csv) + table suitable for e.g. importing into Excel or OOCalc, or + to HTML. Optionally annotating the output with GO terms. + +Build-Type: Simple +Tested-With: GHC==6.8.2 + +Build-Depends: base>3, bio >= 0.3.2, containers, bytestring, array, xhtml, directory +-- Build-Depends: base, bio - GHC 6.6 +-- Build-Depends: base, bio, fps - GHC 6.4 + +data-files: README + +Executable: xml2x +Main-Is: Xml2X.hs +Extensions: Rank2Types +Hs-Source-Dirs: src +Other-modules: Html, Options, Tabulate +Ghc-Options: -Wall -O2 -smp