cgmaptools

#!/usr/bin/env python

"""
    cgmaptools

    Copyright (C) Weilong Guo & Ping Zhu
    Contact: Weilong Guo <guoweilong@126.com>
             Ping Zhu <pingzhu.work@gmail.com>

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in
all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
DEALINGS IN THE SOFTWARE.
"""

import sys, os

#os.system(sys.argv[0])

#print sys.argv[0]
#print sys.argv[1]
#print sys.argv[-1]
DIR=os.path.dirname(sys.argv[0])
#print DIR

import subprocess

#subprocess.call(["ls", "-l", "/etc/resolv.conf"])


argv_len = len(sys.argv)

def PrintVersion() :
   print("Version:  0.1.2")
   print("Updated on: Dec. 14th, 2018")
#

if (argv_len) == 1  or sys.argv[1] in ["-h", "-H", "--help"]:
   print("Program : cgmaptools (Tools for analysis in CGmap/ATCGmap format)")
   PrintVersion()
   print("Usage:    cgmaptools <command> [options]")
   print("Commands:")
   print("  -- File manipulation")
   print("     convert     + data format conversion tools")
   print("     fetch       + fetch a region by random accessing")
   print("     refill        refill the missing columns")
   print("     intersect     intersect two files")
   print("     merge2      + merge two files into one")
   print("     mergelist   + merge a list of files")
   print("     sort          sort lines by chromosome and position")
   print("     split       + split file by chromosomes")
   print("     select      + select lines by region/site")
   print("  -- SNV analysis")
   print("     snv           snv analysis")
   print("  -- Methylation analysis")
   print("     dms           differentially methylated site analysis")
   print("     dmr           differentially methylated region analysis")
   print("     asm           allele-specific methylation analysis")
   print("     mbed          average methylation level in regions")
   print("     mbin        * single sample, mC levels in bins")
   print("     mmbin         multiple samples, mC levels in bins")
   print("     mfg           methlation levels across fragmented region")
   print("     mstat       * methyaltion statistic")
   print("     mtr           methylation level to each region")
   print("  -- Coverage analysis")
   print("     oac        +* overall coverage (for ATCGmap)")
   print("     mec        +* methylation effective coverage (for CGmap)")
   print("  -- Graph related functions")
   print("     lollipop    * show local mC levels as lollipop bars")
   print("     heatmap     * global mC distribution for multiple samples")
   print("     fragreg     * show mC profile across fragmented regions")
   print("     tanghulu    * show local mapped reads in Tanghulu shape")
   print("  -- Other Utils")
   print("     findCCGG      get MspI cutting sites for RRBS")
   print("     bed2fragreg   get fragmented region based on region")
   print("Note: ")
   print("  Commands support figures generation are marked with \"*\" ")
   print("  Commands contain sub-commands are marked with \"+\" ")
   print("Authors:")
   print("  GUO, Weilong; guoweilong@126.com;  http://guoweilong.github.io")
   print("  ZHU, Ping; pingzhu.work@gmail.com; http://perry-zhu.github.io")
   print("")
else :
   code1 = sys.argv[1]
   # -- File manipulation
   if code1 == "convert" :
      if (argv_len) == 2 or sys.argv[2] in ["-h", "-H", "--help"]:
         print("Usage:    cgmaptools convert <command> [options]")
         PrintVersion()
         print("Commands:")
         print("     bam2cgmap        BAM     => CGmap & ATCGmap")
         print("     atcgmap2atcgbz   ATCGmap => ATCGbz")
         print("     atcgbz2atcgmap   ATCGbz  => ATCGmap")
         print("     atcgmap2cgmap    ATCGmap => CGmap")
         print("     cgmap2cgbz       CGamp   => CGbz")
         print("     cgbz2cgmap       CGbz    => CGmap")
         print("     cgmap2wig        CGmap   => WIG")
