Extract peptide counts from count matrix in new fasta files

extractFasta.nim

#Add those lines to lib/system.nim:

iterator pairs*[T](it: iterator(): T {.inline.}): tuple[key: int, val: T] {.inline.} =
  ## iterates over each item of it. Yields ``(index, item)`` pairs.
  var i = 0
  for v in it:
    yield (i, v)
    inc(i)

iterator mpairs*[T](it: iterator(): T {.inline.}): tuple[key: int, val: var T] {.inline.} =
  ## iterates over each item of it. Yields ``(index, item)`` pairs.
  ## ``item`` can be modified.
  var i = 0
  for v in it:
    yield (i, v)
    inc(i)


# $nim-vm rebuild repo
#   CC: docutils_rstgen
#   Error:  execution of an external program failed; rerun with --parallelBuild:1 to see the error message
#   FAILURE
# -- Ho well, lets try:
# $~/Nim/koch boot --parallelBuild:1
#   ...
#   SUCCESS
# $~/Nim/bin/nim c extractFasta.nim
#   extractLists.nim(14, 32) Error: undeclared identifier: 'lines'

#extractFasta.nim:
import os
import strutils

var files: seq[File] = @[]
let file = if paramCount() > 0: open( paramStr( 1 ) )
           else: stdin
for lineNum, line in pairs( file.lines() ):
   var peptideName: string
   let inTokens = split( line, '\t' )
   for tokenNum, token in inTokens:
      if lineNum == 0:
         if tokenNum > 0:
            files.add( open( token&".fasta", FileMode.fmWrite ) )
      else:
         if tokenNum == 1:
            peptideName = token
         elif tokenNum > 1 and parseInt( token ) > 0:
            files[tokenNum-2].write( ">" & peptideName & "|" & token & "\n" )
            files[tokenNum-2].write( peptideName & "\n" )

test.nim

import os
import strutils

iterator pairs*[T](it: iterator(): T {.inline.}): tuple[key: int, val: T] {.inline.} =
  ## iterates over each item of it. Yields ``(index, item)`` pairs.
  var i = 0
  for v in it:
    yield (i, v)
    inc(i)

iterator mpairs*[T](it: iterator(): T {.inline.}): tuple[key: int, val: var T] {.inline.} =
  ## iterates over each item of it. Yields ``(index, item)`` pairs.
  ## ``item`` can be modified.
  var i = 0
  for v in it:
    yield (i, v)
    inc(i)

var files: seq[File] = @[]
let file = if paramCount() > 0: open( paramStr( 1 ) )
           else: stdin
for lineNum, line in pairs( file.lines() ):
   var peptideName: string
   for tokenNum, token in pairs( split( line, '\t' ) ):
      if lineNum == 0:
         if tokenNum > 0:
            files.add( open( token & ".fasta", FileMode.fmWrite ) )
      else:
         if tokenNum == 1:
            peptideName = token
         elif tokenNum > 1 and parseInt( token ) > 0:
            files[tokenNum-2].write( ">" & peptideName & "|" & token & "\n" )
            files[tokenNum-2].write( peptideName & "\n" )