lefse: format_input.py annotate

annotate format_input.py @ 20:a6284ef17bf3 draft default tip

Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea")

author	george-weingart
date	Tue, 07 Jul 2015 13:26:55 -0400
parents	47ac77f2fe68
children

rev	line source
0 47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	1 #!/usr/bin/env python
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	2
20 a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	3 import sys,os,argparse,pickle,re,numpy
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	4
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	5
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	6
0 47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	7
20 a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	8 #***************************************************************************************************************
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	9 #* Log of change *
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	10 #* January 16, 2014 - George Weingart - george.weingart@gmail.com *
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	11 #* *
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	12 #* biom Support *
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	13 #* Modified the program to enable it to accept biom files as input *
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	14 #* *
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	15 #* Added two optional input parameters: *
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	16 #* 1. biom_c is the name of the biom metadata to be used as class *
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	17 #* 2. biom_s is the name of the biom metadata to be used as subclass *
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	18 #* class and subclass are used in the same context as the original *
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	19 #* parameters class and subclass *
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	20 #* These parameters are totally optional, the default is the program *
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	21 #* chooses as class the first metadata received from the conversion *
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	22 #* of the biom file into a sequential (pcl) file as generated by *
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	23 #* breadcrumbs, and similarly, the second metadata is selected as *
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	24 #* subclass. *
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	25 #* The syntax or logic for the original non-biom case was NOT changed. *
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	26 #* *
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	27 #* <***************** IMPORTANT NOTE **********************>
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	28 #* The biom case requires breadcrumbs and therefore there is a *
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	29 #* a conditional import of the breadcrumbs modules *
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	30 #* If the User uses a biom input and breadcrumbs is not detected, *
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	31 #* the run is abnormally ended *
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	32 #* breadcrumbs itself needs a biom environment, so if the immport *
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	33 #* of biom in breadcrumbs fails, the run is also abnormally
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	34 #* ended (Only if the input file was biom) *
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	35 #* *
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	36 #* USAGE EXAMPLES *
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	37 #* -------------- *
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	38 #* Case #1: Using a sequential file as input (Old version - did not change *
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	39 #* ./format_input.py hmp_aerobiosis_small.txt hmp_aerobiosis_small.in -c 1 -s 2 -u 3 -o 1000000 *
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	40 #* Case #2: Using a biom file as input *
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	41 #* ./format_input.py hmp_aerobiosis_small.biom hmp_aerobiosis_small.in -o 1000000 *
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	42 #* Case #3: Using a biom file as input and override the class and subclass *
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	43 #* ./format_input.py lefse.biom hmp_aerobiosis_small.in -biom_c oxygen_availability -biom_s body_site -o 1000000
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	44 #* *
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	45 #***************************************************************************************************************
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	46
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	47 def read_input_file(inp_file, CommonArea):
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	48
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	49 if inp_file.endswith('.biom'): #* If the file format is biom:
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	50 CommonArea = biom_processing(inp_file) #* Process in biom format
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	51 return CommonArea #* And return the CommonArea
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	52
0 47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	53 with open(inp_file) as inp:
20 a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	54 CommonArea['ReturnedData'] = [[v.strip() for v in line.strip().split("\t")] for line in inp.readlines()]
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	55 return CommonArea
0 47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	56
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	57 def transpose(data):
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	58 return zip(*data)
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	59
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	60 def read_params(args):
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	61 parser = argparse.ArgumentParser(description='LEfSe formatting modules')
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	62 parser.add_argument('input_file', metavar='INPUT_FILE', type=str, help="the input file, feature hierarchical level can be specified with \| or . and those symbols must not be present for other reasons in the input file.")
