dump.pbd='pdb' + pdbFile + '_' + 'res' + residMin + '_' residMax + '.pdb'
the program keep giving me syntax error when I run it.
import re
import sys
import os
import time
from sys import argv
import xmltodict
if len(sys.argv) < 3:
message = '\n Get protein file in the form of pdf file from pdb website. \n\n Usage: '+sys.argv[0] + ' [4-letter PDBid] [resid range] \n' + ' Example: ' + sys.argv[0] + ' 2rh1 53-71\n' + ' Output File: pdb2rh1_res53-71.pdb'
print (message)
exit()
pdbID=sys.argv[1]
residRange=sys.argv[2]
residData=residRange.split('-')
residMin=int(residData[0])
residMax=int(residData[1])
twoletter=pdbID[1:3]
xmlfile=pdbID + '.xml'
pdbgzfile=pdbID + '.pdb.gz'
pdbFile=pdbID+'.pdb'
dump.pbd='pdb' + pdbFile + '_' + 'res' + residMin + '_' residMax + '.pdb'
wgetcom='wget https://files.rcsb.org/view/'+pdbFile+' -O '+pdbFile
print(wgetcom)
os.system(wgetcom)
f = open (pdbFile,'r')
k = 0
rc = 0
data = f.readlines()
g = open (dump.pdb, 'w')
for linedata in data:
line=linedata.strip()
words = line.split()
if(words[0] == 'ATOM'):
k=k+1
words[5]=int(line[22:26].strip())
if(words[5] in range(residMin,residMax+1)):
g.write(linedata)
for i in words:
if(i=='CA'):
rc = rc+1
print(rc)
the code is not working because it is giving me a syntax error for line number 22 that states dump.pbd='pdb' + pdbFile + '' + 'res' + residMin + '' residMax + '.pdb'. so can you please help me with that?
Thanks so much on advance!
You've forgotten to add a + sign.
This line should work: dump.pbd='pdb' + pdbFile + '' + 'res' + residMin + '' + residMax + '.pdb'
There must be a + sign between '_' and residMax as this is the Python concatenating strings syntax.
Related
Python 3.8.5 Requests 2.22.0
The API I'm working with requires a unique signature header format.
Please note that this is a header which includes a list of the headers in it as well.
format:
The Header: X-Ca-Signature
stringToSign=HTTPMethod+"\n"+ Headers+"\n"+API_URI+"\n"+FormattedQFStr;
which I believe translates to something like
GET
X-Ca-Key:ACCESSKEY
X-Ca_Nonce:UUID
X-Ca-Timestamp:UNIX_TIMESTAMP
api/open/v1/device/checkMac
mac=MACADDR
I have tried the three following methods of formulating the header
stringToSign = str("GET" + "n\\" + "X-Ca-Key:" + ACCESSID + "n\\" + "X-Ca_Nonce:" + UUID + "n\\" + "X-Ca-Timestamp:" + MILLI_TIMESTAMP_STRIPPED + "n\\" + "api/open/v1/device/checkMac" + "n\\" + "mac=MACADDR")
stringToSign = str("GET" + os.linesep + "X-Ca-Key:" + ACCESSID + os.linesep + "X-Ca_Nonce:" + UUID + os.linesep + "X-Ca-Timestamp:" + MILLI_TIMESTAMP_STRIPPED + os.linesep + "api/open/v1/device/checkMac" + os.linesep + "mac=MACADDR")
stringToSign = str("GET" + "\n" + "X-Ca-Key:" + ACCESSID + "\n" + "X-Ca_Nonce:" + UUID + "\n" + "X-Ca-Timestamp:" + MILLI_TIMESTAMP_STRIPPED + "\n" + "api/open/v1/device/checkMac" + "\n" + "mac=MACADDR")
The last two appear to give me the correct format:
GET
X-Ca-Key:ACCESSKEY
X-Ca_Nonce:UUID
X-Ca-Timestamp:UNIX_TIMESTAMP
api/open/v1/device/checkMac
mac=MACADDR
but on my request
payload = {'mac': MACADDR }
HEADERS = {"X-Ca-Key": ACCESSID, "X-Ca-Timestamp" : MILLI_TIMESTAMP_STRIPPED, "X-Ca-Nonce": UUID, "X-Ca-Signature": stringToSign,}
response = requests.get(URL_ARRAY[3], headers=HEADERS, params=payload)
Requests does not like the linebreaks at all and gives me
requests.exceptions.InvalidHeader: Invalid return character or leading space in header: X-Ca-Signature.
