From e90ecb5b3f4f8b6e27d7f27a4854829aeea07723 Mon Sep 17 00:00:00 2001 From: Keoni Gandall Date: Thu, 9 Nov 2023 23:29:36 -0800 Subject: [PATCH] remove unwanted files --- io/pileup/data/test.pileup | 20 - io/pileup/data/test_not_enough_fields.pileup | 3 - io/pileup/data/test_position_non_int.pileup | 2 - io/pileup/data/test_read_off.pileup | 2 - io/pileup/data/test_readcount_non_int.pileup | 2 - io/pileup/data/test_unknown_rune.pileup | 2 - io/pileup/pileup.go | 382 ------------------- io/pileup/pileup_test.go | 193 ---------- 8 files changed, 606 deletions(-) delete mode 100644 io/pileup/data/test.pileup delete mode 100644 io/pileup/data/test_not_enough_fields.pileup delete mode 100644 io/pileup/data/test_position_non_int.pileup delete mode 100644 io/pileup/data/test_read_off.pileup delete mode 100644 io/pileup/data/test_readcount_non_int.pileup delete mode 100644 io/pileup/data/test_unknown_rune.pileup delete mode 100644 io/pileup/pileup.go delete mode 100644 io/pileup/pileup_test.go diff --git a/io/pileup/data/test.pileup b/io/pileup/data/test.pileup deleted file mode 100644 index 34ef5a1e..00000000 --- a/io/pileup/data/test.pileup +++ /dev/null @@ -1,20 +0,0 @@ -pOpen_v3 1 c 991 ^].^].^,.^].^].^E.^].^].^%.^].^].^6.^].^].^].^].^].^[.^].^].^].^].^].^].^].^].^].^].^].^].^G.^].^,.^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^E.^].^].^].^].^].^].^].^/.^E.^O.^\.^].^E.^].^E.^].^".^].^].^].^].^].^].^].^G.^[.^].^].^A.^].^].^'.^].^].^].^].^].^].^].^].^].^].^].^-.^].^].^&.^].^].^Y.^..^].^].^].^].^].^].^].^].^].^].^].^".^].^E.^].^].^].^].^].^].^].^].^].^W.^].^].^].^].^].^].^].^].^).^E.^].^].^].^].^G.^E.^].^E.^].^].^].^].^].^[.^].^].^].^].^].^].^-.^].^].^].^].^].^].^].^*.^].^].^].^].^].^].^].^].^].^].^9.^G.^>.^].^].^].^].^].^].^].^].^].^].^].^].^].^,.^].^].^].^].^].^].^*.^E.^].^E.^].^].^].^].^].^].^].^].^].^(.^].^].^].^].^].^E.^;.^].^].^].^].^].^].^].^%.^].^".^].^].^].^].^].^].^].^].^].^8.^].^].^E.^].^].^].^].^].^6.^].^?.^].^].^].^].^].^].^(.^].^).^].^].^].^].^].^].^E.^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^*.^].^].^].^].^].^E.^].^].^].^E.^].^].^].^].^].^].^].^].^].^].^].^].^+.^].^].^].^D.^G.^].^].^X.^].^].^].^:.^].^].^].^].^].^/.^].^].^K.^E.^+.^].^].^].^].^>.^].^].^].^].^].^].^].^].^].^*.^].^:.^].^].^>.^].^].^].^6.^].^].^].^].^].^].^].^E.^R.^].^].^].^].^].^].^].^].^].^].^N.^].^].^].^].^6.^].^6.^X.^].^].^].^].^].^].^].^].^].^#.^].^].^].^].^].^].^].^].^#.^[.^].^].^].^].^].^].^].^G.^J.^].^].^].^].^>.^].^].^+.^].^].^].^].^].^].^].^].^].^=.^3.^].^].^].^].^].^].^].^P.^#.^].^].^].^'.^].^].^].^].^].^].^(.^].^].^G.^3.^].^].^].^].^].^].^].^].^".^%.^].^].^E.^].^].^].^].^].^].^].^\.^].^].^E.^].^].^*.^>.^+.^].^].^].^].^].^].^E.^].^G.^].^].^].^].^].^?.^?.^E.^].^].^].^].^].^].^,.^].^].^].^].^].^].^].^].^].^#.^].^V.^].^].^E.^#.^].^].^].^].^].^].^#.^].^].^".^].^].^].^].^].^E.^].^].^].^#.^].^].^].^].^].^>.^].^].^].^].^].^].^].^].^].^#.^].^].^%.^?.^*.^].^].^].^].^].^%.^].^].^].^].^].^W.^].^].^].^].^].^].^].^E.^].^].^].^].^6.^].^W.^+.^V.^].^].^].^].^].^].^].^].^].^].^].^5.^].^].^].^].^].^?.^].^].^0.^].^].^].^>.^].^".^].^].^].^].^].^].^?.^].^].^$.^].^].^].^].^].^].^].^].^].^].^].^].^7.^].^3.^].^G.^].^].^].^E.^].^].^].^].^].^].^].^].^A.^].^].^].^].^@.^>.^].^E.^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^W.^].^].^I.^N.^].^].^P.^].^].^].^].^=.^].^].^].^].^].^].^].^].^].^].^].^].^[.^].^].^].^#.^>.^].^].^].^:.^R.^].^].^O.