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	63 parser.add_argument('output_file', metavar='OUTPUT_FILE', type=str,
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	64 help="the output file containing the data for LEfSe")
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	65 parser.add_argument('--output_table', type=str, required=False, default="",
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	66 help="the formatted table in txt format")
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	67 parser.add_argument('-f',dest="feats_dir", choices=["c","r"], type=str, default="r",
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	68 help="set whether the features are on rows (default) or on columns")
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	69 parser.add_argument('-c',dest="class", metavar="[1..n_feats]", type=int, default=1,
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	70 help="set which feature use as class (default 1)")
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	71 parser.add_argument('-s',dest="subclass", metavar="[1..n_feats]", type=int, default=None,
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	72 help="set which feature use as subclass (default -1 meaning no subclass)")
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	73 parser.add_argument('-o',dest="norm_v", metavar="float", type=float, default=-1.0,
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	74 help="set the normalization value (default -1.0 meaning no normalization)")
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	75 parser.add_argument('-u',dest="subject", metavar="[1..n_feats]", type=int, default=None,
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	76 help="set which feature use as subject (default -1 meaning no subject)")
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	77 parser.add_argument('-m',dest="missing_p", choices=["f","s"], type=str, default="d",
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	78 help="set the policy to adopt with missin values: f removes the features with missing values, s removes samples with missing values (default f)")
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	79 parser.add_argument('-n',dest="subcl_min_card", metavar="int", type=int, default=10,
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	80 help="set the minimum cardinality of each subclass (subclasses with low cardinalities will be grouped together, if the cardinality is still low, no pairwise comparison will be performed with them)")
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	81
20 a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	82 parser.add_argument('-biom_c',dest="biom_class", type=str,
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	83 help="For biom input files: Set which feature use as class ")
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	84 parser.add_argument('-biom_s',dest="biom_subclass", type=str,
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	85 help="For biom input files: set which feature use as subclass ")
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	86
0 47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	87 args = parser.parse_args()
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	88
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	89 return vars(args)
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	90
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	91 def remove_missing(data,roc):
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	92 if roc == "c": data = transpose(data)
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	93 max_len = max([len(r) for r in data])
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	94 to_rem = []
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	95 for i,r in enumerate(data):
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	96 if len([v for v in r if not( v == "" or v.isspace())]) < max_len: to_rem.append(i)
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	97 if len(to_rem):
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	98 for i in to_rem.reverse():
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	99 data.pop(i)
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	100 if roc == "c": return transpose(data)
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	101 return data
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	102
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	103
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	104 def sort_by_cl(data,n,c,s,u):
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	105 def sort_lines1(a,b):
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	106 return int(a[c] > b[c])*2-1
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	107 def sort_lines2u(a,b):
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	108 if a[c] != b[c]: return int(a[c] > b[c])*2-1
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	109 return int(a[u] > b[u])*2-1
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	110 def sort_lines2s(a,b):
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	111 if a[c] != b[c]: return int(a[c] > b[c])*2-1
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	112 return int(a[s] > b[s])*2-1
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	113 def sort_lines3(a,b):
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	114 if a[c] != b[c]: return int(a[c] > b[c])*2-1
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	115 if a[s] != b[s]: return int(a[s] > b[s])*2-1
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	116 return int(a[u] > b[u])*2-1
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	117 if n == 3: data.sort(sort_lines3)
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	118 if n == 2:
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	119 if s is None:
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	120 data.sort(sort_lines2u)
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	121 else:
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	122 data.sort(sort_lines2s)
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	123 if n == 1: data.sort(sort_lines1)
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	124 return data
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	125
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	126 def group_small_subclasses(cls,min_subcl):
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	127 last = ""
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	128 n = 0
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	129 repl = []
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	130 dd = [list(cls['class']),list(cls['subclass'])]
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	131 for d in dd:
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	132 if d[1] != last:
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	133 if n < min_subcl and last != "":
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	134 repl.append(d[1])
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	135 last = d[1]
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	136 n = 1
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	137 for i,d in enumerate(dd):
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	138 if d[1] in repl: dd[i][1] = "other"
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	139 dd[i][1] = str(dd[i][0])+"_"+str(dd[i][1])
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	140 cls['class'] = dd[0]
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	141 cls['subclass'] = dd[1]
