estreps (empty) → 0.1
raw patch · 8 files changed
+642/−0 lines, 8 filesdep +basedep +biodep +bytestringsetup-changed
Dependencies added: base, bio, bytestring, containers, random
Files
- LICENSE +340/−0
- README +49/−0
- Setup.hs +3/−0
- estreps.cabal +34/−0
- src/RSelect.lhs +79/−0
- src/Repeats.lhs +100/−0
- src/Unigene.hs +25/−0
- src/Util.hs +12/−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 +1,49 @@++SYNOPSIS++ rselect - select a random set of sequences from a FASTA file.+ reps - extract exact k-word repeats based that occur in+ sequences grouped in different clusters.+++INSTALLATION++ You'll need GHC or possibly another Haskell system, and the+ Haskell bioinformatics library. The Makefile should work to+ build and install (by default to your home directory) the+ executables.++USAGE++ rselect n [m] input.seq++ Selects n sequences from the file input.seq. If the optional+ m is given, this limits the selection to happen only from the first+ m sequences in the file, which may be more efficient.++ The selected sequences are written to standard output, so you+ probably want to redirect them to a file.++ reps k clustered.seq++ Generate a list of repeated k-words (or k-grams) found in the sequences.+ The sequences are expected to be on UniGene format, i.e. a FASTA file+ with #-initiated comments separating the clusters.++ A k-word is considered repeated if it is found in more than one of the+ clusters.++ reps k clustering.lst sequences.seq++ As above, but take a separate input clustering (and ignore any #'s in the+ sequences. The clustering should consist of one line per cluster, with each+ line containing the sequence identifier (first word after the initial '>'+ in the FASTA header).++BUGS++ Do let me know about them, at <ketil@malde.org>!++HOMEPAGE++ http://malde.org/~ketil/
+ Setup.hs view
@@ -0,0 +1,3 @@+#!/usr/bin/env runhaskell+import Distribution.Simple+main = defaultMain
+ estreps.cabal view
@@ -0,0 +1,34 @@+Name: estreps+Version: 0.1+License: GPL+License-file: LICENSE+Author: Ketil Malde+Maintainer: Ketil Malde <ketil@malde.org>+Stability: Beta+Category: Bioinformatics+Synopsis: Repeats from ESTs+Description: rselect - select a random set of sequences from a FASTA file.+ reps - extract exact k-word repeats based that occur in+ sequences grouped in different clusters.+ .+ The Darcs repository is at: <http://malde.org/~ketil/biohaskell/estreps>.+Homepage: http://malde.org/~ketil/++Tested-With: GHC==6.8.2+Build-Type: Simple+Cabal-Version: >= 1.2++Data-Files: README++Executable rselect+ Hs-source-dirs: src+ Main-Is: RSelect.lhs+ Build-Depends: base>3, random, containers, bio>=0.3.3, bytestring+ ghc-options: -Wall+ Other-Modules: Unigene++Executable reps+ Hs-source-dirs: src+ Main-Is: Repeats.lhs+ Other-Modules: Util+
+ src/RSelect.lhs view
@@ -0,0 +1,79 @@++RSelect - randomly select a number of sequences from a FASTA file++Usage: rselect m < file.seq # prints m random sequences to stdout+ rselect m n < file.seq # print m of the first n seq.s (faster)++\begin{code}++module Main where++import Data.Set+import System.Environment (getArgs)+import System.Random+import System.IO++import Bio.Sequence.Fasta++import Unigene++main :: IO ()+main = do+ as <- getArgs+ case as of [m,f] -> select (read m) Nothing f+ [m,n,f] -> select (read m) (Just (read n)) f+ _ -> error "Usage: rselect n [m] input.seq > output.seq"++-- | Select m out of maybe n sequences from f+-- Not specifying a maximum increases memory consumption+select :: Integer -> Maybe Integer -> FilePath -> IO ()+select m mn f = do+ seed <- newStdGen+ hPutStrLn stderr ("Random seed: "++show seed)+ ss <- ugRead f+ n <- case mn of Nothing -> do hPutStrLn stderr "Counting sequences..."