^].^].^].^G.^].^].^].^].^].^].^].^].^].^].^].^+.^].^].^G.^].^].^].^].^].^].^].^].^].^].^].^].^].^".^].^].^].^].^G.^].^].^].^].^].^].^#.^].^].^].^].^=.^].^].^].^].^].^C.^].^].^].^].^0.^].^].^].^].^G.^].^].^G.^].^].^].^].^A.^M.^].^@.^].^].^].^,.^].^].^].^7.^].^].^].^].^].^].^].^D.^].^].^].^].^].^G.^].^#.^].^].^].^?.^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^?.^].^*.^].^].^].^].^[.^#.^].^].^].^].^].^].^].^].^].^E.^V.^].^].^&.^].^].^].^@.^].^L.^C.^G.^].^B.^].^].^].^].^].^].^].^#.^].^].^(.^].^].^].^].^].^].^].^].^].^].^].^].^].^].^].^#.^].^].^%.^].^].^].^].^O.^6.^].^?.^].^].^].^].^$.^E.^].^I.^].^].^].^..^].^E.^].^].^].^].^?.^].^].^].^].^].^].^].^].^].^].^].^].^].^].^>.^#.^V.^G.^].^].^].^].^].^].^].^].^].^].^].^E.^].^*.^].^].^].^].^].^].^%.^].^].^".^].^].^].^].^].^].^].^?.^].^*. 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EC07@<>5=;E17==@A>EC.A:@E<;5@ED?4=8EEE9E?:;<@0E;;97E9EE1E8B8E5=4=9:1Em3:.EEm80;E?ED.EEDCD9m/4C6=D9E>E;?3E7:m8F;@EADA@E4B9N6.@EK35E?EE9E?/87B>8mEm>B0<60DA>EE<=@3:15E@E876E;m@7D?<=8A6AEBCE?6E>=9B2EJ;@E9::.7m?BEEE:7B?5;E:mEm:E<:4C?53EE:E:AFEEE2DB7;6>5E?9:1>HKA8D8B444/::EEEF77M@1>3AE/03m@.E2EE=?EE=3D?E;7EAD>:AF4;=.=EE3B:7E7=:<7m:;2:2:EJ4E:E1>5:>EAE.M2D9B.C>6?E7@6@3:E46/<><4:EjACEE>?E.EE=@0G8E5EE9C1:?@5EEG@D886>EB;2?:?B>DC?EE/J>?@GE>1:.0=064C;76E8;7E/EE?3m?G8<9mEEEDE.;8EmE2EC6>9EE6EC<269C/EE<6F>:3=@:=BE39ADD@>K16EFEA1E3AD<=3EC>JE?1==E=96873:DE=D==mE6?.B4mEAAmH8CE9 -pOpen_v3 2 a 1006 .....................#........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................ HA2DBD==B?10?>AQB?F1;7CE8>5DBI<5<:AIC1997;:B0>A;78R6REBA@6C4>=D?D<=0>J:G=F@A36ACGA3=;C.0F03C?99G;:>A8=H:D/F9\:9@4B9F.@?=?5B.A@EJK?A?0//45H1;9DH8G85ED/D98?7H>E0?F;A:GB26?4/BG0?AA778IA1BJAH8:/EA/89D/?B@<>G??8=C@1@3AA0.7I@F8A7>D?/B26D>>E5:2C:404/AAC6F:;@=B@I8@E3;E2EB.7CG>C?95B4;B;FEB7<<99=B9BBBC2F>H=3G4C3AA:D;CB/;E>@=A>53MA35:459;>>.?B77C9<371C=1A?4>?D<9><9A?8B65=?A=<>1:>A7;D/=83AA<>09G;HCEE5<<>7O0BH0?29:99>J@1>9HB0=6=714D>7@:@=D???60@A=:CD<91A38E235A8?89E./C5@850:B/7H1IA@D..LA=L5NB@;AL4BB;@GAB6GC6F8=C<;E=9@JC=ER1988@???ADBGFC1=AC898?//7.75?<@AL@9>D0DF?@?K@0@>@H51GEK/9:?5@B23A>@7/EG.8FHDA7AC<2CM65>C?>6/12F>GC8=D@KBC0.?@=8zGG3>B01FCC@>939ECD@93@4EI9A6:8<IG@@?I846JGB@/:.3?=>D@;9ED0@8>66:>:=<8DE=6?A:=>E:B>CA?4;77D1F6:>G71DD25?=;ABCB@;1@A2R=A<@E=<7B;?I0FE<@EA>DFC diff --git a/io/pileup/pileup.go b/io/pileup/pileup.go deleted file mode 100644 index 9efdbbd0..00000000 --- a/io/pileup/pileup.go +++ /dev/null @@ -1,382 +0,0 @@ -/* -Package pileup contains pileup parsers and writers. - -The pileup format is a text-based bioinformatics format to summarize aligned -reads against a reference sequence. In comparison to simply getting a consensus -sequence from sequencing data, pileup files can contain more context about the -mutations in a sequencing run, which is especially useful when analyzing -plasmid sequencing data from Nanopore sequencing runs. - -Pileup files are basically tsv files with 6 columns: Sequence Identifier, Position, -Reference Base, Read Count, Read Results, and Quality. An example from -wikipedia (https://en.wikipedia.org/wiki/Pileup_format) is shown below: - - ``` - seq1 272 T 24 ,.$.....,,.,.,...,,,.,..^+. <<<+;<<<<<<<<<<<=<;<;7<& - seq1 273 T 23 ,.....,,.,.,...,,,.,..A <<<;<<<<<<<<<3<=<<<;<<+ - seq1 274 T 23 ,.$....,,.,.,...,,,.,... 7<7;<;<<<<<<<<<=<;<;<<6 - seq1 275 A 23 ,$....,,.,.,...,,,.,...