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	142 return cls
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	143
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	144 def get_class_slices(data):
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	145 previous_class = data[0][0]
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	146 previous_subclass = data[0][1]
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	147 subclass_slices = []
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	148 class_slices = []
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	149 last_cl = 0
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	150 last_subcl = 0
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	151 class_hierarchy = []
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	152 subcls = []
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	153 for i,d in enumerate(data):
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	154 if d[1] != previous_subclass:
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	155 subclass_slices.append((previous_subclass,(last_subcl,i)))
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	156 last_subcl = i
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	157 subcls.append(previous_subclass)
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	158 if d[0] != previous_class:
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	159 class_slices.append((previous_class,(last_cl,i)))
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	160 class_hierarchy.append((previous_class,subcls))
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	161 subcls = []
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	162 last_cl = i
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	163 previous_subclass = d[1]
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	164 previous_class = d[0]
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	165 subclass_slices.append((previous_subclass,(last_subcl,i+1)))
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	166 subcls.append(previous_subclass)
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	167 class_slices.append((previous_class,(last_cl,i+1)))
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	168 class_hierarchy.append((previous_class,subcls))
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	169 return dict(class_slices), dict(subclass_slices), dict(class_hierarchy)
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	170
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	171 def numerical_values(feats,norm):
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	172 mm = []
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	173 for k,v in feats.items():
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	174 feats[k] = [float(val) for val in v]
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	175 if norm < 0.0: return feats
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	176 tr = zip(*(feats.values()))
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	177 mul = []
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	178 fk = feats.keys()
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	179 hie = True if sum([k.count(".") for k in fk]) > len(fk) else False
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	180 for i in range(len(feats.values()[0])):
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	181 if hie: mul.append(sum([t for j,t in enumerate(tr[i]) if fk[j].count(".") < 1 ]))
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	182 else: mul.append(sum(tr[i]))
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	183 if hie and sum(mul) == 0:
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	184 mul = []
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	185 for i in range(len(feats.values()[0])):
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	186 mul.append(sum(tr[i]))
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	187 for i,m in enumerate(mul):
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	188 if m == 0: mul[i] = 0.0
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	189 else: mul[i] = float(norm) / m
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	190 for k,v in feats.items():
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	191 feats[k] = [val*mul[i] for i,val in enumerate(v)]
20 a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	192 if numpy.mean(feats[k]) and (numpy.std(feats[k])/numpy.mean(feats[k])) < 1e-10:
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	193 feats[k] = [ float(round(kv*1e6)/1e6) for kv in feats[k]]
0 47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	194 return feats
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	195
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	196 def add_missing_levels2(ff):
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	197
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	198 if sum( [f.count(".") for f in ff] ) < 1: return ff
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	199
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	200 dn = {}
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	201
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	202 added = True
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	203 while added:
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	204 added = False
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	205 for f in ff:
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	206 lev = f.count(".")
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	207 if lev == 0: continue
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	208 if lev not in dn: dn[lev] = [f]
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	209 else: dn[lev].append(f)
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	210 for fn in sorted(dn,reverse=True):
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	211 for f in dn[fn]:
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	212 fc = ".".join(f.split('.')[:-1])
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	213 if fc not in ff:
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	214 ab_all = [ff[fg] for fg in ff if (fg.count(".") == 0 and fg == fc) or (fg.count(".") > 0 and fc == ".".join(fg.split('.')[:-1]))]
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	215 ab =[]
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	216 for l in [f for f in zip(*ab_all)]:
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	217 ab.append(sum([float(ll) for ll in l]))
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	218 ff[fc] = ab
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	219 added = True
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	220 if added:
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	221 break
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	222
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	223 return ff
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	224
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	225
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	226 def add_missing_levels(ff):
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	227 if sum( [f.count(".") for f in ff] ) < 1: return ff
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	228
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	229 clades2leaves = {}
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	230 for f in ff:
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	231 fs = f.split(".")
