python脚本在两个相似的输入文件中显示不同的结果（有一个错误）

时间：2016-08-16 10:24:27

标签： python

最初从（http://globplot.embl.de/）获取和修改的脚本：

#!/usr/bin/env python
# Copyright (C) 2003 Rune Linding - EMBL
# GlobPlot TM
# GlobPlot is licensed under the Academic Free license

from string import *
from sys import argv
from Bio import File
from Bio import SeqIO
import fpformat
import sys
import tempfile
import os
from os import system,popen3
import math

# Russell/Linding
RL =     {'N':0.229885057471264,'P':0.552316012226663,'Q':-0.187676577424997,'A':-0.261538461538462,'R':-0.176592654077609, \
  'S':0.142883029808825,'C':-0.0151515151515152,'T':0.00887797506611258,'D':0.227629796839729,'E':-0.204684629516228, \
  'V':-0.386174834235195,'F':-0.225572305974316,'W':-0.243375458622095,'G':0.433225711769886,'H':-0.00121743364986608, \
  'Y':-0.20750516775322,'I':-0.422234699606962,'K':-0.100092289621613,'L':-0.337933495925287,'M':-0.225903614457831}

def Sum(seq,par_dict):
sum = 0
results = []
raws = []
sums = []
p = 1
for residue in seq:
    try:
        parameter = par_dict[residue]
    except:
        parameter = 0
    if p == 1:
        sum = parameter
    else:
        sum = sum + parameter#*math.log10(p)
    ssum = float(fpformat.fix(sum,10))
    sums.append(ssum)
    p +=1
return sums

def getSlices(dydx_data, DOM_join_frame, DOM_peak_frame, DIS_join_frame,     DIS_peak_frame):
DOMslices = []
DISslices = []
in_DOMslice = 0
in_DISslice = 0
beginDOMslice = 0
endDOMslice = 0
beginDISslice = 0
endDISslice = 0
for i in range( len(dydx_data) ):
#close dom slice
    if in_DOMslice and dydx_data[i] > 0:
        DOMslices.append([beginDOMslice, endDOMslice])
        in_DOMslice = 0
#close dis slice
    elif in_DISslice and dydx_data[i] < 0:
        DISslices.append([beginDISslice, endDISslice])
        in_DISslice = 0
    # elseif inSlice expandslice
    elif in_DOMslice:
        endDOMslice += 1
    elif in_DISslice:
        endDISslice += 1
# if not in slice and dydx !== 0 start slice
    if dydx_data[i] > 0 and not in_DISslice:
        beginDISslice = i
        endDISslice = i
        in_DISslice = 1
    elif dydx_data[i] < 0 and not in_DOMslice:
        beginDOMslice = i
        endDOMslice = i
        in_DOMslice = 1
#last slice
if in_DOMslice:
    DOMslices.append([beginDOMslice, endDOMslice])
if in_DISslice:
    DISslices.append([beginDISslice,endDISslice])
k = 0
l = 0
while k < len(DOMslices):
    if k+1 < len(DOMslices) and DOMslices[k+1][0]-DOMslices[k][1] < DOM_join_frame:
        DOMslices[k] = [ DOMslices[k][0], DOMslices[k+1][1] ]
        del DOMslices[k+1]
    elif DOMslices[k][1]-DOMslices[k][0]+1 < DOM_peak_frame:
        del DOMslices[k]
    else:
        k += 1
while l < len(DISslices):
    if l+1 < len(DISslices) and DISslices[l+1][0]-DISslices[l][1] < DIS_join_frame:
        DISslices[l] = [ DISslices[l][0], DISslices[l+1][1] ]
        del DISslices[l+1]
    elif DISslices[l][1]-DISslices[l][0]+1 < DIS_peak_frame:
        del DISslices[l]
    else:
        l += 1
return DOMslices, DISslices


def SavitzkyGolay(window,derivative,datalist):
SG_bin = 'sav_gol'
stdin, stdout, stderr = popen3(SG_bin + '-D' + str(derivative) + ' -n' + str(window)+','+str(window))
for data in datalist:
    stdin.write(`data`+'\n')
try:
    stdin.close()
except:
    print stderr.readlines()
results = stdout.readlines()
stdout.close()
SG_results = []
for result in results:
    SG_results.append(float(fpformat.fix(result,6)))
return SG_results