^l. <+;9*<<<<<<<<<=<<:;<<<< - seq1 276 G 22 ...T,,.,.,...,,,.,.... 33;+<<7=7<<7<&<<1;<<6< - seq1 277 T 22 ....,,.,.,.C.,,,.,..G. +7<;<<<<<<<&<=<<:;<<&< - seq1 278 G 23 ....,,.,.,...,,,.,....^k. %38*<<;<7<<7<=<<<;<<<<< - seq1 279 C 23 A..T,,.,.,...,,,.,..... 75&<<<<<<<<<=<<<9<<:<<< - ``` - - 1. Sequence Identifier: The sequence identifier of the reference sequence - 2. Position: Position of row in the reference sequence (indexed at 1) - 3. Reference Base: Base pair in reference sequence - 4. Read Count: Number of aligned reads to this particular base pair - 5. Read Results: The resultant alignments - 6. Quality: Phred quality scores associated with each base - -This package provides a parser and writer for working with pileup files. -*/ -package pileup - -import ( - "bufio" - "bytes" - "errors" - "fmt" - "io" - "math" - "os" - "regexp" - "strconv" - "strings" - "unicode" -) - -// https://en.wikipedia.org/wiki/Pileup_format - -// Pileup struct is a single position in a pileup file. Pileup files "pile" -// a bunch of separate bam/sam alignments into something more readable at a per -// base pair level, so are only useful as a grouping. -type Pileup struct { - Sequence string `json:"sequence"` - Position uint `json:"position"` - ReferenceBase string `json:"reference_base"` - ReadCount uint `json:"read_count"` - ReadResults []string `json:"read_results"` - Quality string `json:"quality"` -} - -// Parse parses a given Pileup file into an array of Pileup structs. -func Parse(r io.Reader) ([]Pileup, error) { - // 32kB is a magic number often used by the Go stdlib for parsing. We multiply it by two. - const maxLineSize = 2 * 32 * 1024 - parser := NewParser(r, maxLineSize) - return parser.ParseAll() -} - -// Parser is a pileup parser. -type Parser struct { - reader bufio.Reader - line uint -} - -// NewParser creates a parser from an io.Reader for pileup data. -func NewParser(r io.Reader, maxLineSize int) *Parser { - return &Parser{ - reader: *bufio.NewReaderSize(r, maxLineSize), - } -} - -// ParseAll parses all sequences in underlying reader only returning non-EOF errors. -// It returns all valid pileup sequences up to error if encountered. -func (parser *Parser) ParseAll() ([]Pileup, error) { - return parser.ParseN(math.MaxInt) -} - -// ParseN parses up to maxRows pileup sequences from the Parser's underlying reader. -// ParseN does not return EOF if encountered. -// If an non-EOF error is encountered it returns it and all correctly parsed sequences up to then. -func (parser *Parser) ParseN(maxRows int) (pileups []Pileup, err error) { - for counter := 0; counter < maxRows; counter++ { - pileup, err := parser.ParseNext() - if err != nil { - if errors.Is(err, io.EOF) { - err = nil // EOF not treated as parsing error. - } - return pileups, err - } - pileups = append(pileups, pileup) - } - return pileups, nil -} - -// ParseNext parses the next pileup row in a pileup file. -// ParseNext returns an EOF if encountered. -func (parser *Parser) ParseNext() (Pileup, error) { - if _, err := parser.reader.Peek(1); err != nil { - // Early return on error. Probably will be EOF. - return Pileup{}, err - } - // Parse out a single line - lineBytes, err := parser.reader.ReadSlice('\n') - if err != nil { - return Pileup{}, err - } - parser.line++ - line := string(lineBytes) - line = line[:len(line)-1] // Exclude newline delimiter. - - // Check that there are 6 