osprai/trunk/io_module.py

"""
io_module
---------

Input/Output module for converting files to Biosensor Array class.
Supported sensorgram types include Biosensor, CLAMP, SPRit, and Plexera ICM.
Supported microarray types include GAL and ISB Map.

.. moduleauthor:: Christopher Lausted, 
                  Institute for Systems Biology, 
                  OSPRAI developers.                      
Examples::

  >>> import io_module as io
  >>> ba1 = io.readsprit("spritdata.txt")
  >>> ba1 = io.readclamp("spritdata.txt")
  >>> ba1 = io.readicmtxt("icmdata.txt")
  >>> ba1 = io.readbiosensor("icmdata.txt")
  >>> ba1 = io.readcsv("rawdata.csv")
  >>> ba2 = io.applygal(ba1, "galfile.gal")
  >>> ba2 = io.applykey(ba1, "keyfile.tsv")
  >>> ba3 = io.applymethod(ba2, "icmmethod.xls")
  >>> io.writesprit(ba3, "newspritfile.txt")
  >>> io.writeclamp(ba3, "newclampfile.txt")
"""
__version__ = "110208"


## Import libraries.
from copy import deepcopy
from os import getcwd
from time import mktime
import numpy as np                  ## Numpy array library.
import ba_class as ba               ## Our Biosensor Array class.
reload(ba)

def readsprit(fname):
    """
    Read a SPRit text file into a ba class.
    It has two tab-delimited columns and two header lines.
    Here is a very simple example with 2 rois and 3 datapoints::
    
      Elapsed Time (Seconds)   Average Intensity (Pixel Intensity)
      BEGIN
      0.000000e+000            2.863145e+003
      5.013000e+000            2.863367e+003
      1.002500e+001            2.862950e+003
      0.000000e+000            2.862875e+003
      5.013000e+000            2.862510e+003
    """
    
    ## Try to open file. Return tiny ba object if it fails.
    ba0 = ba.BiosensorArray(1,1)
    try:
        fp = open(fname, "r")
    except IOError:
        print 'Error: Cannot open file %s for reading' % fname
        return ba0
    
    ## Check header lines for signature text.
    txt = fp.readline()  # 'Elapsed Time...'
    txt = fp.readline()  # 'BEGIN'
    if ('BEGIN' not in txt):
        print "Error: Second line is not BEGIN."
        fp.close()
        return ba0
    
    ## Put data into one big text string and close.
    txtfile = fp.readlines()
    fp.close()
    
    ## Change text into array
    sprtable = np.zeros((len(txtfile),2), dtype=float)  ## Redimension Nx2
    for i in range(len(txtfile)):
        txt = txtfile[i].split('\t')
        sprtable[i,0] = float(txt[0])  ## Time column.
        sprtable[i,1] = float(txt[1])  ## Signal column.
    
    ## Find number of ROIs in file.
    for i in range(1,len(sprtable)):
        ## See when the time drops back to zero.
        if (sprtable[i,0] < sprtable[i-1,0]): break
    rows = i  ## Datapoints or new array rows.
    rois = int(len(sprtable) / rows)
    
    ## Move data the old-fashioned iterative way.
    ba0 = ba.BiosensorArray(rois,rows)
    k = 0
    for i in range(rois):
        for j in range(rows):
            ba0.roi[i].time[j] = sprtable[k,0]
            ba0.roi[i].value[j] = sprtable[k,1]
            k +=1
            
    return ba0
    """End of readsprit() function"""
    
    
def writesprit(ba0, fname):
    """
    Write a ba class to a SPRit text file.
    """
    fp=file(fname,'w')
    fp.write("Elapsed Time (Seconds)\tAverage Intensity (Pixel Intensity)\r\n")
    fp.write("BEGIN\r\n")
    for roi in range(len(ba0.roi)):                   ## Could also use ba.rois.
        for dpoint in range(len(ba0.roi[0].time)):    ## Could also use ba.dpoints.
            txt = "%f\t%f\r\n" % (ba0.roi[roi].time[dpoint], ba0.roi[roi].value[dpoint])
            fp.write(txt)
    fp.close
    print "File %s saved in %s." % (fname, getcwd())
    return
    """End of writesprit() function"""
    
    
def readclamp(fname):
    """
    Read a Clamp text file into a ba class.
    It has two tab-delimited columns per SPR flowcell/roi..
    It has a varying number of header lines with injection information.
    Here is a very simple example with 2 rois and 3 datapoints::
    
