diff --git a/TxtSushi/IO.hs b/TxtSushi/IO.hs --- a/TxtSushi/IO.hs +++ b/TxtSushi/IO.hs @@ -73,19 +73,6 @@ maxRowFieldWidths :: [String] -> [Int] -> [Int] maxRowFieldWidths row prevMaxValues = zipWithD max (map length row) prevMaxValues -{- - let colLengths = map length row - lengthOfRow = length row - lengthOfPrevMax = length prevMaxValues - maxPrefixList = zipWith max colLengths prevMaxValues - in - if lengthOfRow == lengthOfPrevMax then - maxPrefixList - else if lengthOfRow > lengthOfPrevMax then - maxPrefixList ++ (drop lengthOfPrevMax colLengths) - else - maxPrefixList ++ (drop lengthOfRow prevMaxValues) --} zipWithD :: (a -> a -> a) -> [a] -> [a] -> [a] zipWithD f (x:xt) (y:yt) = (f x y):(zipWithD f xt yt) diff --git a/TxtSushi/SQLExecution.hs b/TxtSushi/SQLExecution.hs --- a/TxtSushi/SQLExecution.hs +++ b/TxtSushi/SQLExecution.hs @@ -19,6 +19,7 @@ import Data.Char import Data.List import qualified Data.Map as Map +import Text.Regex.Posix import TxtSushi.SQLParser import TxtSushi.Transform @@ -62,8 +63,8 @@ boolExpression bool = EvaluatedExpression { preferredType = BoolType, - maybeIntValue = Just $ if bool then 1 else 0, - maybeRealValue = Just $ if bool then 1.0 else 0.0, + maybeIntValue = Nothing, + maybeRealValue = Nothing, stringValue = show bool, maybeBoolValue = Just bool} @@ -71,21 +72,21 @@ intValue evalExpr = case maybeIntValue evalExpr of Just int -> int Nothing -> - error $ "failed to parse \"" ++ (stringValue evalExpr) ++ - "\" as an integer value" + error $ "could not convert \"" ++ (stringValue evalExpr) ++ + "\" to an integer value" realValue :: EvaluatedExpression -> Double realValue evalExpr = case maybeRealValue evalExpr of Just real -> real Nothing -> - error $ "failed to parse \"" ++ (stringValue evalExpr) ++ + error $ "could not convert \"" ++ (stringValue evalExpr) ++ "\" to a numeric value" boolValue :: EvaluatedExpression -> Bool boolValue evalExpr = case maybeBoolValue evalExpr of Just bool -> bool Nothing -> - error $ "failed to parse \"" ++ (stringValue evalExpr) ++ + error $ "could not convert \"" ++ (stringValue evalExpr) ++ "\" to a boolean value" data ExpressionType = StringType | RealType | IntType | BoolType deriving Eq @@ -112,21 +113,30 @@ expr1 == expr2 = compare expr1 expr2 == EQ instance Ord EvaluatedExpression where - -- compare on bool based on preferred type - compare (EvaluatedExpression BoolType _ _ _ (Just b1)) (EvaluatedExpression _ _ _ _ (Just b2)) = compare b1 b2 - compare (EvaluatedExpression _ _ _ _ (Just b1)) (EvaluatedExpression BoolType _ _ _ (Just b2)) = compare b1 b2 - - -- compare on int based on preferred type - compare (EvaluatedExpression IntType _ _ (Just i1) _) (EvaluatedExpression _ _ _ (Just i2) _) = compare i1 i2 - compare (EvaluatedExpression _ _ _ (Just i1) _) (EvaluatedExpression IntType _ _ (Just i2) _) = compare i1 i2 + compare expr1 expr2 + | type1 == RealType || type2 == RealType = realCompare expr1 expr2 + | type1 == IntType || type2 == IntType = intCompare expr1 expr2 + | type1 == BoolType || type2 == BoolType = boolCompare expr1 expr2 + | otherwise = stringCompare expr1 expr2 + + where + type1 = preferredType expr1 + type2 = preferredType expr2 - -- compare on real based on preferred type - compare (EvaluatedExpression RealType _ (Just r1) _ _) (EvaluatedExpression _ _ (Just r2) _ _) = compare r1 r2 - compare (EvaluatedExpression _ _ (Just r1) _ _) (EvaluatedExpression RealType _ (Just r2) _ _) = compare r1 r2 - - -- fall back on string type - compare expr1 expr2 = compare (stringValue expr1) (stringValue expr2) +realCompare (EvaluatedExpression _ _ (Just r1) _ _) (EvaluatedExpression _ _ (Just r2) _ _) = + compare r1 r2 +realCompare expr1 expr2 = stringCompare expr1 expr2 +intCompare (EvaluatedExpression _ _ _ (Just i1) _) (EvaluatedExpression _ _ _ (Just i2) _) = + compare i1 i2 +intCompare expr1 expr2 = realCompare expr1 expr2 + +boolCompare (EvaluatedExpression _ _ _ _ (Just b1)) (EvaluatedExpression _ _ _ _ (Just b2)) = + compare b1 b2 +boolCompare expr1 expr2 = stringCompare expr1 expr2 + +stringCompare expr1 expr2 = stringValue expr1 `compare` stringValue expr2 + -- convert a text table to a database table by using the 1st row as column IDs textTableToDatabaseTable :: String -> [[String]] -> DatabaseTable textTableToDatabaseTable tableName (headerNames:tblRows) = @@ -363,17 +373,35 @@ -- this is where the action is. evaluate a function evalExpression (FunctionExpression sqlFun funArgs) columnIds tblRow -- String functions - | sqlFun == upperFunction = stringExpression $ map toUpper (stringValue (head evaluatedArgs)) - | sqlFun == lowerFunction = stringExpression $ map toLower (stringValue (head evaluatedArgs)) - | sqlFun == trimFunction = stringExpression $ trimSpace (stringValue (head evaluatedArgs)) + | sqlFun == upperFunction = stringExpression $ map toUpper (stringValue arg1) + | sqlFun == lowerFunction = stringExpression $ map toLower (stringValue arg1) + | sqlFun == trimFunction = stringExpression $ trimSpace (stringValue arg1) + | sqlFun == concatenateFunction = stringExpression $ concat (map stringValue evaluatedArgs) + | sqlFun == substringFromToFunction = + stringExpression $ take (intValue arg3) (drop (intValue arg2 - 1) (stringValue arg1)) + | sqlFun == substringFromFunction = + stringExpression $ drop (intValue arg2 - 1) (stringValue arg1) + | sqlFun == regexMatchFunction = boolExpression $ (stringValue arg1) =~ (stringValue arg2) - -- algebraic infix functions + -- negate + | sqlFun == negateFunction = + if length evaluatedArgs /= 1 then + error "internal error: found a negate function with multiple args" + else + let evaldArg = head evaluatedArgs + in + if useRealAlgebra evaldArg then + realExpression $ negate (realValue evaldArg) + else + intExpression $ negate (intValue evaldArg) + + -- algebraic | sqlFun == multiplyFunction = algebraWithCoercion (*) (*) evaluatedArgs | sqlFun == divideFunction = realExpression $ foldl1' (/) (map realValue evaluatedArgs) | sqlFun == plusFunction = algebraWithCoercion (+) (+) evaluatedArgs | sqlFun == minusFunction = algebraWithCoercion (-) (-) evaluatedArgs - -- boolean infix functions + -- boolean | sqlFun == isFunction = boolExpression (arg1 == arg2) | sqlFun == isNotFunction = boolExpression (arg1 /= arg2) | sqlFun == lessThanFunction = boolExpression (arg1 < arg2) @@ -382,10 +410,13 @@ | sqlFun == greaterThanOrEqualToFunction = boolExpression (arg1 >= arg2) | sqlFun == andFunction = boolExpression $ (boolValue arg1) && (boolValue arg2) | sqlFun == orFunction = boolExpression $ (boolValue arg1) || (boolValue arg2) + | sqlFun == notFunction = boolExpression $ not (boolValue arg1) where arg1 = head evaluatedArgs arg2 = evaluatedArgs !! 1 + arg3 = evaluatedArgs !! 