         print("     bismark2cgmap    Bismark => CGmap")
      else :
         code2 = sys.argv[2]
         if code2 == "bam2cgmap" :
            subprocess.call([DIR + "/bin/CGmapFromBAM"]+ sys.argv[3:])
         elif code2 == "cgmap2wig" :
            subprocess.call([DIR + "/bin/CGmapToWig"]+ sys.argv[3:])
         elif code2 == "atcgbz2atcgmap" :
            subprocess.call([DIR + "/bin/ATCGbzToATCGmap"]+ sys.argv[3:])
         elif code2 == "atcgmap2atcgbz" :
            subprocess.call([DIR + "/bin/ATCGmapToATCGbz"]+ sys.argv[3:])
         elif code2 == "cgbz2cgmap" :
            subprocess.call([DIR + "/bin/CGbzToCGmap"]+ sys.argv[3:])
         elif code2 == "cgmap2cgbz" :
            subprocess.call([DIR + "/bin/CGmapToCGbz"]+ sys.argv[3:])
         elif code2 == "atcgmap2cgmap" :
            subprocess.call([DIR + "/bin/ATCGmapToCGmapWig"]+ sys.argv[3:])
         elif code2 == "bismark2cgmap" :
            subprocess.call([DIR + "/bin/BismarkToCGmap"]+ sys.argv[3:])
         else :
            print("Wrong parameter. Enter \"cgmaptools convert -h\" for more information.")
         #
      #
   elif code1 == "fetch" :
      if (argv_len) == 2 or sys.argv[2] in ["-h", "-H", "--help"]:
         print("Usage:    cgmaptools fetch <command> [options]")
         PrintVersion()
         print("Commands:")
         print("     atcgbz      fetch lines from ATCGbz")
         print("     cgbz        fetch lines from CGbz")
      else :
         code2 = sys.argv[2]
         if code2 == "atcgbz" :
            subprocess.call([DIR + "/bin/ATCGbzFetchRegion"]+ sys.argv[3:])
         elif code2 == "cgbz" :
            subprocess.call([DIR + "/bin/CGbzFetchRegion"]+ sys.argv[3:])
         else :
            print("Wrong parameter. Enter \"cgmaptools fetch -h\" for more information.")
         #
      #
   elif code1 == "refill" :
      subprocess.call([DIR + "/bin/CGmapFillContext"]+ sys.argv[2:])
   elif code1 == "intersect" :
      subprocess.call([DIR + "/bin/CGmapIntersect"]+ sys.argv[2:])
   elif code1 == "merge2" :
      if (argv_len) == 2 or sys.argv[2] in ["-h", "-H", "--help"]:
         print("Usage:    cgmaptools merge2 <command> [options]")
         PrintVersion()
         print("Commands:")
         print("     atcgmap      merge two ATCGmap files into one")
         print("     cgmap        merge two CGmap files into one")
      else :
         code2 = sys.argv[2]
         if code2 == "atcgmap" :
            subprocess.call([DIR + "/bin/ATCGmapMerge"]+ sys.argv[3:])
         elif code2 == "cgmap" :
            subprocess.call([DIR + "/bin/CGmapMerge"]+ sys.argv[3:])
         else :
            print("Wrong parameter. Enter \"cgmaptools merge2 -h\" for more information.")
         #
      #
   elif code1 == "mergelist" :
      if (argv_len) == 2 or sys.argv[2] in ["-h", "-H", "--help"]:
         print("Usage:    cgmaptools mergelist <command> [options]")
         PrintVersion()
         print("Commands:")
         print("     tomatrix   mC levels matrix from multiple files")
         print("     tosingle   merge list of input files into one")
      else :
         code2 = sys.argv[2]
         if code2 == "tomatrix" :
            subprocess.call([DIR + "/bin/CGmapFillIndex"]+ sys.argv[3:])
         elif code2 == "tosingle" :
            subprocess.call([DIR + "/bin/MergeListOfCGmap"]+ sys.argv[3:])
         else :
            print("Wrong parameter. Enter \"cgmaptools mergelist -h\" for more information.")
         #
      #
   elif code1 == "sort" :
      subprocess.call([DIR + "/bin/Sort_chr_pos"]+ sys.argv[2:])
   elif code1 == "split" :
      subprocess.call([DIR + "/bin/CGmapSplitByChr"]+ sys.argv[2:])
   elif code1 == "select" :
      if (argv_len) == 2 or sys.argv[2] in ["-h", "-H", "--help"]:
         print("Usage:    cgmaptools select <command> [options]")