      Vers 3.41 Data
      Conc1   0       0       0       0
      Start1  301.5   301.5   301.5   301.5
      Stop1   949.8   949.8   949.8   949.8
      RInd1   0       0       0       0
      Conc2   0       0       0       0
      Start2  986.4   0       0       0
      Stop2   1626    0       0       0
      RInd2   0       0       0       0
      Flow    1       1       1       1
      Time1   Data1   Time2   Data2
      0.094   0.062   0.094   0.053
      1.094   0.026   1.094   0.05
      2.094   0.119   2.094   0.055
    """
    
    print "This feature is under construction."
    return
    """"End of readclamp() function"""
    
    
def writeclamp(ba0, fname):
    """
    Write a ba class to a Clamp text file.
    """
    
    fp=file(fname,'w')
    ## First header line.
    fp.write("Vers 3.41 Data\r\n")
    
    ## Next write injection information.
    for inj in range(len(ba0.roi[0].injconc)):
        fp.write("Conc%i" % (inj+1))
        for roi in ba0.roi: fp.write("\t%.3f" % roi.injconc[inj])
        fp.write("\r\nStart%i" % (inj+1))
        for roi in ba0.roi: fp.write("\t%.3f" % roi.injstart[inj])
        fp.write("\r\nStop%i" % (inj+1))
        for roi in ba0.roi: fp.write("\t%.3f" % roi.injstop[inj])
        fp.write("\r\nRInd%i" % (inj+1))
        for roi in ba0.roi: fp.write("\t%.3f" % roi.injrind[inj])
    ## Next write flowrate line.
    fp.write("\r\nFlow")
    for roi in ba0.roi: fp.write("\t%.3f" % roi.flow)
    fp.write("\r\n")
    
    ## Write sensorgram data header line.
    for i,roi in enumerate(ba0.roi):
        if (i>0): fp.write("\t")
        fp.write("Time%i" % (i+1))
        fp.write("\t")
        fp.write(roi.name)
    fp.write("\r\n")
    ## Write sensorgram data lines. Three decimal places.
    for dpoint in range(len(ba0.roi[0].time)):
        for i,roi in enumerate(ba0.roi):
            if (i>0): fp.write("\t")
            fp.write("%.3f\t%.3f" % (roi.time[dpoint], roi.value[dpoint]))
        fp.write("\r\n")
        
    ## Close file handle and print message.
    fp.close
    print "File %s saved in %s." % (fname, getcwd())
    return
    """End of writeclamp() function"""
    
    
def readicmtxt(fname):
    """
    Read a ICM text file into a ba class.
    Here is a very simple example of the tab-delimited format::
    
      03/05/2010 13:37:21.312   249.408   0.000   0.000
      03/05/2010 13:37:22.312   249.306   0.000   0.000
    """ 

    ## Try to open file. Return tiny ba object if it fails.
    ba0 = ba.BiosensorArray(1,1)
    try:
        fp = open(fname, "r")
    except IOError:
        print 'Error: Cannot open file %s for reading' % fname
        return ba0
    
    ## Put data into one big text string and close.
    txtfile = fp.readlines()
    fp.close()
    dpoints = len(txtfile)
    rois = txtfile[0].count("\t")  ## Usually 25.
    
    ## Create and size ba object.
    print "This ICM file has %i datapoints for %i ROIs." % (dpoints, rois)
    ba0 = ba.BiosensorArray(rois, dpoints)
    
    ## Determine experiment start time so we can make other times relative.
    x = txtfile[0].split("\t")  ## E.g. "03/05/2010 13:37:20.218"
    t0 = __icmtime2sec(x[0])      ## E.g. 1267825040.22
    
    ## Move the data from txtfile to ba0.
    for i, txtline in enumerate(txtfile):
        x = txtline.split("\t")
        tx = __icmtime2sec(x[0]) - t0
        for j in range(1,rois):
            ba0.roi[j].time[i] = tx
            ba0.roi[j].value[i] = float(x[j])
            
    return ba0
    """End of readicmtxt"""


def __icmtime2sec(timetxt):
    """
    Take a time of the form "03/05/2010 15:19:27.312" and return seconds.
    """
    cal, clock = timetxt.split(" ")
    mm, dd, yy = cal.split("/")
    hh, min, ss = clock.split(":")
    stime = (int(yy), int(mm), int(dd), int(hh), int(min), 0, 0, 0, 0)
    return mktime(stime) + float(ss)
    """End of __icmtime2sec"""
    
    
def readbiosensor(fname):
    """
    Read a Biacore-style text file into a ba class.
    Here is a very simple example of the tab-delimited format::
    
      Ab1 Fc=4- 1_X  Ab1 Fc=4 -1_Y  Ab2 Fc=4 -1_X  Ab2 Fc=4 -1_Y
      13.1           23.7644        93.1           0.713912
      13.6           23.4265        93.6           0.0541172
      14.1           23.1625        94.1           0.332768
      14.6           23.5752        94.6           0.849459
    """ 

