xml2x (empty) → 0.2
raw patch · 8 files changed
+865/−0 lines, 8 filesdep +arraydep +basedep +biosetup-changed
Dependencies added: array, base, bio, bytestring, containers, directory, xhtml
Files
- LICENSE +340/−0
- README +47/−0
- Setup.hs +5/−0
- src/Html.hs +111/−0
- src/Options.hs +84/−0
- src/Tabulate.hs +35/−0
- src/Xml2X.hs +213/−0
- xml2x.cabal +30/−0
+ LICENSE view
@@ -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.++ <one line to give the program's name and a brief idea of what it does.>+ Copyright (C) <year> <name of author>++ 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.++ <signature of Ty Coon>, 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.
+ README view
@@ -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.
+ Setup.hs view
@@ -0,0 +1,5 @@+#!/usr/bin/env runhaskell+ +import Distribution.Simple+main = defaultMain+
+ src/Html.hs view
@@ -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 = "<!DOCTYPE html PUBLIC \"-//W3C//DTD XHTML 1.0 Transitional//EN\" \"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd\">\n"++htmlheader :: BlastResult -> [String] -> String+htmlheader b hs = doctype ++ "<html>" ++ renderHtmlFragment (header << thetitle << "Blast") + ++ "<body>" ++ renderHtmlFragment pagehdr ++ "\n<table border=\"1\">\n" + ++ renderHtmlFragment (tr << map (th <<) hs)+ where pagehdr = (h1 << "Blast results") + +++ p ((toHtml ("Program: "++unpack (blastversion b)))+ +++ br +++ toHtml ("Database: "++ unpack (database b)))++htmlfooter = " </table>\n </body>\n</html>"++-- 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 <tr>+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 $ "<!--"++xs++"-->"++
+ src/Options.hs view
@@ -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+
+ src/Tabulate.hs view
@@ -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'<t' then (f',t') else (t',f')+ w1 = max (f-p) 0+ w2 = max (t-(p+w1)) 0+ in Cell w1 0 Nothing+ : Cell w2 (floor (50*bits b) `div` (t-f)) (Just $ aux b)+ : go (p+w1+w2) bs'++
+ src/Xml2X.hs view
@@ -0,0 +1,213 @@+{- | Annotate sequences with GO terms, via BLASTX hits to UniProt -}++module Main where++import Data.ByteString.Lazy.Char8 (ByteString,unpack,pack)+import qualified Data.ByteString.Lazy.Char8 as B+import Data.Map (Map)+import qualified Data.Map as M+import Data.Set (Set)+import qualified Data.Set as S+import Data.List (intersperse,sortBy,partition,group,nub)+import Control.Monad+import Data.Maybe+import System.IO+import System.Directory (doesDirectoryExist, createDirectory)+import Data.Array.Unboxed+import Data.Word++import Bio.Sequence.GOA+import qualified Bio.Alignment.BlastData as BD+import Bio.Alignment.BlastData (BlastResult)+import Bio.Alignment.BlastFlat+import Bio.Alignment.BlastXML++import Options+import Html++main :: IO ()+main = getOptions >>= 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
+ xml2x.cabal view
@@ -0,0 +1,30 @@+Name: xml2x+Version: 0.2+License: GPL+License-File: LICENSE++Author: Ketil Malde+Maintainer: Ketil Malde <ketil@malde.org>++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