2 + subStringF start extent string = take extent (drop start string) evaluatedArgs = map evalArgExpr funArgs evalArgExpr expr = evalExpression expr columnIds tblRow algebraWithCoercion intFunc realFunc args = @@ -395,8 +426,11 @@ intExpression $ foldl1' intFunc (map intValue args) useRealAlgebra expr = - let prefType = preferredType expr - in prefType == StringType || prefType == RealType + let + prefType = preferredType expr + maybeInt = maybeIntValue expr + in + prefType == RealType || maybeInt == Nothing -- | trims leading and trailing spaces trimSpace :: String -> String diff --git a/TxtSushi/SQLParser.hs b/TxtSushi/SQLParser.hs --- a/TxtSushi/SQLParser.hs +++ b/TxtSushi/SQLParser.hs @@ -25,18 +25,22 @@ prettyFormatWithArgs, SQLFunction(..), - -- SQL functions with "normal" syntax + -- String SQL function + concatenateFunction, upperFunction, lowerFunction, trimFunction, + substringFromFunction, + substringFromToFunction, - -- Algebraic infix SQL functions + -- Algebraic SQL functions multiplyFunction, divideFunction, plusFunction, minusFunction, + negateFunction, - -- Boolean infix SQL functions + -- Boolean SQL functions isFunction, isNotFunction, lessThanFunction, @@ -45,6 +49,8 @@ greaterThanOrEqualToFunction, andFunction, orFunction, + notFunction, + regexMatchFunction, -- Etc... maybeReadInt, @@ -154,6 +160,11 @@ prettyFormatWithArgs sqlFunc funcArgs | sqlFunc `elem` normalSyntaxFunctions = prettyFormatNormalFunctionExpression sqlFunc funcArgs | or (map (sqlFunc `elem`) infixFunctions) = prettyFormatInfixFunctionExpression sqlFunc funcArgs + | sqlFunc == negateFunction = "-" ++ toArgString (head funcArgs) + | sqlFunc == substringFromToFunction || + sqlFunc == substringFromFunction || + sqlFunc == notFunction = + prettyFormatNormalFunctionExpression sqlFunc funcArgs prettyFormatInfixFunctionExpression :: SQLFunction -> [Expression] -> String prettyFormatInfixFunctionExpression sqlFunc funcArgs = @@ -364,13 +375,17 @@ parenthesize parseExpression <|> parseStringConstant <|> try parseRealConstant <|> - parseIntConstant <|> + try parseIntConstant <|> parseAnyNormalFunction <|> + parseNegateFunction <|> + parseSubstringFunction <|> + parseNotFunction <|> (parseColumnId >>= (\colId -> return $ ColumnExpression colId)) parseStringConstant :: GenParser Char st Expression parseStringConstant = - quotedText True '"' >>= (\txt -> return $ StringConstantExpression txt) + (quotedText True '"' <|> quotedText True '\'') >>= + (\txt -> return $ StringConstantExpression txt) parseIntConstant :: GenParser Char st Expression parseIntConstant = @@ -458,9 +473,11 @@ infixFunctions = [[multiplyFunction, divideFunction], [plusFunction, minusFunction], + [concatenateFunction], [isFunction, isNotFunction, lessThanFunction, lessThanOrEqualToFunction, - greaterThanFunction, greaterThanOrEqualToFunction], - [andFunction, orFunction]] + greaterThanFunction, greaterThanOrEqualToFunction, regexMatchFunction], + [andFunction], + [orFunction]] -- | This function parses the operator part of the infix function and returns -- a function that excepts a left expression and right expression to form @@ -482,9 +499,10 @@ sqlFunction = infixFunc, functionArguments = [leftSubExpr, rightSubExpr]} funcIsAlphaNum = any isAlphaNum (functionName infixFunc) - notOpChar = - notFollowedBy $ oneOf "*/+-=<>^" +notOpChar = + notFollowedBy $ oneOf "*/+-=<>^|~" + -- Algebraic multiplyFunction = SQLFunction { functionName = "*", @@ -547,15 +565,25 @@ minArgCount = 2, argCountIsFixed = True} +concatenateFunction = SQLFunction { + functionName = "||", + minArgCount = 2, + argCountIsFixed = True} +regexMatchFunction = SQLFunction { + functionName = "=~", + minArgCount = 2, + argCountIsFixed = True} -- Functions with special syntax -- specialFunctions = [substringFromFunction, - substringFromToFunction] + substringFromToFunction, + negateFunction, + notFunction] -- | SUBSTRING(extraction_string FROM starting_position [FOR length] -- [COLLATE collation_name]) --- TODO implement these +-- TODO implement COLLATE part substringFromFunction = SQLFunction { functionName = "SUBSTRING", minArgCount = 2, @@ -565,6 +593,47 @@ minArgCount = 3, argCountIsFixed = True} +parseSubstringFunction :: GenParser Char st Expression +parseSubstringFunction = do + try $ upperOrLower (functionName substringFromFunction) >> spaces >> char '(' + spaces + strExpr <- parseExpression + spaces1 + upperOrLower "FROM" + spaces1 + startExpr <- parseExpression + -- TODO doesn't need to be spaces. it can just be '(' + maybeLength <- maybeParse $ spaces1 >> upperOrLower "FOR" >> spaces1 >> parseExpression + spaces + char ')' + + return $ case maybeLength of + Nothing -> FunctionExpression substringFromFunction [strExpr, startExpr] + Just len -> FunctionExpression substringFromToFunction [strExpr, startExpr, len] + +negateFunction = SQLFunction { + functionName = "-", + minArgCount = 1, + argCountIsFixed = True} + +parseNegateFunction :: GenParser Char st Expression +parseNegateFunction = do + try $ char '-' >> notOpChar + expr <- parseAnyNonInfixExpression + return $ FunctionExpression negateFunction [expr] + +notFunction = SQLFunction { + functionName = "NOT", + minArgCount = 1, + argCountIsFixed = True} + +parseNotFunction = do + try $ upperOrLower (functionName notFunction) >> + genNotFollowedBy (anyChar `exceptChar` (space <|> char '(')) + spaces + expr <- parseAnyNonInfixExpression + return $ FunctionExpression notFunction [expr] + -------------------------------------------------------------------------------- -- Parse utility functions -------------------------------------------------------------------------------- @@ -577,6 +646,8 @@ quotedText False '`' <|> many1 idChar (parseId `genExcept` parseReservedWord) "identifier" +-- | quoted text which allows escaping by doubling the quote char +-- like "escaped quote char here:""" quotedText allowEmpty quoteChar = do let quote = char quoteChar manyFunc = if allowEmpty then many else many1 @@ -644,7 +715,7 @@ map functionName normalSyntaxFunctions ++ map functionName (concat infixFunctions) ++ map functionName specialFunctions ++ - ["BY","CROSS", "FROM", "GROUP", "HAVING", "INNER", "JOIN", "ON", "ORDER", "SELECT", "WHERE"] + ["BY","CROSS", "FROM", "FOR", "GROUP", "HAVING", "INNER", "JOIN", "ON", "ORDER", "SELECT", "WHERE"] -- | tries parsing both the upper and lower case versions of the given string upperOrLower :: String -> GenParser Char st String diff --git a/_darcs/format b/_darcs/format new file mode 100644 --- /dev/null +++ b/_darcs/format @@ -0,0 +1,2 @@ +hashed +darcs-2 diff --git a/_darcs/hashed_inventory b/_darcs/hashed_inventory new file mode 100644 --- /dev/null +++ b/_darcs/hashed_inventory @@ -0,0 +1,8 @@ +pristine:0000001506-5eac01f7311f45389d1fc10325ff7b83a4cdd71d1532f04f07800936c5acb260 +Starting with inventory: +0000001260-8f8e2c077c4bae8cc2094386214bd292379b1ee72540673d89e1514e19f69207 +[TAG release 0.2 +keithshep@gmail.com**20090521033210 + Ignore-this: b0ed58fccf2f95a610521713d9c1a499 +] +hash: 0000000773-b36b71d0a85a717f6642b9f04da20921fb1e3d4e2044508833e676d094046526 diff --git 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a/_darcs/patches/0000070374-475515c8f051c8c3f01a02e1bd957749267881da8f7a853a7b9be4efac61 b/_darcs/patches/0000070374-475515c8f051c8c3f01a02e1bd957749267881da8f7a853a7b9be4efac61 new file mode 100644 Binary files /dev/null and b/_darcs/patches/0000070374-475515c8f051c8c3f01a02e1bd957749267881da8f7a853a7b9be4efac61 differ diff --git a/_darcs/patches/pending.tentative b/_darcs/patches/pending.tentative new file mode 100644 --- /dev/null +++ b/_darcs/patches/pending.tentative @@ -0,0 +1,2 @@ +{ +} diff --git a/_darcs/prefs/binaries b/_darcs/prefs/binaries new file mode 100644 --- /dev/null +++ b/_darcs/prefs/binaries @@ -0,0 +1,59 @@ +# Binary file regexps: +\.png$ +\.PNG$ +\.gz$ +\.GZ$ +\.pdf$ +\.PDF$ +\.jpg$ +\.JPG$ +\.jpeg$ +\.JPEG$ +\.gif$ +\.GIF$ +\.tif$ +\.TIF$ +\.tiff$ +\.TIFF$ +\.pnm$ +\.PNM$ +\.pbm$ +\.PBM$ +\.pgm$ +\.PGM$ +\.ppm$ +\.PPM$ +\.bmp$ +\.BMP$ +\.mng$ +\.MNG$ +\.tar$ +\.TAR$ +\.bz2$ +\.BZ2$ +\.z$ +\.Z$ +\.zip$ +\.ZIP$ +\.jar$ +\.JAR$ +\.so$ +\.SO$ +\.a$ +\.A$ +\.tgz$ +\.TGZ$ +\.mpg$ +\.MPG$ +\.mpeg$ +\.MPEG$ +\.iso$ +\.ISO$ +\.exe$ +\.EXE$ +\.doc$ +\.DOC$ +\.elc$ +\.ELC$ +\.pyc$ +\.PYC$ diff --git a/_darcs/prefs/boring b/_darcs/prefs/boring new file mode 100644 --- /dev/null +++ b/_darcs/prefs/boring @@ -0,0 +1,113 @@ +# Boring file regexps: + +### compiler and interpreter intermediate files +# haskell (ghc) interfaces +\.hi$ +\.hi-boot$ +\.o-boot$ +# object files +\.o$ +\.o\.cmd$ +# profiling haskell +\.p_hi$ +\.p_o$ +# haskell program coverage resp. profiling info +\.tix$ +\.prof$ +# fortran module files +\.mod$ +# linux kernel +\.ko\.cmd$ +\.mod\.c$ +(^|/)\.tmp_versions($|/) +# *.ko files aren't boring by default because they might +# be Korean translations rather than kernel modules +# \.ko$ +# python, emacs, java byte code +\.py[co]$ +\.elc$ +\.class$ +# objects and libraries; lo and la are libtool things +\.(obj|a|exe|so|lo|la)$ +# compiled zsh configuration files +\.zwc$ +# Common LISP output files for CLISP and CMUCL +\.(fas|fasl|sparcf|x86f)$ + +### build and packaging systems +# cabal intermediates +\.installed-pkg-config +\.setup-config +# standard cabal build dir, might not be boring for everybody +# ^dist(/|$) +# autotools +(^|/)autom4te\.cache($|/) +(^|/)config\.(log|status)$ +# microsoft web expression, visual studio metadata directories +\_vti_cnf$ +\_vti_pvt$ +# gentoo tools +\.revdep-rebuild.* +# generated dependencies +^\.depend$ + +### version control systems +# cvs +(^|/)CVS($|/) +\.cvsignore$ +# cvs, emacs locks +^\.# +# rcs +(^|/)RCS($|/) +,v$ +# subversion +(^|/)\.svn($|/) +# mercurial +(^|/)\.hg($|/) +# git +(^|/)\.git($|/) +# bzr +\.bzr$ +# sccs +(^|/)SCCS($|/) +# darcs +(^|/)_darcs($|/) +(^|/)\.darcsrepo($|/) +^\.darcs-temp-mail$ +-darcs-backup[[:digit:]]+$ +# gnu arch +(^|/)(\+|,) +(^|/)vssver\.scc$ +\.swp$ +(^|/)MT($|/) +(^|/)\{arch\}($|/) +(^|/).arch-ids($|/) +# bitkeeper +(^|/)BitKeeper($|/) +(^|/)ChangeSet($|/) + +### miscellaneous +# backup files +~$ +\.bak$ +\.BAK$ +# patch originals and rejects +\.orig$ +\.rej$ +# X server +\..serverauth.