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	232 if len(fs) < 2:
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	233 continue
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	234 for l in range(len(fs)):
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	235 n = ".".join( fs[:l] )
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	236 if n in clades2leaves:
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	237 clades2leaves[n].append( f )
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	238 else:
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	239 clades2leaves[n] = [f]
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	240 for k,v in clades2leaves.items():
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	241 if k and k not in ff:
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	242 ff[k] = [sum(a) for a in zip(*[[float(fn) for fn in ff[vv]] for vv in v])]
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	243 return ff
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	244
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	245
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	246
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	247 def modify_feature_names(fn):
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	248 ret = fn
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	249
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	250 for v in [' ',r'\$',r'\@',r'#',r'%',r'\^',r'\&',r'\*',r'\"',r'\'']:
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	251 ret = [re.sub(v,"",f) for f in ret]
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	252 for v in ["/",r'$',r'$',r'-',r'\+',r'=',r'{',r'}',r'\[',r'\]',
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	253 r',',r'\.',r';',r':',r'\?',r'\<',r'\>',r'\.',r'\,']:
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	254 ret = [re.sub(v,"_",f) for f in ret]
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	255 for v in ["\\|"]:
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	256 ret = [re.sub(v,".",f) for f in ret]
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	257
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	258 ret2 = []
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	259 for r in ret:
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	260 if r[0] in ['0','1','2','3','4','5','6','7','8','9']:
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	261 ret2.append("f_"+r)
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	262 else: ret2.append(r)
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	263
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	264 return ret2
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	265
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	266
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	267 def rename_same_subcl(cl,subcl):
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	268 toc = []
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	269 for sc in set(subcl):
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	270 if len(set([cl[i] for i in range(len(subcl)) if sc == subcl[i]])) > 1:
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	271 toc.append(sc)
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	272 new_subcl = []
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	273 for i,sc in enumerate(subcl):
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	274 if sc in toc: new_subcl.append(cl[i]+"_"+sc)
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	275 else: new_subcl.append(sc)
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	276 return new_subcl
20 a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	277
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	278
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	279 #*************************************************************************************
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	280 #* Modifications by George Weingart, Jan 15, 2014 *
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	281 #* If the input file is biom: *
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	282 #* a. Load an AbundanceTable (Using breadcrumbs) *
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	283 #* b. Create a sequential file from the AbundanceTable (de-facto - pcl) *
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	284 #* c. Use that file as input to the rest of the program *
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	285 #* d. Calculate the c,s,and u parameters, either from the values the User entered *
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	286 #* from the meta data values in the biom file or set up defaults *
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	287 #* <<<------------- I M P O R T A N T N O T E ------------------->> *
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	288 #* breadcrumbs src directory must be included in the PYTHONPATH *
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	289 #* <<<------------- I M P O R T A N T N O T E ------------------->> *
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	290 #*************************************************************************************
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	291 def biom_processing(inp_file):
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	292 CommonArea = dict() #* Set up a dictionary to return
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	293 CommonArea['abndData'] = AbundanceTable.funcMakeFromFile(inp_file, #* Create AbundanceTable from input biom file
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	294 cDelimiter = None,
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	295 sMetadataID = None,
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	296 sLastMetadataRow = None,
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	297 sLastMetadata = None,
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	298 strFormat = None)
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	299
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	300 #****************************************************************
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	301 #* Building the data element here *
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	302 #****************************************************************
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	303 ResolvedData = list() #This is the Resolved data that will be returned
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	304 IDMetadataName = CommonArea['abndData'].funcGetIDMetadataName() #* ID Metadataname
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	305 IDMetadata = [CommonArea['abndData'].funcGetIDMetadataName()] #* The first Row
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	306 for IDMetadataEntry in CommonArea['abndData'].funcGetMetadataCopy()[IDMetadataName]: #* Loop on all the metadata values
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	307 IDMetadata.append(IDMetadataEntry)
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	308 ResolvedData.append(IDMetadata) #Add the IDMetadata with all its values to the resolved area
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	309 for key, value in CommonArea['abndData'].funcGetMetadataCopy().iteritems():