    ## Try to open file. Return tiny ba object if it fails.
    ba0 = ba.BiosensorArray(1,1)
    try:
        fp = open(fname, "r")
    except IOError:
        print 'Error: Cannot open file %s for reading' % fname
        return ba0
    
    ## Read header line.  Check number of pairs of _X and _Y labels.
    txthdr = fp.readline()
    cols = txthdr.count("Fc=")
    xys = txthdr.count("_X\t") + txthdr.count("_Y\t")+1
    if ((cols != xys) or ((cols%2) != 0)):
        print "Error: This is not a valid Biosensor file."
        return ba0
        
    ## Put data into one big text string and close.
    txtfile = fp.readlines()
    fp.close()
    dpoints = len(txtfile)
    rois = int(cols/2)
    
    ## Create and size ba object.
    print "This Biosensor file has %i datapoints for %i ROIs." % (dpoints, rois)
    ba0 = ba.BiosensorArray(rois, dpoints)
    
    ## Get names of ROIs from header like "Ab1 Fc=4 - 1_Y"
    txthdr = txthdr.replace(" -","-").replace("- ","-") ## Remove unwanted spaces.
    names = txthdr.split("\t")                          ## Use tab delimiter.
    for j in range(rois):
        name = names[j*2+1].replace("_Y","").strip(" -")
        name = name.partition("Fc=")          ## Now a 3-tuple.
        ba0.roi[j].name = name[0]             ## Text left of Fc.
        ba0.roi[j].desc = ("Fc=" + name[2])   ## Text right of Fc.
        
    ## Move the data from txtfile to ba0.
    for i, txtline in enumerate(txtfile):
        x = txtline.split("\t")
        for j in range(rois):
            ba0.roi[j].time[i] = float(x[j*2+0])
            ba0.roi[j].value[i] = float(x[j*2+1])
    
    return ba0
    """End of readbiosensor()"""


def writebiosensor(ba0, fname):
    """
    Write a ba class to a Biosensor text file.
    """
    
    ## This is like a simplified Clamp file.
    fp=file(fname,'w')
    ## Write sensorgram data header line.
    for i,roi in enumerate(ba0.roi):
        if (i>0): fp.write("\t")
        name = roi.name.strip() + " " + roi.desc.strip()
        fp.write("%s_X\t%s_Y" % (name, name))
    ## Write sensorgram data lines. Three decimal places.
    for dpoint in range(len(ba0.roi[0].time)):
        fp.write("\r\n")
        for i,roi in enumerate(ba0.roi):
            if (i>0): fp.write("\t")
            fp.write("%.3f\t%.3f" % (roi.time[dpoint], roi.value[dpoint]))
    
    ## Close file handle and print message.
    fp.close
    print "File %s saved in %s." % (fname, getcwd())
    return
    """End of writebiosensor()"""


def readcsv(fname):
    """
    Read a comma-separated value text file into a ba class.
    The first column contains time data while the others contain response data.
    Here is a very simple example of the format::
    
      1.0001, 23.7644, 0.7139
      2.0001, 23.4265, 0.0541
      3.0001, 23.1625, 0.3327
      4.0001, 23.5752, 0.8494
    """ 

    ## Try to open file. Return tiny ba object if it fails.
    ba0 = ba.BiosensorArray(1,1)
    try:
        fp = open(fname, "r")
    except IOError:
        print 'Error: Cannot open file %s for reading' % fname
        return ba0
      
    ## Put data into one big text string, determine array size, and close.
    txtfile = fp.readlines()  ## One big text string.
    fp.close()
    dpoints = len(txtfile)  ## Rows in the csv file.
    rois = len(txtfile[0].split(',')) - 1  ## Columns are comma-delimited.
    
    ## Move the data from txtfile to ba0.
    ba0 = ba.BiosensorArray(rois, dpoints)
    for i, txtline in enumerate(txtfile):
        x = txtline.split(',')
        for j in range(rois):
            ba0.roi[j].time[i] = float(x[0])
            ba0.roi[j].value[i] = float(x[j+1])
    
    print "The file %s has %i ROIs and %i datapoints." % (fname, rois, dpoints)
    return ba0
    """End of readcsv()"""


def applygal(ba0, fname):
    """
    Read a Gal file and apply its microarray information.
    