Any advice to steer me in the right direction is very much appreciated.
UPDATE : I have corrected my code and below is working fine as expected
Basically i need an output like below in mail.
I achieved this. but need to know if any efficient code then below one.
name 5001 5010 9000 4 %
name 5002 5010 9000 4 %
name 5003 5010 9000 4 %
name 5004 5010 9000 4 %
Storing the values in list.
Below are dummy values
container = []
for server in range(1,5):
container.append('name')
container.append(server + 5000)
container.append(5000+10)
container.append(4000+5000)
container.append(2500 % 12)
print('\n' + str(container))
Assign list of values to msgBody in order to send it via email
I'm just putting piece of code here. Below also working fine
msgBody1 = ''
for count in range(4):
if count == 0:
tempValue = '\n' + '\n' + str(container[count]) + '\t' + str(container[count+1]) + '\t' + str(container[count+2]) + '\t'
+ str(container[count+3]) + '\t' + str(container[count+4])
msgBody1 = msgBody1 + str(tempValue) + ' %'
elif count == 1:
tempValue = '\n' + '\n' + str(container[count+4]) + '\t' + str(container[count+5]) + '\t' + str(container[count+6]) + '\t'
+ str(container[count+7]) + '\t' + str(container[count+8])
msgBody1 = msgBody1 + str(tempValue) + ' %'
elif count == 2:
tempValue = '\n' + '\n' + str(container[count+8]) + '\t' + str(container[count+9]) + '\t' + str(container[count+10]) + '\t'
+ str(container[count+11]) + '\t' + str(container[count+12])
msgBody1 = msgBody1 + str(tempValue) + ' %'
elif count == 3:
tempValue = '\n' + '\n' + str(container[count+12]) + '\t' + str(container[count+13]) + '\t' + str(container[count+14]) + '\t'
+ str(container[count+15]) + '\t' + str(container[count+16])
msgBody1 = msgBody1 + str(tempValue) + ' %'
Any other better and short code to replace msgBody1
Thanks in advance
Your question is not clear; the code example does not make any sense. But from the structure of it, it seems like you are trying to use dict, but you are defining or sourcing lists.
Not sure why for server in servers, I hope your servers list is collection of numerical value, which does not make any sense.
Please go through list Vs dict, and list.append() and how to add new key, value pairs to dictionary.
In the code below, my problem is that it's writing output to all folders based on only one input file. Can some one give me a hint and check if my code is looping properly?
import libxml2
import os.path
from numpy import *
from cfs_utils import *
np=[1,2,3,4,5,6,7,8]
n=[20,30,40,60,80,100,130]
solver=["CG_iluk", "CG_saamg", "CG_ssor", "BiCGSTABL_iluk", "BiCGSTABL_saamg", "BiCGSTABL_ssor", "cholmod", "ilu" ]
file_list=["eval_CG_iluk_default","eval_CG_saamg_default", "eval_CG_ssor_default", "eval_BiCGSTABL_iluk", "eval_BiCGSTABL_saamg", "eval_BiCGSTABL_ssor","simp_cholmod_solver_3D_evaluate ", "simp_ilu_solver_3D_evaluate" ]
for sol in solver:
i=0
for cnt_np in np:
#open write_file= "Graphs/" + "Np"+ cnt_np + "/CG_iluk.dat"
#"Graphs/Np1/CG_iluk.dat"
write_file = open("Graphs/"+ "Np"+ str(cnt_np) + "/" + sol + ".dat", "w")
#loop through different unknowns
for cnt_n in n:
#open file "cfs_calculations_" + cnt_n +"np"+ cnt_np+ "/" + file_list(i) + "_default.info.xml"
read_file = "cfs_calculations_" +str(cnt_n) +"np"+ str(cnt_np) + "/" + file_list[i] + ".info.xml"
#read wall and cpu time and write
if os.path.exists(read_file):
doc = libxml2.parseFile(read_file)
xml = doc.xpathNewContext()
walltime = xpath(xml, "//cfsInfo/sequenceStep/OLAS/mechanic/solver/summary/setup/timer/#wall")
cputime = xpath(xml, "//cfsInfo/sequenceStep/OLAS/mechanic/solver/summary/setup/timer/#cpu")
unknowns = 3*cnt_n*cnt_n*cnt_n
write_file.write(str(unknowns) + "\t" + walltime + "\t" + cputime + "\n")
doc.freeDoc()
write_file.close()
i=i+1
Problem solved, I = o, was outside the loop
I have the following code which creates the txt file I require from a shp.file with the data I need. I have a folder called profiles containing a few number of shape files named (profil1.shp, profil2.shp, profil3.shp etc.). I was wondering how to create a loop so that the script creates for each file a txt file with the same name (eg. for profil1.shp create profil1.txt, profil2.shp create profil2.txt and so on).