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	310 if key != IDMetadataName:
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	311 MetadataEntry = list() #* Set it up
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	312 MetadataEntry.append(key) #* And post it to the area
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	313 for x in value:
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	314 MetadataEntry.append(x) #* Append the metadata value name
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	315 ResolvedData.append(MetadataEntry)
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	316 for AbundanceDataEntry in CommonArea['abndData'].funcGetAbundanceCopy(): #* The Abundance Data
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	317 lstAbundanceDataEntry = list(AbundanceDataEntry) #Convert tuple to list
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	318 ResolvedData.append(lstAbundanceDataEntry) #Append the list to the metadata list
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	319 CommonArea['ReturnedData'] = ResolvedData #Post the results
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	320 return CommonArea
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	321
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	322
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	323 #*******************************************************************************
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	324 #* Check the params and override in the case of biom *
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	325 #*******************************************************************************
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	326 def check_params_for_biom_case(params, CommonArea):
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	327 CommonArea['MetadataNames'] = list() #Metadata names
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	328 params['original_class'] = params['class'] #Save the original class
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	329 params['original_subclass'] = params['subclass'] #Save the original subclass
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	330 params['original_subject'] = params['subject'] #Save the original subclass
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	331
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	332
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	333 TotalMetadataEntriesAndIDInBiomFile = len(CommonArea['abndData'].funcGetMetadataCopy()) # The number of metadata entries
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	334 for i in range(0,TotalMetadataEntriesAndIDInBiomFile): #* Populate the meta data names table
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	335 CommonArea['MetadataNames'].append(CommonArea['ReturnedData'][i][0]) #Add the metadata name
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	336
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	337
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	338 #****************************************************
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	339 #* Setting the params here *
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	340 #****************************************************
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	341
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	342 if TotalMetadataEntriesAndIDInBiomFile > 0: #If there is at least one entry - has to be the subject
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	343 params['subject'] = 1
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	344 if TotalMetadataEntriesAndIDInBiomFile == 2: #If there are 2 - The first is the subject and the second has to be the metadata, and that is the class
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	345 params['class'] = 2
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	346 if TotalMetadataEntriesAndIDInBiomFile == 3: #If there are 3: Set up default that the second entry is the class and the third is the subclass
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	347 params['class'] = 2
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	348 params['subclass'] = 3
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	349 FlagError = False #Set up error flag
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	350
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	351 if not params['biom_class'] is None and not params['biom_subclass'] is None: #Check if the User passed a valid class and subclass
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	352 if params['biom_class'] in CommonArea['MetadataNames']:
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	353 params['class'] = CommonArea['MetadataNames'].index(params['biom_class']) +1 #* Set up the index for that metadata
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	354 else:
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	355 FlagError = True
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	356 if params['biom_subclass'] in CommonArea['MetadataNames']:
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	357 params['subclass'] = CommonArea['MetadataNames'].index(params['biom_subclass']) +1 #* Set up the index for that metadata
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	358 else:
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	359 FlagError = True
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	360 if FlagError == True: #* If the User passed an invalid class
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	361 print "**Invalid biom class or subclass passed - Using defaults: First metadata=class, Second Metadata=subclass\n"
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	362 params['class'] = 2
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	363 params['subclass'] = 3
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	364 return params
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	365
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	366
0 47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	367
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	368 if __name__ == '__main__':
20 a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	369 CommonArea = dict() #Build a Common Area to pass variables in the biom case
0 47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	370 params = read_params(sys.argv)
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	371
20 a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	372 #*************************************************************
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	373 #* Conditionally import breadcrumbs if file is a biom file *
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	374 #* If it is and no breadcrumbs found - abnormally exit *
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	375 #*************************************************************
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	376 if params['input_file'].endswith('.biom'):
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	377 try:
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	378 from lefsebiom.ConstantsBreadCrumbs import *
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	379 from lefsebiom.AbundanceTable import *