    *(This function is under construction)*
    """
    print "This feature is under construction."
    return
    """End of applygal()"""
    
    
def applykey(ba0, fname):
    """
    Read a Key file and apply its microarray information.
    Multiple background ROIs are not yet supported.
    Here is a very simple example::
    
      No. Description1    Description2    Background ROI  Col     Row
      1   Rat TNF         Antibody01      2               1       1
      2   ratIgG          Antibody02      4               2       1
      3   Hum TNF         Antibody03      4               3       1
      4   humIgG          Antibody04      2               4       1
    """
    
    ## Try to open file. Return unchanged ba object if it fails.
    try:
        fp = open(fname, "r")
    except IOError:
        print 'Cannot open file %s for reading' % fname
        return ba0
    ## Check header lines for signature text.
    txt = fp.readline()
    if ("No." not in txt):
        print "Error: The header line is unfamiliar."
        fp.close()
        return ba0
    
    ## Read all text, convert to 2d list, then six lists (one for each column).
    ## There's probably an easier way to do this. Maybe in CSV module.
    txtfile = fp.readlines()
    fp.close()
    ## Change text into array
    keytable = txtfile[:]  ## Dimension rows in new 2d list.
    for i in range(len(txtfile)):
        txt = str(txtfile[i].strip())
        keytable[i] = txt.split('\t')
    ## Use list comprehensions to get one list for each column.
    id = [int(x[0]) for x in keytable]    ## First column is integer.
    desc1 = [x[1] for x in keytable]      ## Second column is text.
    desc2 = [x[2] for x in keytable]      ## Third column is text.
    bg = [int(x[3]) for x in keytable]    ## Fourth column is integer. Change base1 to base0?
    col = [int(x[4]) for x in keytable]   ## Fifth column is integer.
    row = [int(x[5]) for x in keytable]   ## Sixth column is integer.
    
    ## Check if key file looks valid.  These tests are not very thorough!
    keys = 1 + max(id) - min(id)
    if (ba0.rois != keys):
        print "Error: We have %i ROIs but %i keyfile entries." % (ba0.rois, keys)
        return ba0
    if ((min(bg) < min(id)) or (max(bg) > max (id))):
        print "Error: at least one specified background ROI does not exist"
        print "Identifiers (id) range from %i to %i." % (min(id), max(id))
        print "Background references range from %i to %i." % (min(bg), max(bg))
        return ba0
        
    ## Create new object and put data in it.
    ba1 = deepcopy(ba0)
    for i in range(len(id)):
        ba1.roi[id[i]-1].name = desc1[i] 
        ba1.roi[id[i]-1].desc = desc2[i]
        ba1.roi[id[i]-1].bgroi = [bg[i]]  ## ToDo: Decide if bg will be id or index. Base1 now.
        ba1.roi[id[i]-1].spotx = col[i]
        ba1.roi[id[i]-1].spoty = row[i]
    
    print "Successfully loaded information for %i ROIs." % keys
    return ba1
    """End of applykey()"""
    
    
def applymethod(ba0, fname):
    """
    Read a ICM Analyte/Method xls file and apply its information.
    
    *(This feature is under construction.)*
    """
    print "This feature is under construction."
    return
    """End of applymethod()"""
    
    
def outputbindinglevels(ba0, fname, interval, *baselines):
    """
    Measure the binding level changes at multiple intervals along a sensorgram.
    Write the data to a file.  If interval is 500 and baselines are [100, 1100] then
    binding levels are changes between 100-600s and between 1100-01600s.
    Average 30s of data.
    """
    fp=file(fname,'w')
    
    ## Measurements
    for iroi in ba0.roi:
        fp.write("%i\t%s" % (iroi.index, iroi.name))
        for j in baselines:
            t1 = j
            t2 = j + interval
            y1 = np.average(iroi.time2val(t1-15, t1+15))
            y2 = np.average(iroi.time2val(t2-15, t2+15))
            fp.write("\t%.3f" % (y2-y1))
        fp.write("\n")
    fp.close
    print "File %s saved in %s." % (fname, getcwd())
    return
    """End of outputbindinglevels()"""