values, as defined by the pileup format - values := strings.Split(line, "\t") - if len(values) != 6 { - return Pileup{}, fmt.Errorf("Error on line %d: Got %d values, expected 6.", parser.line, len(values)) - } - - // Convert Position and ReadCount to integers - positionInteger, err := strconv.Atoi(values[1]) - if err != nil { - return Pileup{}, fmt.Errorf("Error on line %d. Got error: %w", parser.line, err) - } - readCountInteger, err := strconv.Atoi(values[3]) - if err != nil { - return Pileup{}, fmt.Errorf("Error on line %d. Got error: %w", parser.line, err) - } - - // Parse ReadResults - var readResults []string - var starts uint - var ends uint - var skip int - var readCount uint - resultsString := values[4] - for resultIndex := range resultsString { - if skip != 0 { - skip = skip - 1 - continue - } - resultRune := resultsString[resultIndex] - switch resultRune { - case '^': - starts = starts + 1 - skip = skip + 2 - readResults = append(readResults, resultsString[resultIndex:resultIndex+3]) - case '$': - ends = ends + 1 - // This applies to the last read segement - readResults[len(readResults)-1] = readResults[len(readResults)-1] + "$" - case '.', ',', '*', 'A', 'T', 'G', 'C', 'N', 'a', 't', 'g', 'c', 'n': - readResults = append(readResults, string(resultRune)) - case '-', '+': - // formatted in `+4ATGC` format. We need to know the number of jumps - // because you can have +10AAAAAAAAAA - var numberOfJumps string - for numberIndex := range resultsString[resultIndex:] { - runeToCheck := resultsString[resultIndex+numberIndex+1] - if unicode.IsDigit(rune(runeToCheck)) { - numberOfJumps = numberOfJumps + string(runeToCheck) - continue - } - break - } - regularExpressionInt, _ := strconv.Atoi(numberOfJumps) // Because of the above check, this will never err - readResult := resultsString[resultIndex : resultIndex+regularExpressionInt+2] - for _, letter := range readResult { - switch letter { - case '0', '1', '2', '3', '4', '5', '6', '7', '8', '9', 'A', 'T', 'G', 'C', 'N', 'a', 't', 'g', 'c', 'n', '-', '+': - continue - default: - return Pileup{}, fmt.Errorf("Rune within +,- not found on line %d. Got %c: only runes allowed are: [0 1 2 3 4 5 6 7 8 9 A T G C N a t g c n - +]", parser.line, letter) - } - } - readResults = append(readResults, readResult) - skip = skip + regularExpressionInt + len(numberOfJumps) // The 1 makes sure to include the regularExpressionInt in readResult string - default: - return Pileup{}, fmt.Errorf("Rune not found on line %d. Got %c: only runes allowed are: [^ $ . , * A T G C N a t g c n - +]", parser.line, resultRune) - } - readCount = readCount + 1 - } - - return Pileup{Sequence: values[0], Position: uint(positionInteger), ReferenceBase: values[2], ReadCount: uint(readCountInteger), ReadResults: readResults, Quality: values[5]}, nil -} - -// Reset discards all data in buffer and resets state. -func (parser *Parser) Reset(r io.Reader) { - parser.reader.Reset(r) - parser.line = 0 -} - -/****************************************************************************** - -Start of Read functions - -******************************************************************************/ - -// Read reads a file into an array of Pileup structs -func Read(path string) ([]Pileup, error) { - file, err := os.Open(path) - if err != nil { - return nil, err - } - defer file.Close() - return