* +# image spam +\# +(^|/)Thumbs\.db$ +# vi, emacs tags +(^|/)(tags|TAGS)$ +#(^|/)\.[^/] +# core dumps +(^|/|\.)core$ +# partial broken files (KIO copy operations) +\.part$ +# waf files, see http://code.google.com/p/waf/ +(^|/)\.waf-[[:digit:].]+-[[:digit:]]+($|/) +(^|/)\.lock-wscript$ +# mac os finder +(^|/)\.DS_Store$ diff --git a/_darcs/prefs/defaultrepo b/_darcs/prefs/defaultrepo new file mode 100644 --- /dev/null +++ b/_darcs/prefs/defaultrepo @@ -0,0 +1,1 @@ +http://patch-tag.com/r/txt-sushi/pullrepo diff --git a/_darcs/prefs/motd b/_darcs/prefs/motd new file mode 100644 --- /dev/null +++ b/_darcs/prefs/motd diff --git a/_darcs/prefs/prefs b/_darcs/prefs/prefs new file mode 100644 --- /dev/null +++ b/_darcs/prefs/prefs @@ -0,0 +1,1 @@ +boringfile .boring diff --git a/_darcs/prefs/repos b/_darcs/prefs/repos new file mode 100644 --- /dev/null +++ b/_darcs/prefs/repos @@ -0,0 +1,1 @@ +http://patch-tag.com/r/txt-sushi/pullrepo diff --git a/_darcs/prefs/sources b/_darcs/prefs/sources new file mode 100644 --- /dev/null +++ b/_darcs/prefs/sources @@ -0,0 +1,3 @@ +repo:http://patch-tag.com/r/txt-sushi/pullrepo +thisrepo:/Users/keith/temp/txt-sushi-0.2 +cache:/Users/keith/.darcs/cache diff --git a/_darcs/pristine.hashed/0000000088-2061bfc1d7e7ec5e518faee92edbbe7e4472e558cbae9ce84fc8 b/_darcs/pristine.hashed/0000000088-2061bfc1d7e7ec5e518faee92edbbe7e4472e558cbae9ce84fc8 new file mode 100644 Binary files /dev/null and b/_darcs/pristine.hashed/0000000088-2061bfc1d7e7ec5e518faee92edbbe7e4472e558cbae9ce84fc8 differ diff --git a/_darcs/pristine.hashed/0000000111-2eb4b905deb944c0862657c882064532176f86535181e46e7bce b/_darcs/pristine.hashed/0000000111-2eb4b905deb944c0862657c882064532176f86535181e46e7bce new file mode 100644 Binary files /dev/null and b/_darcs/pristine.hashed/0000000111-2eb4b905deb944c0862657c882064532176f86535181e46e7bce differ diff --git 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a/_darcs/pristine.hashed/da39a3ee5e6b4b0d3255bfef95601890afd80709 b/_darcs/pristine.hashed/da39a3ee5e6b4b0d3255bfef95601890afd80709 new file mode 100644 --- /dev/null +++ b/_darcs/pristine.hashed/da39a3ee5e6b4b0d3255bfef95601890afd80709 diff --git a/_darcs/tentative_hashed_inventory b/_darcs/tentative_hashed_inventory new file mode 100644 --- /dev/null +++ b/_darcs/tentative_hashed_inventory @@ -0,0 +1,8 @@ +pristine:0000001506-5eac01f7311f45389d1fc10325ff7b83a4cdd71d1532f04f07800936c5acb260 +Starting with inventory: +0000001260-8f8e2c077c4bae8cc2094386214bd292379b1ee72540673d89e1514e19f69207 +[TAG release 0.2 +keithshep@gmail.com**20090521033210 + Ignore-this: b0ed58fccf2f95a610521713d9c1a499 +] +hash: 0000000773-b36b71d0a85a717f6642b9f04da20921fb1e3d4e2044508833e676d094046526 diff --git a/_darcs/tentative_pristine b/_darcs/tentative_pristine new file mode 100644 --- /dev/null +++ b/_darcs/tentative_pristine @@ -0,0 +1,1 @@ +pristine:0000001506-5eac01f7311f45389d1fc10325ff7b83a4cdd71d1532f04f07800936c5acb260 diff --git a/examples/query-imputed-SNPs-regex.bash b/examples/query-imputed-SNPs-regex.bash new file mode 100644 --- /dev/null +++ b/examples/query-imputed-SNPs-regex.bash @@ -0,0 +1,15 @@ +#!