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	380 except ImportError:
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	381 sys.stderr.write("************************************************************************************************************ \n")
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	382 sys.stderr.write("* Error: Breadcrumbs libraries not detected - required to process biom files - run abnormally terminated * \n")
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	383 sys.stderr.write("************************************************************************************************************ \n")
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	384 exit(1)
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	385
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	386
0 47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	387 if type(params['subclass']) is int and int(params['subclass']) < 1:
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	388 params['subclass'] = None
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	389 if type(params['subject']) is int and int(params['subject']) < 1:
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	390 params['subject'] = None
20 a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	391
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	392
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	393 CommonArea = read_input_file(sys.argv[1], CommonArea) #Pass The CommonArea to the Read
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	394 data = CommonArea['ReturnedData'] #Select the data
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	395
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	396 if sys.argv[1].endswith('biom'): #* Check if biom:
a6284ef17bf3 Fixed bug due to numerical approximation after normalization affecting root-level clades (e.g. "Bacteria" or "Archaea") george-weingart parents: 0 diff changeset	397 params = check_params_for_biom_case(params, CommonArea) #Check the params for the biom case
0 47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	398
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	399 if params['feats_dir'] == "c":
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	400 data = transpose(data)
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	401
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	402 ncl = 1
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	403 if not params['subclass'] is None: ncl += 1
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	404 if not params['subject'] is None: ncl += 1
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	405
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	406 first_line = zip(*data)[0]
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	407
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	408 first_line = modify_feature_names(list(first_line))
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	409
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	410 data = zip( first_line,
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	411 sort_by_cl(zip(data)[1:],
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	412 ncl,
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	413 params['class']-1,
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	414 params['subclass']-1 if not params['subclass'] is None else None,
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	415 params['subject']-1 if not params['subject'] is None else None))
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	416 # data.insert(0,first_line)
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	417 # data = remove_missing(data,params['missing_p'])
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	418 cls = {}
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	419
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	420 cls_i = [('class',params['class']-1)]
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	421 if params['subclass'] > 0: cls_i.append(('subclass',params['subclass']-1))
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	422 if params['subject'] > 0: cls_i.append(('subject',params['subject']-1))
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	423 cls_i.sort(lambda x, y: -cmp(x[1],y[1]))
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	424 for v in cls_i: cls[v[0]] = data.pop(v[1])[1:]
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	425 if not params['subclass'] > 0: cls['subclass'] = [str(cl)+"_subcl" for cl in cls['class']]
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	426
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	427 cls['subclass'] = rename_same_subcl(cls['class'],cls['subclass'])
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	428 # if 'subclass' in cls.keys(): cls = group_small_subclasses(cls,params['subcl_min_card'])
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	429 class_sl,subclass_sl,class_hierarchy = get_class_slices(zip(*cls.values()))
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	430
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	431 feats = dict([(d[0],d[1:]) for d in data])
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	432
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	433 feats = add_missing_levels(feats)
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	434
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	435 feats = numerical_values(feats,params['norm_v'])
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	436 out = {}
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	437 out['feats'] = feats
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	438 out['norm'] = params['norm_v']
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	439 out['cls'] = cls
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	440 out['class_sl'] = class_sl
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	441 out['subclass_sl'] = subclass_sl
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	442 out['class_hierarchy'] = class_hierarchy
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	443
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	444 if params['output_table']:
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	445 with open( params['output_table'], "w") as outf:
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	446 if 'class' in cls: outf.write( "\t".join(list(["class"])+list(cls['class'])) + "\n" )
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	447 if 'subclass' in cls: outf.write( "\t".join(list(["subclass"])+list(cls['subclass'])) + "\n" )
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	448 if 'subject' in cls: outf.write( "\t".join(list(["subject"])+list(cls['subject'])) + "\n" )
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	449 for k,v in out['feats'].items(): outf.write( "\t".join([k]+[str(vv) for vv in v]) + "\n" )
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	450
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	451 with open(params['output_file'], 'wb') as back_file:
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	452 pickle.dump(out,back_file)
47ac77f2fe68 First version of lefse in this toolshed george-weingart parents: diff changeset	453

Mercurial > repos > george-weingart > lefse

annotate format_input.py @ 20:a6284ef17bf3 draft default tip