## Here are a few lines to test this module.
if __name__ == '__main__':
    print "This module isn't a stand-alone app."

################################# End of module #################################
Revision:	51
Committed:	Wed Feb 9 01:09:05 2011 UTC (8 years, 8 months ago) by clausted
File size:	16581 byte(s)
Log Message:	Fix minor docstring error.
Line	File contents
1	"""
2	io_module
3	---------
4
5	Input/Output module for converting files to Biosensor Array class.
6	Supported sensorgram types include Biosensor, CLAMP, SPRit, and Plexera ICM.
7	Supported microarray types include GAL and ISB Map.
8
9	.. moduleauthor:: Christopher Lausted,
10	Institute for Systems Biology,
11	OSPRAI developers.
12	Examples::
13
14	>>> import io_module as io
15	>>> ba1 = io.readsprit("spritdata.txt")
16	>>> ba1 = io.readclamp("spritdata.txt")
17	>>> ba1 = io.readicmtxt("icmdata.txt")
18	>>> ba1 = io.readbiosensor("icmdata.txt")
19	>>> ba1 = io.readcsv("rawdata.csv")
20	>>> ba2 = io.applygal(ba1, "galfile.gal")
21	>>> ba2 = io.applykey(ba1, "keyfile.tsv")
22	>>> ba3 = io.applymethod(ba2, "icmmethod.xls")
23	>>> io.writesprit(ba3, "newspritfile.txt")
24	>>> io.writeclamp(ba3, "newclampfile.txt")
25	"""
26	__version__ = "110208"
27
28
29	## Import libraries.
30	from copy import deepcopy
31	from os import getcwd
32	from time import mktime
33	import numpy as np ## Numpy array library.
34	import ba_class as ba ## Our Biosensor Array class.
35	reload(ba)
36
37	def readsprit(fname):
38	"""
39	Read a SPRit text file into a ba class.
40	It has two tab-delimited columns and two header lines.
41	Here is a very simple example with 2 rois and 3 datapoints::
42
43	Elapsed Time (Seconds) Average Intensity (Pixel Intensity)
44	BEGIN
45	0.000000e+000 2.863145e+003
46	5.013000e+000 2.863367e+003
47	1.002500e+001 2.862950e+003
48	0.000000e+000 2.862875e+003
49	5.013000e+000 2.862510e+003
50	"""
51
52	## Try to open file. Return tiny ba object if it fails.
53	ba0 = ba.BiosensorArray(1,1)
54	try:
55	fp = open(fname, "r")
56	except IOError:
57	print 'Error: Cannot open file %s for reading' % fname
58	return ba0
59
60	## Check header lines for signature text.
61	txt = fp.readline() # 'Elapsed Time...'
62	txt = fp.readline() # 'BEGIN'
63	if ('BEGIN' not in txt):
64	print "Error: Second line is not BEGIN."
65	fp.close()
66	return ba0
67
68	## Put data into one big text string and close.
69	txtfile = fp.readlines()
70	fp.close()
71
72	## Change text into array
73	sprtable = np.zeros((len(txtfile),2), dtype=float) ## Redimension Nx2
74	for i in range(len(txtfile)):
75	txt = txtfile[i].split('\t')
76	sprtable[i,0] = float(txt[0]) ## Time column.
77	sprtable[i,1] = float(txt[1]) ## Signal column.
78
79	## Find number of ROIs in file.
80	for i in range(1,len(sprtable)):
81	## See when the time drops back to zero.
82	if (sprtable[i,0] < sprtable[i-1,0]): break
83	rows = i ## Datapoints or new array rows.
84	rois = int(len(sprtable) / rows)
85
86	## Move data the old-fashioned iterative way.
87	ba0 = ba.BiosensorArray(rois,rows)
88	k = 0
89	for i in range(rois):
90	for j in range(rows):
91	ba0.roi[i].time[j] = sprtable[k,0]
92	ba0.roi[i].value[j] = sprtable[k,1]
93	k +=1
94
95	return ba0
96	"""End of readsprit() function"""
97
98
99	def writesprit(ba0, fname):
100	"""
101	Write a ba class to a SPRit text file.
102	"""
103	fp=file(fname,'w')
104	fp.write("Elapsed Time (Seconds)\tAverage Intensity (Pixel Intensity)\r\n")
105	fp.write("BEGIN\r\n")
106	for roi in range(len(ba0.roi)): ## Could also use ba.rois.
107	for dpoint in range(len(ba0.roi[0].time)): ## Could also use ba.dpoints.
108	txt = "%f\t%f\r\n" % (ba0.roi[roi].time[dpoint], ba0.roi[roi].value[dpoint])
109	fp.write(txt)
110	fp.close
111	print "File %s saved in %s." % (fname, getcwd())
112	return
113	"""End of writesprit() function"""
114
115
116	def readclamp(fname):
117	"""
118	Read a Clamp text file into a ba class.