/bin/bash + +# An example of using TxtSushi to query one of the CGD (center for genome dynamics) +# datasets +# +# Selects chromosome, base pair position, data source and a couple of strains. +# Filters out any rows from perlegen and any rows where A/J and BPH/2J differ + +curl -s http://cgd.jax.org/ImputedSNPData/v1.1/PBupdatedv1.1_HMM_filleddata/PBupdatedv1.1_SNP_genoData_chr4.csv.gz \ +| zcat \ +| ../dist/build/tssql/tssql -table cgd - \ +'select ChrID, `build 36 bp Position`, Source, `BPH/2J`, `A/J`, (Source =~ "Celera2"), (Source =~ "^Celera2"), not (Source =~ "^Celera2") from cgd +where not (Source =~ "^Perlegen36_b03$") and `A/J` = `BPH/2J` +order by `build 36 bp Position` + 0 desc' \ +| ../dist/build/csvtopretty/csvtopretty - diff --git a/examples/query-imputed-SNPs.bash b/examples/query-imputed-SNPs.bash new file mode 100644 --- /dev/null +++ b/examples/query-imputed-SNPs.bash @@ -0,0 +1,15 @@ +#!/bin/bash + +# An example of using TxtSushi to query one of the CGD (center for genome dynamics) +# datasets +# +# Selects chromosome, base pair position, data source and a couple of strains. +# Filters out any rows from perlegen and any rows where A/J and BPH/2J differ + +curl -s http://cgd.jax.org/ImputedSNPData/v1.1/PBupdatedv1.1_HMM_filleddata/PBupdatedv1.1_SNP_genoData_chr4.csv.gz \ +| zcat \ +| ../dist/build/tssql/tssql -table cgd - \ +'select ChrID, `build 36 bp Position`, Source, `BPH/2J`, `A/J` from cgd +where Source <> "Perlegen36_b03" and `A/J` = `BPH/2J` +order by `build 36 bp Position` + 0 desc' \ +| ../dist/build/csvtopretty/csvtopretty - diff --git a/examples/query-mgi-markers.bash b/examples/query-mgi-markers.bash --- a/examples/query-mgi-markers.bash +++ b/examples/query-mgi-markers.bash @@ -2,11 +2,17 @@ # An example of using TxtSushi to query one of the MGI (mouse genome informatics) # database reports +# +# Selects accession ID, Symbol, chromosome, ID and centimorgan position (without +# the "trim" we end up with extra spaces). +# Only select chromosomes 1, 8 and 19 and look for "N/A" positions +# Sort the rows by chromosome (the "+0" coerces the chromosome from text to an +# integer) then symbol -wget -q -O - ftp://ftp.informatics.jax.org/pub/reports/MRK_List2.rpt | tabtocsv - \ -| tssql -table mgi - \ -'select `MGI Accession ID`, Symbol, Chr, trim(`cM Position`) +wget -q -O - ftp://ftp.informatics.jax.org/pub/reports/MRK_List2.rpt \ +| ../dist/build/tabtocsv/tabtocsv - \ +| ../dist/build/tssql/tssql -table mgi - \ +'select substring(`MGI Accession ID` from 5), substring(`MGI Accession ID` from 5 for 3), `MGI Accession ID`, Symbol, Chr, trim(`cM Position`) from mgi where (Chr = 1 or Chr = 8 or Chr = 19) and trim(`cM Position`) = "N/A" order by Chr+0, Symbol' \ -| csvtopretty - - +| ../dist/build/csvtopretty/csvtopretty - diff --git a/txt-sushi.cabal b/txt-sushi.cabal --- a/txt-sushi.cabal +++ b/txt-sushi.cabal @@ -1,6 +1,6 @@ Name: txt-sushi -Version: 0.1 -Synopsis: A collection of command line utilities for processing text tables +Version: 0.2 +Synopsis: Spreadsheets are databases! Description: TxtSushi is a collection of command line utilities for processing comma-separated and tab-delimited files (AKA flat files, spreadsheets). @@ -18,7 +18,7 @@ Executable tssql Main-Is: tssql.hs - Build-Depends: base,haskell98,directory,containers,parsec + Build-Depends: base,haskell98,directory,containers,parsec,regex-posix -- creates highly optimized code (slow compile) GHC-Options: -O2 -fvia-C