Parse(file) -} - -/****************************************************************************** - -Start of Write functions - -******************************************************************************/ - -// WritePileups writes a pileup array to an io.Writer -func WritePileups(pileups []Pileup, w io.Writer) error { - for _, pileup := range pileups { - _, err := w.Write([]byte( - strings.Join( - []string{ - pileup.Sequence, - strconv.FormatUint(uint64(pileup.Position), 10), - pileup.ReferenceBase, - strconv.FormatUint(uint64(pileup.ReadCount), 10), - strings.Join(pileup.ReadResults, ""), - pileup.Quality, - }, - "\t") + "\n")) - if err != nil { - return err - } - } - return nil -} - -// Write writes a pileup array to a file -func Write(pileups []Pileup, path string) error { - var b bytes.Buffer - if err := WritePileups(pileups, &b); err != nil { - return err - } - return os.WriteFile(path, b.Bytes(), 0644) -} - -/****************************************************************************** - -Sequencing - -The primary use of pileup files are to have a visual way of looking at -SNP/indels in alignment data. In particular, it can be used analyze plasmid -sequencing data to see if there any mutations in the DNA. - - - -******************************************************************************/ - -type MutationType string - -const ( - NoMutation MutationType = "no_mutation" - Point MutationType = "point" - PointIndel MutationType = "point_indel" - Indel MutationType = "indel" - Insertion MutationType = "insertion" - Noisy MutationType = "noisy" -) - -type Mutation struct { - Type MutationType - To string - Length int // Only for Indel and Insertions - TotalCorrect int - TotalMutated int - TotalAligned int -} - -func CallMutations(readResults []string, minimalRatio float64) Mutation { - reads := make(map[string]int) - for _, readResult := range readResults { - if len(readResult) == 1 { - // This will include simple point mutations and - // correct sequences. - reads[string(readResult[0])]++ - } else { - // This includes more complicated Sequences - switch { - case strings.Contains(readResult, "$"): - // An "end" will always start with the base called - reads[string(readResults[0])]++ - case strings.Contains(readResult, "^"): - // A "start" will end with the base called - reads[string(readResult[len(readResults)-1])]++ - default: - // The default case would be a deletion or an insertion. - // We handle those by inserting the entire thing. - reads[readResult]++ - } - } - } - // First, check how many correct alignments we have. - noMutation := reads["."] + reads[","] - - // ratioFunction is a function that returns "true" if a mutation - // has a greater than or equal ratio than the minimalRatio. - ratioFunction := func(mutation int) bool { - if mutation+noMutation == 0 { - return false - } - return float64((mutation / (mutation + noMutation))) >= minimalRatio - } - - // Next, let's check for point mutations. - aMutation := reads["A"] + reads["a"] - tMutation := reads["T"] + reads["t"] - gMutation := reads["G"] + reads["g"] - cMutation := reads["C"] + reads["c"] - pointIndel := reads["*"] - - // First, let's check if the mutation is a point mutation - switch { - case ratioFunction(aMutation): - return Mutation{Type: Point, To: "A", TotalCorrect: noMutation, TotalMutated: aMutation, TotalAligned: len(readResults)} - case ratioFunction(tMutation): - return