import ogr, os, sys, osr
os.chdir('..\profiles')
file = open('profil1.txt', 'w')
driver = ogr.GetDriverByName('ESRI Shapefile')
datasource = driver.Open('profil1.shp', 0)
if datasource is None:
print 'Could not open file'
sys.exit(1)
layer = datasource.GetLayer()
feature = layer.GetNextFeature()
while feature:
id = feature.GetFieldAsString('ID')
Distanta = feature.GetFieldAsString('DIST')
Z = feature.GetFieldAsString('Z')
geom = feature.GetGeometryRef()
x = str(geom.GetX())
y = str(geom.GetY())
file.write(id + " " + Distanta + " " + "[X]:" + " " + x + ' ' + '[Y]:' + " " + y + " " + " " + "[Z]" + Z + " " + "\n")
feature.Destroy()
feature = layer.GetNextFeature()
datasource.Destroy()
file.close()
edit: the code is returning a Could not open file.Photo of the folder containing the files and their respective names. Safe to assume I am doing something wrong.
import ogr, os, sys, osr,os.path
os.chdir = ('C:\Users\Andrei\Desktop\profil3')
l = os.listdir('C:\Users\Andrei\Desktop\profil3')
for i in l:
if i.endswith('.shp'):
s1 = s.split('.')[0] + '.txt'
file = open(s1, 'w')
driver = ogr.GetDriverByName('ESRI Shapefile')
datasource = driver.Open(i, 0)
if datasource is None:
print 'Could not open file'
sys.exit(1)
layer = datasource.GetLayer()
feature = layer.GetNextFeature()
while feature:
id = feature.GetFieldAsString('ID')
Distanta = feature.GetFieldAsString('DIST')
Z = feature.GetFieldAsString('Z')
geom = feature.GetGeometryRef()
x = str(geom.GetX())
y = str(geom.GetY())
file.write(id + " " + Distanta + " " + "[X]:" + " " + x + ' ' + '[Y]:' + " " + y + " " + " " + "[Z]" + Z + " " + "\n")
feature.Destroy()
feature = layer.GetNextFeature()
datasource.Destroy()
file.close()
You can use os.listdir() to list the files and folders in the current directory.
This returns a list of all files in the current directory (or the directory given to it as parameter , if no parameter is specified it checks the current directory) .
Then you can check for files with the name ending with .shp using string.endswith() function and then use that to create your new files.
Example of a small portion -
import os , os.path
l = os.listdir()
for i in l:
if i.endswith('.shp'):
s1 = s.split('.')[0] + '.txt'
At the end s1 would contain the file with extension as .txt .
Then you can do your logic on this file, and keep on doing like this.
Full code would look something like -
import ogr, os, sys, osr,os.path
os.chdir('..\profiles')
l = os.listdir()
for i in l:
if i.endswith('.shp'):
s1 = s.split('.')[0] + '.txt'
file = open(s1, 'w')
driver = ogr.GetDriverByName('ESRI Shapefile')
datasource = driver.Open(i, 0)
if datasource is None:
print 'Could not open file'
sys.exit(1)
layer = datasource.GetLayer()
feature = layer.GetNextFeature()
while feature:
id = feature.GetFieldAsString('ID')
Distanta = feature.GetFieldAsString('DIST')
Z = feature.GetFieldAsString('Z')
geom = feature.GetGeometryRef()
x = str(geom.GetX())
y = str(geom.GetY())
file.write(id + " " + Distanta + " " + "[X]:" + " " + x + ' ' + '[Y]:' + " " + y + " " + " " + "[Z]" + Z + " " + "\n")
feature.Destroy()
feature = layer.GetNextFeature()
datasource.Destroy()
file.close()
A better way of openning files, etc is using with statement. Look up its tutorial here.