119	It has two tab-delimited columns per SPR flowcell/roi..
120	It has a varying number of header lines with injection information.
121	Here is a very simple example with 2 rois and 3 datapoints::
122
123	Vers 3.41 Data
124	Conc1 0 0 0 0
125	Start1 301.5 301.5 301.5 301.5
126	Stop1 949.8 949.8 949.8 949.8
127	RInd1 0 0 0 0
128	Conc2 0 0 0 0
129	Start2 986.4 0 0 0
130	Stop2 1626 0 0 0
131	RInd2 0 0 0 0
132	Flow 1 1 1 1
133	Time1 Data1 Time2 Data2
134	0.094 0.062 0.094 0.053
135	1.094 0.026 1.094 0.05
136	2.094 0.119 2.094 0.055
137	"""
138
139	print "This feature is under construction."
140	return
141	""""End of readclamp() function"""
142
143
144	def writeclamp(ba0, fname):
145	"""
146	Write a ba class to a Clamp text file.
147	"""
148
149	fp=file(fname,'w')
150	## First header line.
151	fp.write("Vers 3.41 Data\r\n")
152
153	## Next write injection information.
154	for inj in range(len(ba0.roi[0].injconc)):
155	fp.write("Conc%i" % (inj+1))
156	for roi in ba0.roi: fp.write("\t%.3f" % roi.injconc[inj])
157	fp.write("\r\nStart%i" % (inj+1))
158	for roi in ba0.roi: fp.write("\t%.3f" % roi.injstart[inj])
159	fp.write("\r\nStop%i" % (inj+1))
160	for roi in ba0.roi: fp.write("\t%.3f" % roi.injstop[inj])
161	fp.write("\r\nRInd%i" % (inj+1))
162	for roi in ba0.roi: fp.write("\t%.3f" % roi.injrind[inj])
163	## Next write flowrate line.
164	fp.write("\r\nFlow")
165	for roi in ba0.roi: fp.write("\t%.3f" % roi.flow)
166	fp.write("\r\n")
167
168	## Write sensorgram data header line.
169	for i,roi in enumerate(ba0.roi):
170	if (i>0): fp.write("\t")
171	fp.write("Time%i" % (i+1))
172	fp.write("\t")
173	fp.write(roi.name)
174	fp.write("\r\n")
175	## Write sensorgram data lines. Three decimal places.
176	for dpoint in range(len(ba0.roi[0].time)):
177	for i,roi in enumerate(ba0.roi):
178	if (i>0): fp.write("\t")
179	fp.write("%.3f\t%.3f" % (roi.time[dpoint], roi.value[dpoint]))
180	fp.write("\r\n")
181
182	## Close file handle and print message.
183	fp.close
184	print "File %s saved in %s." % (fname, getcwd())
185	return
186	"""End of writeclamp() function"""
187
188
189	def readicmtxt(fname):
190	"""
191	Read a ICM text file into a ba class.
192	Here is a very simple example of the tab-delimited format::
193
194	03/05/2010 13:37:21.312 249.408 0.000 0.000
195	03/05/2010 13:37:22.312 249.306 0.000 0.000
196	"""
197
198	## Try to open file. Return tiny ba object if it fails.
199	ba0 = ba.BiosensorArray(1,1)
200	try:
201	fp = open(fname, "r")
202	except IOError:
203	print 'Error: Cannot open file %s for reading' % fname
204	return ba0
205
206	## Put data into one big text string and close.
207	txtfile = fp.readlines()
208	fp.close()
209	dpoints = len(txtfile)
210	rois = txtfile[0].count("\t") ## Usually 25.
211
212	## Create and size ba object.
213	print "This ICM file has %i datapoints for %i ROIs." % (dpoints, rois)
214	ba0 = ba.BiosensorArray(rois, dpoints)
215
216	## Determine experiment start time so we can make other times relative.
217	x = txtfile[0].split("\t") ## E.g. "03/05/2010 13:37:20.218"
218	t0 = __icmtime2sec(x[0]) ## E.g. 1267825040.22
219
220	## Move the data from txtfile to ba0.
221	for i, txtline in enumerate(txtfile):
222	x = txtline.split("\t")
223	tx = __icmtime2sec(x[0]) - t0
224	for j in range(1,rois):
225	ba0.roi[j].time[i] = tx
226	ba0.roi[j].value[i] = float(x[j])
227
228	return ba0
229	"""End of readicmtxt"""
230
231
232	def __icmtime2sec(timetxt):
233	"""
234	Take a time of the form "03/05/2010 15:19:27.312" and return seconds.
235	"""
236	cal, clock = timetxt.split(" ")
237	mm, dd, yy = cal.split("/")
238	hh, min, ss = clock.split(":")
239	stime = (int(yy), int(mm), int(dd), int(hh), int(min), 0, 0, 0, 0)
240	return mktime(stime) + float(ss)
241	"""End of __icmtime2sec"""
242
243
244	def readbiosensor(fname):
245	"""
246	Read a Biacore-style text file into a ba class.
247	Here is a very simple example of the tab-delimited format::
248
249	Ab1 Fc=4- 1_X Ab1 Fc=4 -1_Y Ab2 Fc=4 -1_X Ab2 Fc=4 -1_Y