Mutation{Type: Point, To: "T", TotalCorrect: noMutation, TotalMutated: tMutation, TotalAligned: len(readResults)} - case ratioFunction(gMutation): - return Mutation{Type: Point, To: "G", TotalCorrect: noMutation, TotalMutated: gMutation, TotalAligned: len(readResults)} - case ratioFunction(cMutation): - return Mutation{Type: Point, To: "C", TotalCorrect: noMutation, TotalMutated: cMutation, TotalAligned: len(readResults)} - case ratioFunction(pointIndel): - return Mutation{Type: PointIndel, To: "*", TotalCorrect: noMutation, TotalMutated: pointIndel, TotalAligned: len(readResults)} - } - - // Ok, we know there is no point mutation. That means there is an insertion or indel. Let's call it. - for key, value := range reads { - if len(key) > 1 { - var mutationType MutationType - switch key[0] { - case '-': - mutationType = Indel - case '+': - mutationType = Insertion - default: - panic(fmt.Sprintf("Unknown readResult! got: %s", key)) - } - if ratioFunction(value) { - // Let's get the length of the insertion / indel - re := regexp.MustCompile(`-?\d+`) - match := re.FindString(key) - if match == "" { - panic("no num found!") - } - // Given the regex, this will never fail - length, _ := strconv.Atoi(match) - return Mutation{Type: mutationType, To: key, TotalCorrect: noMutation, TotalMutated: value, TotalAligned: len(readResults), Length: length} - } - } - } - - // Now we know it is not a point mutation, not an indel, and not an insertion. Maybe the read - // is just noisy though, so let's check that now - var noisyCount int - for key, value := range reads { - if key != "." && key != "," { - noisyCount += value - } - } - if ratioFunction(noisyCount) { - return Mutation{Type: Noisy, To: "?", TotalCorrect: noMutation, TotalMutated: noisyCount, TotalAligned: len(readResults)} - } - - return Mutation{Type: NoMutation, To: ".", TotalCorrect: noMutation, TotalMutated: noisyCount, TotalAligned: len(readResults)} -} diff --git a/io/pileup/pileup_test.go b/io/pileup/pileup_test.go deleted file mode 100644 index 65521fd4..00000000 --- a/io/pileup/pileup_test.go +++ /dev/null @@ -1,193 +0,0 @@ -package pileup - -import ( - "bytes" - "errors" - "fmt" - "io" - "os" - "strings" - "testing" -) - -func TestParse(t *testing.T) { - file, err := os.Open("data/test.pileup") - if err != nil { - t.Errorf("Failed to open test.pileup: %s", err) - } - defer file.Close() - const maxLineSize = 2 * 32 * 1024 - parser := NewParser(file, maxLineSize) - var pileupReads []Pileup - for { - pileupRead, err := parser.ParseNext() - if err != nil { - if !errors.Is(err, io.EOF) { - t.Errorf("Got unknown error: %s", err) - } - break - } - pileupReads = append(pileupReads, pileupRead) - } - if pileupReads[2].ReadCount != 1401 { - t.Errorf("Expected 1401 read counts. Got: %d", pileupReads[2].ReadCount) - } - - // Test not enough fields - file2, err := os.Open("data/test_not_enough_fields.pileup") - if err != nil { - t.Errorf("Failed to open test_not_enough_fields.pileup: %s", err) - } - defer file2.Close() - parser = NewParser(file2, maxLineSize) - for { - _, err = parser.ParseNext() - if err != nil { - if !strings.Contains(fmt.Sprint(err), "values, expected 6.") { - t.Errorf("Got unknown error: %s", err) - } - break - } - } - - // Test Position Int - file3, err := os.Open("data/test_position_non_int.pileup") - if err != nil { - t.Errorf("Failed to open