+ n' <- countSeqs f+ return (fromIntegral n')+ Just n' -> return n'+ let ds = if m>n then error "rselect: m is larger than n, that won't work."+ else if m==n then take (fromIntegral n) $ repeat 1+ else if m<=n `div` 2 then diffs $ pick m $ randomRs (1,n) seed+ else diffs $ invert n 1 $ pick (n-m) $ randomRs (1,n) seed+ out = Prelude.filter (not.Prelude.null) $ choose ds ss+ n `seq` hPutStrLn stderr ("N = "++show n++", M = "++show m)+ mapM_ (\o -> putStrLn "# cluster delimiter" >> hWriteFasta stdout o) out++-- | choose elements according to a list of deltas+choose :: Show a => [Integer] -> [[a]] -> [[a]]+choose = choose' []++choose' :: Show a => [a] -> [Integer] -> [[a]] -> [[a]]+choose' acc [] _ = [reverse acc]+choose' acc (0:ds) xss = choose' acc ds xss+choose' acc (d:ds) (xs:xss) = let ys = drop (fromIntegral d-1) xs+ in if not (Prelude.null ys) then choose' (head ys:acc) ds (tail ys:xss)+ else reverse acc : choose' [] ((d-fromIntegral (length xs)):ds) xss+choose' _ _ [] = error "rselect: cannot choose from empty list.\nPerhaps you specified 'n' too large?"++-- | convert indices to deltas+diffs :: [Integer] -> [Integer]+diffs xs = diffs' (0:xs)+ where+ diffs' (a:b:cs) = if b<=a then error ("diffs needs a monotonically increasing sequence"++show (take 10 (a:b:cs)))+ else (b-a) : diffs' (b:cs)+ diffs' [_] = []++-- | convert a list to the list of missing values+invert :: Integer -> Integer -> [Integer] -> [Integer]+invert n i (a:cs) = [i..a-1] ++ invert n (a+1) cs+invert n i [] = [i..n]+++-- | pick m unique integers+pick :: Integer -> [Integer] -> [Integer]+pick = pick' empty+ where pick' tmp 0 _ = elems tmp+ pick' tmp m (i:is) = if member i tmp then pick' tmp m is+ else pick' (insert i tmp) (m-1) is++\end{code}
+ src/Repeats.lhs view
@@ -0,0 +1,100 @@++Cluster all ESTs against the genome++Construct the de-Bruijn graph for each cluster+(i.e. collect the set of all k-words in each cluster)+What about multiplicity?++For each pair of clusters, calculate the intersection.+Repeat words = U (Ci /\ Cj) -- also keep count of each word.++(Can we use a more sophisticated data structure? I.e. keep track of+longest common exact string?)++Check each repeat word against: repbase, simple repeats, complexity++Parameters: word length k, and file to read clusters from++\begin{code}++module Main where++import qualified Data.Set as S+import qualified Data.Map as M++import qualified Data.ByteString.Lazy.Char8 as B+import Bio.Sequence+import Bio.Sequence.HashWord++import Unigene++import Control.Monad (when)+import Data.List+import Data.Maybe+import System.Environment (getArgs)++import Util++-- type Word = Int++main = do+ args <- getArgs+ when (length args < 2 || length args > 3)+ (error "usage: reps k ugfile\n or: reps k clusterfile sequencefile")+ (k,rs,rl) <- initialize args+ if (k>16)+ then putStrLn (myshow k rl)+ else putStrLn (myshow k rs)++myshow k = unlines . map show1+ where show1 (key,count) = ">" ++ show key ++ " " ++ show count ++ "\n" ++ B.unpack (k2n k key) ++ "\n"++initialize args = do+ let k = case reads (head args) of [(k',"")] -> k'+ _ -> error "k must be a positive integer"+ case tail args of [csfile,sqsfile] -> do+ cs <- {- countIO 10 "clusters: " . -} return . filter (not.null) . map words . lines =<< readFile csfile+ sqs <- readFasta sqsfile+ let rs = repeats k $ clusters cs sqs :: [(Int,Int)]+ rl = repeats k $ clusters cs sqs :: [(Integer,Int)]+ return (k,rs,rl)+ [ugfile] -> do+ ugdata <- {- countIO 10 "clusters: " =<< -} ugRead ugfile+ let rs = repeats k ugdata :: [(Int,Int)]+ rl = repeats k ugdata :: [(Integer,Int)]+ return (k,rs,rl)++-- build clusters from [[Label]] and [Seq Label sdata]+clusters :: [[String]] -> [Sequence] -> [[Sequence]]+clusters labels seqs = map (map mylookup) labels+ where smap = M.fromListWith (error "duplicate sequences in input!") $+ map (\s -> (B.dropWhile (=='>') $ seqlabel s,s)) seqs+ mylookup s = case (flip M.lookup $ smap) . B.pack $ s of+ Nothing -> error ("sequence '"++s++"' in the clustering is not found in data set")+ Just x -> x++-- extract words from clusters+debruijn :: Integral w => Int -> [Sequence] -> S.Set w+debruijn k = foldl1' S.union . map (S.fromList . keys k . seqdata)+-- slightly faster than: "foldl' (flip S.insert) S.empty . concatMap (keys k)"++keys k = map fst . hashes (rcontig k)++-- calculate word counts+freqs :: Integral w => [S.Set w] -> M.Map w Int+freqs = foldl' union M.empty+ where union :: Integral w => M.Map w Int -> S.Set w -> M.Map w Int+ union a b = foldl' insert a $ S.toList b+ insert a k = case M.lookup k a of+ Just x -> let v' = x+1 in v' `seq` M.insert k v' a+ Nothing -> M.insert k 1 a++-- inefficient?+toMap :: Integral w => S.Set w -> M.Map w Int+toMap = M.fromList . map (\x -> (x,1)) . S.toList++-- given word length k, calculate repeats from clusters+repeats :: Integral w => Int -> [[Sequence]] -> [(w,Int)]+repeats k = filter ((>1).snd) . M.toList . freqs . map (debruijn k)++\end{code}
+ src/Unigene.hs view
@@ -0,0 +1,25 @@+-- read a clustering on Unigene format+-- each cluster separated by '^#.*$'++module Unigene (ugRead) where++import Control.Monad+import System.IO+import qualified Data.ByteString.Lazy.Char8 as B++import Bio.Sequence (Sequence(..))+import Bio.Sequence.Fasta (mkSeqs)+import Data.List (groupBy)++-- Isn't this lazy?+ugRead :: FilePath -> IO [[Sequence]]+ugRead f = do+ s <- B.readFile f+ let ls = dropWhile B.null $ B.lines $ s+ when (B.head (head ls) /= '#') (hPutStrLn stderr ("Warning: '"++f++"' does not look like Unigene format"))+ return (clusters $ ls)++clusters :: [B.ByteString] -> [[Sequence]]+clusters (l:ls) = let ls' = if B.head l == '#' then (l:ls) else (B.pack "# dummy UG hdr" :l:ls)+ ss = groupBy (const (('#' /=) . B.head)) $ filter (not . B.null) ls'+ in map (mkSeqs . tail) ss
+ src/Util.hs view
@@ -0,0 +1,12 @@+module Util where++import System.IO+import System.IO.Unsafe++countIO step msg xs = sequence $ map unsafeInterleaveIO $ ct 0 xs+ where ct s xs = let (a,b) = splitAt (step-1) xs+ next = s+step+ output c = hPutStr stderr ((take (length (show c)+2+length msg) $ repeat ' ')++'\r':msg++show c) >> hFlush stderr+ in if null b then map return a ++ []+ else map return a ++ [output next >> return (head b)]+ ++ ct next (tail b)