def reportSlicesTXT(slices, sequence, maskFlag):
if maskFlag == 'DOM':
    coordstr = '|GlobDoms:'
elif maskFlag == 'DIS':
    coordstr = '|Disorder:'
else:
    raise SystemExit
if slices == []:
    #by default the sequence is in uppercase which is our search space
    s = sequence
else:
    # insert seq before first slide
    if slices[0][0] > 0:
        s = sequence[0:slices[0][0]]
    else:
        s = ''
    for i in range(len(slices)):
        #skip first slice
        if i > 0:
            coordstr = coordstr + ', '
        coordstr = coordstr + str(slices[i][0]+1) + '-' + str(slices[i][1]+1)
        #insert the actual slice
        if maskFlag == 'DOM':
            s = s + lower(sequence[slices[i][0]:(slices[i][1]+1)])
            if i < len(slices)-1:
                s = s + upper(sequence[(slices[i][1]+1):(slices[i+1][0])])
            #last slice
            elif slices[i][1] < len(sequence)-1:
                s = s + lower(sequence[(slices[i][1]+1):(len(sequence))])
        elif maskFlag == 'DIS':
            s = s + upper(sequence[slices[i][0]:(slices[i][1]+1)])
            #insert untouched seq between disorder segments, 2-run labelling
            if i < len(slices)-1:
                s = s + sequence[(slices[i][1]+1):(slices[i+1][0])]
            #last slice
            elif slices[i][1] < len(sequence)-1:
                s = s + sequence[(slices[i][1]+1):(len(sequence))]
return s,coordstr


def runGlobPlot():
try:
    smoothFrame = int(sys.argv[1])
    DOM_joinFrame = int(sys.argv[2])
    DOM_peakFrame = int(sys.argv[3])
    DIS_joinFrame = int(sys.argv[4])
    DIS_peakFrame = int(sys.argv[5])
    file = str(sys.argv[6])
    db = open(file,'r')
except:
    print 'Usage:'
    print '         ./GlobPipe.py SmoothFrame DOMjoinFrame DOMpeakFrame DISjoinFrame DISpeakFrame FASTAfile'
    print '         Optimised for ELM: ./GlobPlot.py 10 8 75 8 8 sequence_file'
    print '         Webserver settings: ./GlobPlot.py 10 15 74 4 5 sequence_file'
    raise SystemExit
for cur_record in SeqIO.parse(db, "fasta"):
    #uppercase is searchspace
    seq = upper(str(cur_record.seq))
    # sum function
    sum_vector = Sum(seq,RL)
    # Run Savitzky-Golay
    smooth = SavitzkyGolay('smoothFrame',0, sum_vector)
    dydx_vector = SavitzkyGolay('smoothFrame',1, sum_vector)
    #test
    sumHEAD = sum_vector[:smoothFrame]
    sumTAIL = sum_vector[len(sum_vector)-smoothFrame:]
    newHEAD = []
    newTAIL = []
    for i in range(len(sumHEAD)):
        try:
            dHEAD = (sumHEAD[i+1]-sumHEAD[i])/2
        except:
            dHEAD = (sumHEAD[i]-sumHEAD[i-1])/2
        try:
            dTAIL = (sumTAIL[i+1]-sumTAIL[i])/2
        except:
            dTAIL = (sumTAIL[i]-sumTAIL[i-1])/2
        newHEAD.append(dHEAD)
        newTAIL.append(dTAIL)
    dydx_vector[:smoothFrame] = newHEAD
    dydx_vector[len(dydx_vector)-smoothFrame:] = newTAIL
    globdoms, globdis = getSlices(dydx_vector, DOM_joinFrame, DOM_peakFrame, DIS_joinFrame, DIS_peakFrame)
    s_domMask, coordstrDOM = reportSlicesTXT(globdoms, seq, 'DOM')
    s_final, coordstrDIS = reportSlicesTXT(globdis, s_domMask, 'DIS')
    sys.stdout.write('>'+cur_record.id+coordstrDOM+coordstrDIS+'\n')
    print s_final
    print '\n'
return

runGlobPlot()

我的输入和输出文件位于：link

此脚本接受输入（input1.fa）并提供以下输出output1.txt

但是当我尝试使用类似类型但更大的输入文件（input2.fa）运行此脚本时..它显示以下错误：

Traceback (most recent call last):
  File "final_script_globpipe.py", line 207, in <module>
    runGlobPlot()
  File "final_script_globpipe.py", line 179, in runGlobPlot
    smooth = SavitzkyGolay('smoothFrame',0, sum_vector)
  File "final_script_globpipe.py", line 105, in SavitzkyGolay
    stdin.write(`data`+'\n')
IOError: [Errno 22] Invalid argument

我不知道问题出在哪里。任何类型的建议都是适用的。

我在windows 7机器上使用python 2.7。我还附加了运行脚本所需的Savitzky Golay模块。

由于

1 个答案:

答案 0 :(得分：0)

更新： 在尝试重现linux上的错误后，它显示了类似的行为，与第一个文件一起正常工作但第二个文件正在返回Errno32。 回溯：

Traceback (most recent call last):
  File "Glob.py", line 207, in <module>
    runGlobPlot()
  File "Glob.py", line 179, in runGlobPlot
    smooth = SavitzkyGolay('smoothFrame',0, sum_vector)
  File "Glob.py", line 105, in SavitzkyGolay
    stdin.write(`data`+'\n')
IOError: [Errno 32] Broken pipe

更新

SG_bin 的某些调用返回 -n参数是错误的类型。

Wrong type of parameter for flag -n. Has to be unsigned,unsigned

此参数来自传递给 SavitzkyGolay 函数的 window 变量。

使用trycatch块围绕stdin.write会发现它已经破坏了很多次。

try:
   for data in datalist:
        stdin.write(repr(data)+'\n')
except:
    print "It broke"
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