Procs for reading and writing DNA alignments in Phylip format

Example:

import src/bioseq/phylip
import bioseq
let 
  str = """
      2 8
      Sample1 ATGC
      Sample2 TTGC
      ATGC
      ATGC
      2 8
      Sample3 GTGC
      Sample4 CTGC
      ATGC
      ATGC
      """
  a = parsePhylipString(str, DNA, Interleaved)
echo a
# Sample1 ATGCATGC
# Sample2 TTGCATGC

for i in iterPhylipString(str, DNA, Interleaved): 
  echo i
# Sample1 ATGCATGC
# Sample2 TTGCATGC
# Sample3 GTGCATGC
# Sample4 CTGCATGC

let a = parsePhylipFile("input.phy", DNA, Sequential)

Imports

alignment

Types

PhylipError = object of CatchableError: Source Edit
PhylipFormat = enum Interleaved, Sequential: Source Edit

Procs

proc parsePhylipFile(path: string; typ: typedesc; fmt: PhylipFormat): Alignment[ typ]: Read relaxed Phylip formatted file. Source Edit
proc parsePhylipStream(stream: Stream; typ: typedesc; fmt: PhylipFormat): Alignment[ typ]: Read relaxed Phylip formatted stream. Source Edit
proc parsePhylipString(str: string; typ: typedesc; fmt: PhylipFormat): Alignment[ typ]: Read relaxed Phylip formatted string. Source Edit
proc toPhylipFile[T](a: Alignment[T]; path: string; fmt: PhylipFormat; lineLength = 80; mode: FileMode = fmWrite): Write data to file in Phylip format. Use fmt=fmAppend to append rather than overwrite. Source Edit
proc toPhylipString[T](a: Alignment[T]; fmt: PhylipFormat; lineLength = 80): string: Write data to string in Phylip format. Source Edit

Iterators

iterator iterPhylipFile(path: string; typ: typedesc; fmt: PhylipFormat): Alignment[ typ]: Source Edit
iterator iterPhylipStream(stream: Stream; typ: typedesc; fmt: PhylipFormat): Alignment[ typ]: Source Edit
iterator iterPhylipString(str: string; typ: typedesc; fmt: PhylipFormat): Alignment[ typ]: Source Edit
iterator toPhylip[T](a: Alignment[T]; fmt: PhylipFormat; lineLength = 80): string: Iterable yielding lines for a Phylip string or file. Source Edit