test_position_non_int.pileup: %s", err) - } - defer file3.Close() - parser = NewParser(file3, maxLineSize) - for { - _, err = parser.ParseNext() - if err != nil { - if !strings.Contains(fmt.Sprint(err), "Error on line") { - t.Errorf("Got unknown error: %s", err) - } - break - } - } - - // Test ReadCount Int - file4, err := os.Open("data/test_readcount_non_int.pileup") - if err != nil { - t.Errorf("Failed to open test_readcount_non_int.pileup: %s", err) - } - defer file4.Close() - parser = NewParser(file4, maxLineSize) - for { - _, err = parser.ParseNext() - if err != nil { - if !strings.Contains(fmt.Sprint(err), "Error on line") { - t.Errorf("Got unknown error: %s", err) - } - break - } - } - - // Test +,- Rune - file5, err := os.Open("data/test_read_off.pileup") - if err != nil { - t.Errorf("Failed to open test_read_off.pileup: %s", err) - } - defer file5.Close() - parser = NewParser(file5, maxLineSize) - for { - _, err = parser.ParseNext() - if err != nil { - if !strings.Contains(fmt.Sprint(err), "Rune within +,- not found on line") { - t.Errorf("Got unknown error: %s", err) - } - break - } - } - - // Test Unknown Rune - file6, err := os.Open("data/test_unknown_rune.pileup") - if err != nil { - t.Errorf("Failed to open test_unknown_rune.pileup: %s", err) - } - defer file6.Close() - parser = NewParser(file6, maxLineSize) - for { - _, err = parser.ParseNext() - if err != nil { - if !strings.Contains(fmt.Sprint(err), "Rune not found on line") { - t.Errorf("Got unknown error: %s", err) - } - break - } - } - - // Test ParseN - file7, err := os.Open("data/test.pileup") - if err != nil { - t.Errorf("Failed to open test.pileup: %s", err) - } - defer file7.Close() - parser = NewParser(file7, maxLineSize) - _, err = parser.ParseN(2) - if err != nil { - t.Errorf("Got unknown error: %s", err) - } -} - -func TestBuild(t *testing.T) { - file, err := os.Open("data/test.pileup") - if err != nil { - t.Errorf("Failed to open test.pileup: %s", err) - } - const maxLineSize = 2 * 32 * 1024 - parser := NewParser(file, maxLineSize) - pileups, err := parser.ParseAll() // Parse all - if err != nil { - t.Errorf("Failed to parse pileup: %s", err) - } - parser.Reset(file) - var b bytes.Buffer - if err := WritePileups(pileups, &b); err != nil { - t.Errorf("Failed to write pileups: %v", err) - } - newBody := b.Bytes() - file.Close() - - // Open file again, read all - file, err = os.Open("data/test.pileup") - if err != nil { - t.Errorf("Failed to open test.pileup: %s", err) - } - body, err := io.ReadAll(file) // Read them bytes - if err != nil { - t.Errorf("Failed to readall: %s", err) - } - if string(body) != string(newBody) { - t.Errorf("input bytes do not equal output bytes of build") - } -} - -func TestRead(t *testing.T) { - _, err := Read("data/DOESNT_EXIST.pileup") - if err == nil { - t.Errorf("Should have failed on empty file") - } - _, err = Read("data/test.pileup") - if err != nil { - t.Errorf("Should have succeeded in reading pileup file") - } -} - -func TestWrite(t *testing.T) { - pileups, _ := Read("data/test.pileup") - err := Write(pileups, "tmp.pileup") - if err != nil { - t.Errorf("Failed to write temporary pileup") - } - err = os.Remove("tmp.pileup") - if err != nil { - t.Errorf("Failed to delete temporary pileup") - } -} - -func TestCallMutations(t *testing.T) { - pileups, _ := Read("data/real/134_from_D20.pileup") - fmt.Println(pileups[0]) -}