250	13.1 23.7644 93.1 0.713912
251	13.6 23.4265 93.6 0.0541172
252	14.1 23.1625 94.1 0.332768
253	14.6 23.5752 94.6 0.849459
254	"""
255
256	## Try to open file. Return tiny ba object if it fails.
257	ba0 = ba.BiosensorArray(1,1)
258	try:
259	fp = open(fname, "r")
260	except IOError:
261	print 'Error: Cannot open file %s for reading' % fname
262	return ba0
263
264	## Read header line. Check number of pairs of _X and _Y labels.
265	txthdr = fp.readline()
266	cols = txthdr.count("Fc=")
267	xys = txthdr.count("_X\t") + txthdr.count("_Y\t")+1
268	if ((cols != xys) or ((cols%2) != 0)):
269	print "Error: This is not a valid Biosensor file."
270	return ba0
271
272	## Put data into one big text string and close.
273	txtfile = fp.readlines()
274	fp.close()
275	dpoints = len(txtfile)
276	rois = int(cols/2)
277
278	## Create and size ba object.
279	print "This Biosensor file has %i datapoints for %i ROIs." % (dpoints, rois)
280	ba0 = ba.BiosensorArray(rois, dpoints)
281
282	## Get names of ROIs from header like "Ab1 Fc=4 - 1_Y"
283	txthdr = txthdr.replace(" -","-").replace("- ","-") ## Remove unwanted spaces.
284	names = txthdr.split("\t") ## Use tab delimiter.
285	for j in range(rois):
286	name = names[j*2+1].replace("_Y","").strip(" -")
287	name = name.partition("Fc=") ## Now a 3-tuple.
288	ba0.roi[j].name = name[0] ## Text left of Fc.
289	ba0.roi[j].desc = ("Fc=" + name[2]) ## Text right of Fc.
290
291	## Move the data from txtfile to ba0.
292	for i, txtline in enumerate(txtfile):
293	x = txtline.split("\t")
294	for j in range(rois):
295	ba0.roi[j].time[i] = float(x[j*2+0])
296	ba0.roi[j].value[i] = float(x[j*2+1])
297
298	return ba0
299	"""End of readbiosensor()"""
300
301
302	def writebiosensor(ba0, fname):
303	"""
304	Write a ba class to a Biosensor text file.
305	"""
306
307	## This is like a simplified Clamp file.
308	fp=file(fname,'w')
309	## Write sensorgram data header line.
310	for i,roi in enumerate(ba0.roi):
311	if (i>0): fp.write("\t")
312	name = roi.name.strip() + " " + roi.desc.strip()
313	fp.write("%s_X\t%s_Y" % (name, name))
314	## Write sensorgram data lines. Three decimal places.
315	for dpoint in range(len(ba0.roi[0].time)):
316	fp.write("\r\n")
317	for i,roi in enumerate(ba0.roi):
318	if (i>0): fp.write("\t")
319	fp.write("%.3f\t%.3f" % (roi.time[dpoint], roi.value[dpoint]))
320
321	## Close file handle and print message.
322	fp.close
323	print "File %s saved in %s." % (fname, getcwd())
324	return
325	"""End of writebiosensor()"""
326
327
328	def readcsv(fname):
329	"""
330	Read a comma-separated value text file into a ba class.
331	The first column contains time data while the others contain response data.
332	Here is a very simple example of the format::
333
334	1.0001, 23.7644, 0.7139
335	2.0001, 23.4265, 0.0541
336	3.0001, 23.1625, 0.3327
337	4.0001, 23.5752, 0.8494
338	"""
339
340	## Try to open file. Return tiny ba object if it fails.
341	ba0 = ba.BiosensorArray(1,1)
342	try:
343	fp = open(fname, "r")
344	except IOError:
345	print 'Error: Cannot open file %s for reading' % fname
346	return ba0
347
348	## Put data into one big text string, determine array size, and close.
349	txtfile = fp.readlines() ## One big text string.
350	fp.close()
351	dpoints = len(txtfile) ## Rows in the csv file.
352	rois = len(txtfile[0].split(',')) - 1 ## Columns are comma-delimited.
353
354	## Move the data from txtfile to ba0.
355	ba0 = ba.BiosensorArray(rois, dpoints)
356	for i, txtline in enumerate(txtfile):
357	x = txtline.split(',')
358	for j in range(rois):
359	ba0.roi[j].time[i] = float(x[0])
360	ba0.roi[j].value[i] = float(x[j+1])
361
362	print "The file %s has %i ROIs and %i datapoints." % (fname, rois, dpoints)
363	return ba0
364	"""End of readcsv()"""
365
366
367	def applygal(ba0, fname):
368	"""
369	Read a Gal file and apply its microarray information.
370
371	(This function is under construction)
372	"""
373	print "This feature is under construction."