         PrintVersion()
         print("Commands:")
         print("     region     select or exclude liens by region lists")
         print("     site       select or exclude lines by site list")
      else :
         code2 = sys.argv[2]
         if code2 == "region" :
            subprocess.call([DIR + "/bin/CGmapSelectByRegion"]+ sys.argv[3:])
         elif code2 == "site" :
            subprocess.call([DIR + "/bin/CGmapSelectBySite"]+ sys.argv[3:])
         else :
            print("Wrong parameter. Enter \"cgmaptools select -h\" for more information.")
         #
      #
   # -- SNV analysis
   elif code1 == "snv" :
      subprocess.call([DIR + "/bin/SNVFromATCGmap"]+ sys.argv[2:])
   # -- Methylation analysis
   elif code1 == "dms" :
      subprocess.call([DIR + "/bin/CGmapInterDiffSite"]+ sys.argv[2:])
   elif code1 == "dmr" :
      subprocess.call([DIR + "/bin/CGmapInterDiffReg"]+ sys.argv[2:])
   elif code1 == "asm" :
      subprocess.call([DIR + "/bin/ASM"]+ sys.argv[2:])
   elif code1 == "mbed" :
      subprocess.call([DIR + "/bin/CGmapMethInBed"]+ sys.argv[2:])
   elif code1 == "mbin" :
      subprocess.call([DIR + "/bin/CGmapMethInBins"]+ sys.argv[2:])
   elif code1 == "mmbin" :
      subprocess.call([DIR + "/bin/CGmapsMethInBins"]+ sys.argv[2:])
   elif code1 == "mfg" :
      subprocess.call([DIR + "/bin/CGmapMethInFragReg"]+ sys.argv[2:])
   elif code1 == "mstat" :
      subprocess.call([DIR + "/bin/CGmapStatMeth"]+ sys.argv[2:])
   elif code1 == "mtr" :
      subprocess.call([DIR + "/bin/CGmapToRegion"]+ sys.argv[2:])
   # -- Coverage analysis
   elif code1 == "oac" :
      if (argv_len) == 2 or sys.argv[2] in ["-h", "-H", "--help"]:
         print("Usage:    cgmaptools oac <command> [options]")
         PrintVersion()
         print("Commands:")
         print("     bin      * overall coverage in bins")
         print("     stat     * overall coverage statistics globally")
      else :
         code2 = sys.argv[2]
         if code2 == "bin" :
            subprocess.call([DIR + "/bin/ATCGmapCovInBins"]+ sys.argv[3:])
         elif code2 == "stat" :
            subprocess.call([DIR + "/bin/ATCGmapStatCov"]+ sys.argv[3:])
         else :
            print("Wrong parameter. Enter \"cgmaptools oac -h\" for more information.")
         #
      #
   elif code1 == "mec" :
      if (argv_len) == 2 or sys.argv[2] in ["-h", "-H", "--help"]:
         print("Usage:    cgmaptools mec <command> [options]")
         PrintVersion()
         print("Commands:")
         print("     bin      * methylation effective coverage in bins")
         print("     stat     * methylation effective coverage statistics globally")
      else :
         code2 = sys.argv[2]
         if code2 == "bin" :
            subprocess.call([DIR + "/bin/CGmapCovInBins"]+ sys.argv[3:])
         elif code2 == "stat" :
            subprocess.call([DIR + "/bin/CGmapStatCov"]+ sys.argv[3:])
         else :
            print("Wrong parameter. Enter \"cgmaptools mec -h\" for more information.")
         #
      #
   # -- Graph related funtion
   elif code1 == "lollipop" :
      subprocess.call([DIR + "/bin/mCLollipop"]+ sys.argv[2:])
   elif code1 == "heatmap" :
      subprocess.call([DIR + "/bin/mCBinHeatmap"]+ sys.argv[2:])
   elif code1 == "fragreg" :
      subprocess.call([DIR + "/bin/mCFragRegView"]+ sys.argv[2:])
   elif code1 == "tanghulu" :
      subprocess.call([DIR + "/bin/mCTanghulu"]+ sys.argv[2:])
   # -- other utilities
   elif code1 == "findCCGG" :
      subprocess.call([DIR + "/bin/FindCCGG"]+ sys.argv[2:])
   elif code1 == "combinestrands" :
      subprocess.call([DIR + "/bin/CGmapCombineStrands"]+ sys.argv[2:])
   elif code1 == "bed2fragreg" :
      subprocess.call([DIR + "/bin/FragRegFromBED"]+ sys.argv[2:])
   else :
      print("Wrong parameter. Enter \"cgmaptools -h\" for more information.")
   #
#