I am receiving the following error when running a script to parse contents of an XML file.
if iteration.findtext("Iteration_query-def") in ecdict:
KeyError: 'XLOC_000434'
I was under the impression that using "if in dict" would mean that if the key is not found in the dictionary, the script will continue past the if statement and proceed with the rest of the code. Below is the problematic section of the code I am using. I realise this is quite a basic question, but I am unsure what else I can say, and I don't understand why I am receiving this error.
import xml.etree.ElementTree as ET
tree = ET.parse('507.FINAL_14.2.14_2_nr.out_fmt5.out')
blast_iteration = tree.find("BlastOutput_iterations")
for iteration in blast_iteration.findall("Iteration"):
query = iteration.findtext("Iteration_query-def").strip().strip("\n")
if query in score:
continue
if iteration.findtext("Iteration_message") == "No hits found":
if iteration.findtext("Iteration_query-def") in tair:
tairid = tair[iteration.findtext("Iteration_query-def")][0]
tairdes = tair[iteration.findtext("Iteration_query-def")][1]
else:
tairid = "-"
tairdes = "-"
goterms = ""
ecterms = ""
if iteration.findtext("Iteration_query-def") in godict:
for x in godict[iteration.findtext("Iteration_query-def")][:-1]:
goterms = goterms + x + ";"
goterms = goterms + godict[iteration.findtext("Iteration_query-def")][-1]
else:
goterms = "-"
if iteration.findtext("Iteration_query-def") in ecdict:
for x in ecdict[iteration.findtext("Iteration_query-def")][:-1]:
ecterms = ecterms + x + ";"
ecterms = ecterms + ecdict[iteration.findtext("Iteration_query-def")][-1]
else:
ecterms = "-"
if iteration.findtext("Iteration_query-def") in godescr:
desc = godescr[iteration.findtext("Iteration_query-def")]
else:
desc = "-"
n += 1
p = "PvOAK_up"+str(n) + "\t" + tranlen[iteration.findtext("Iteration_query-def")] + "\t" + orflen[iteration.findtext("Iteration_query-def")] + "\t" + "-" + "\t" + "-" + "\t" + tairid + "\t" + tairdes + "\t" + goterms + "\t" + ecterms + "\t" + desc + "\t" + str(flower[query][2]) + "\t" + str('{0:.2e}'.format(float(flower[query][1]))) + "\t" + str('{0:.2f}'.format(float(flower[query][0]))) + "\t" + str('{0:.2f}'.format(float(leaf[query][2]))) + "\t" + str('{0:.2f}'.format(float(leaf[query][1]))) + "\t" + str('{0:.2f}'.format(float(leaf[query][0])))
print p
Hope you can help,
Thanks.
edit: I should say that godict and ecdict were previously created as follows - I can submit the entire code if needs be:
godict = {}
ecdict = {}
godescr = {}
f = open("507.FINAL_14.2.14_2_nr.out_fmt5.out.annot")
for line in f:
line = line.split("\t")
if len(line) > 2:
godescr[line[0]] = line[2]
line[1] = line[1].strip("\n")
if line[1].startswith("EC"):
if line[0] in ecdict:
a = ecdict[line[0]]
a.append(line[1])
ecdict[line[0]] = a
else:
ecdict[line[0]] = [line[1]]
else:
if line[0] in godict:
a = godict[line[0]]
a.append(line[1])
godict[line[0]] = a
else:
godict[line[0]] = [line[1]]
Traceback:
Traceback (most recent call last):
File "2d.test.py", line 170, in <module>
p = "PvOAK_up"+str(n) + "\t" + tranlen[iteration.findtext("Iteration_query-def")] + "\t" + orflen[iteration.findtext("Iteration_query-def")] + "\t" + "-" + "\t" + "-" + "\t" + tairid + "\t" + tairdes + "\t" + goterms + "\t" + ecterms + "\t" + desc + "\t" + str(flower[query][2]) + "\t" + str('{0:.2e}'.format(float(flower[query][1]))) + "\t" + str('{0:.2f}'.format(float(flower[query][0]))) + "\t" + str('{0:.2f}'.format(float(leaf[query][2]))) + "\t" + str('{0:.2f}'.format(float(leaf[query][1]))) + "\t" + str('{0:.2f}'.format(float(leaf[query][0])))
KeyError: 'XLOC_000434'