374	return
375	"""End of applygal()"""
376
377
378	def applykey(ba0, fname):
379	"""
380	Read a Key file and apply its microarray information.
381	Multiple background ROIs are not yet supported.
382	Here is a very simple example::
383
384	No. Description1 Description2 Background ROI Col Row
385	1 Rat TNF Antibody01 2 1 1
386	2 ratIgG Antibody02 4 2 1
387	3 Hum TNF Antibody03 4 3 1
388	4 humIgG Antibody04 2 4 1
389	"""
390
391	## Try to open file. Return unchanged ba object if it fails.
392	try:
393	fp = open(fname, "r")
394	except IOError:
395	print 'Cannot open file %s for reading' % fname
396	return ba0
397	## Check header lines for signature text.
398	txt = fp.readline()
399	if ("No." not in txt):
400	print "Error: The header line is unfamiliar."
401	fp.close()
402	return ba0
403
404	## Read all text, convert to 2d list, then six lists (one for each column).
405	## There's probably an easier way to do this. Maybe in CSV module.
406	txtfile = fp.readlines()
407	fp.close()
408	## Change text into array
409	keytable = txtfile[:] ## Dimension rows in new 2d list.
410	for i in range(len(txtfile)):
411	txt = str(txtfile[i].strip())
412	keytable[i] = txt.split('\t')
413	## Use list comprehensions to get one list for each column.
414	id = [int(x[0]) for x in keytable] ## First column is integer.
415	desc1 = [x[1] for x in keytable] ## Second column is text.
416	desc2 = [x[2] for x in keytable] ## Third column is text.
417	bg = [int(x[3]) for x in keytable] ## Fourth column is integer. Change base1 to base0?
418	col = [int(x[4]) for x in keytable] ## Fifth column is integer.
419	row = [int(x[5]) for x in keytable] ## Sixth column is integer.
420
421	## Check if key file looks valid. These tests are not very thorough!
422	keys = 1 + max(id) - min(id)
423	if (ba0.rois != keys):
424	print "Error: We have %i ROIs but %i keyfile entries." % (ba0.rois, keys)
425	return ba0
426	if ((min(bg) < min(id)) or (max(bg) > max (id))):
427	print "Error: at least one specified background ROI does not exist"
428	print "Identifiers (id) range from %i to %i." % (min(id), max(id))
429	print "Background references range from %i to %i." % (min(bg), max(bg))
430	return ba0
431
432	## Create new object and put data in it.
433	ba1 = deepcopy(ba0)
434	for i in range(len(id)):
435	ba1.roi[id[i]-1].name = desc1[i]
436	ba1.roi[id[i]-1].desc = desc2[i]
437	ba1.roi[id[i]-1].bgroi = [bg[i]] ## ToDo: Decide if bg will be id or index. Base1 now.
438	ba1.roi[id[i]-1].spotx = col[i]
439	ba1.roi[id[i]-1].spoty = row[i]
440
441	print "Successfully loaded information for %i ROIs." % keys
442	return ba1
443	"""End of applykey()"""
444
445
446	def applymethod(ba0, fname):
447	"""
448	Read a ICM Analyte/Method xls file and apply its information.
449
450	(This feature is under construction.)
451	"""
452	print "This feature is under construction."
453	return
454	"""End of applymethod()"""
455
456
457
458	def outputbindinglevels(ba0, fname, interval, *baselines):
459	"""
460	Measure the binding level changes at multiple intervals along a sensorgram.
461	Write the data to a file. If interval is 500 and baselines are [100, 1100] then
462	binding levels are changes between 100-600s and between 1100-01600s.
463	Average 30s of data.
464	"""
465	fp=file(fname,'w')
466
467	## Measurements
468	for iroi in ba0.roi:
469	fp.write("%i\t%s" % (iroi.index, iroi.name))
470	for j in baselines:
471	t1 = j
472	t2 = j + interval
473	y1 = np.average(iroi.time2val(t1-15, t1+15))
474	y2 = np.average(iroi.time2val(t2-15, t2+15))
475	fp.write("\t%.3f" % (y2-y1))
476	fp.write("\n")
477	fp.close
478	print "File %s saved in %s." % (fname, getcwd())
479	return
480	"""End of outputbindinglevels()"""
481
482
483	## Here are a few lines to test this module.
484	if __name__ == '__main__':
485	print "This module isn't a stand-alone app."
486
487	################################# End of module #################################