Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

To v0.8.1; apply black formatting to python #82

Merged
merged 1 commit into from
Aug 29, 2024
Merged

To v0.8.1; apply black formatting to python #82

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
1 change: 1 addition & 0 deletions .gitignore
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -105,3 +105,4 @@ arm64
/examples/test/images/c302_C1_Pharyngeal.net.nml
/examples/test/images/c302_C1_Social.net.nml
/examples/test/images/c302_C1_Syns.net.nml
*ken.sh
101 changes: 78 additions & 23 deletions c302/CompareMain.py
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,11 +1,11 @@
__author__ = 'Ari'
__author__ = "Ari"

from operator import itemgetter
import xlrd
import os

def comparitor(fName1, fName2):

def comparitor(fName1, fName2):
path1 = fName1
path2 = fName2
dir = os.path.dirname(__file__)
Expand All @@ -28,17 +28,54 @@ def comparitor(fName1, fName2):
# Print results. Give number of pairs that are matched, remained from unmatched files, and associated pairs.
print("Number of matching pairs: " + str(len(matches[indexName2[0]])))
for p in range(len(matches[indexName2[0]])):
print(str(matches[indexName2[0]][p])+" -> "+str(matches[indexName2[1]][p])+" ("+str(matches[indexName2[2]][p])+", "+str(matches[indexName2[3]][p])+")")
print("\nNumber of pairs unmatched in " + fName1 + " is: " + str(len(col1[indexName2[0]])))
print(
str(matches[indexName2[0]][p])
+ " -> "
+ str(matches[indexName2[1]][p])
+ " ("
+ str(matches[indexName2[2]][p])
+ ", "
+ str(matches[indexName2[3]][p])
+ ")"
)
print(
"\nNumber of pairs unmatched in "
+ fName1
+ " is: "
+ str(len(col1[indexName2[0]]))
)
for p in range(len(col1[indexName2[0]])):
print(str(col1[indexName2[0]][p])+" -> "+str(col1[indexName2[1]][p])+" ("+str(col1[indexName2[2]][p])+", "+str(col1[indexName2[3]][p])+")")
print("\nNumber of pairs unmatched in " + fName2 + " is: " + str(len(col2[indexName1[0]])))
print(
str(col1[indexName2[0]][p])
+ " -> "
+ str(col1[indexName2[1]][p])
+ " ("
+ str(col1[indexName2[2]][p])
+ ", "
+ str(col1[indexName2[3]][p])
+ ")"
)
print(
"\nNumber of pairs unmatched in "
+ fName2
+ " is: "
+ str(len(col2[indexName1[0]]))
)
for p in range(len(col2[indexName1[0]])):
print(str(col2[indexName1[0]][p])+" -> "+str(col2[indexName1[1]][p])+" ("+str(col2[indexName1[2]][p])+", "+str(col2[indexName1[3]][p])+")")
print(
str(col2[indexName1[0]][p])
+ " -> "
+ str(col2[indexName1[1]][p])
+ " ("
+ str(col2[indexName1[2]][p])
+ ", "
+ str(col2[indexName1[3]][p])
+ ")"
)


# Get columns from .txt files
def getColumns(fileIn, delim = "\t", header = True):
def getColumns(fileIn, delim="\t", header=True):
cols = {}
indexName = {}
for lineNum, line in enumerate(fileIn):
Expand All @@ -63,6 +100,7 @@ def getColumns(fileIn, delim = "\t", header = True):
i += 1
return cols, indexName


# Get columns from .xls files
def getColumnsXls(fileIn):
cols = {}
Expand Down Expand Up @@ -92,16 +130,19 @@ def getColumnsXls(fileIn):
cols[indexName[curr_cell]] += [cell_value]
return cols, indexName


# Sort dictionaries by first two column (From/To Neurons), first by one, then the other.
def sortTwoColumns(cols):
cols = sorted(cols, key = itemgetter(0,1))
cols = sorted(cols, key=itemgetter(0, 1))


# Formatting involved removing any filler zeros from the middle of strings.
def formatNames(cols, indexName):
for i in range(2):
for char in cols[indexName[i]]:
if char[-1] != '0':
char = "".join(char.split("0",1))
if char[-1] != "0":
char = "".join(char.split("0", 1))


# Compare two lists, create new list of matching pairs, remove pairs from respective original lists.
def matchLists(cols1, cols2, indexName1, indexName2):
Expand Down Expand Up @@ -134,7 +175,9 @@ def matchLists(cols1, cols2, indexName1, indexName2):
if x2 == pair:
index2 = p2
# If matches array does not contain current pair from long array, add it
if not zip(matches[indexNames1[0]], matches[indexNames1[1]]).__contains__(([pair[0]],[pair[1]])):
if not zip(matches[indexNames1[0]], matches[indexNames1[1]]).__contains__(
([pair[0]], [pair[1]])
):
# print(matches[indexNames1[0]], matches[indexNames1[1]])
for i in range(len(indexNames1)):
if col1[indexNames1[i]][index1] == col2[indexNames2[i]][index2]:
Expand All @@ -144,17 +187,23 @@ def matchLists(cols1, cols2, indexName1, indexName2):
del col2[indexNames2[i]][index2]
del col1[indexNames1[i]][index1]
else:
matches[indexNames1[i]] += [[col1[indexNames1[i]][index1], col2[indexNames2[i]][index2]]]
matches[indexNames1[i]] += [
[col1[indexNames1[i]][index1], col2[indexNames2[i]][index2]]
]
del col2[indexNames2[i]][index2]
del col1[indexNames1[i]][index1]
# If pair is already in array, add value from last two columns to array
else:
for p3, x3 in enumerate(zip(matches[indexNames1[0]], matches[indexNames1[1]])):
for p3, x3 in enumerate(
zip(matches[indexNames1[0]], matches[indexNames1[1]])
):
if x3 == ([pair[0]], [pair[1]]):
index3 = p3
for i in range(len(indexNames1)):
if i > 1:
matches[indexNames1[i]][index3] += [col1[indexNames1[i]][index1]]
matches[indexNames1[i]][index3] += [
col1[indexNames1[i]][index1]
]
del col1[indexNames1[i]][index1]
del col2[indexNames2[i]][index2]

Expand All @@ -164,8 +213,12 @@ def matchLists(cols1, cols2, indexName1, indexName2):
if x1 == pair:
index1 = p1
# If matches array does contain current pair from long array, add its conn. type and number
if zip(matches[indexNames1[0]], matches[indexNames1[1]]).__contains__(([pair[0]],[pair[1]])):
for p3, x3 in enumerate(zip(matches[indexNames1[0]], matches[indexNames1[1]])):
if zip(matches[indexNames1[0]], matches[indexNames1[1]]).__contains__(
([pair[0]], [pair[1]])
):
for p3, x3 in enumerate(
zip(matches[indexNames1[0]], matches[indexNames1[1]])
):
if x3 == ([pair[0]], [pair[1]]):
index3 = p3
for i in range(len(indexNames1)):
Expand All @@ -183,7 +236,9 @@ def matchLists(cols1, cols2, indexName1, indexName2):
for p4, x4 in enumerate(zip(matches[indexNames1[0]], matches[indexNames1[1]])):
if x4 == ([pair[1]], [pair[0]]):
index4 = p4
if zip(matches[indexNames1[0]], matches[indexNames1[1]]).__contains__(([pair[1]], [pair[0]])):
if zip(matches[indexNames1[0]], matches[indexNames1[1]]).__contains__(
([pair[1]], [pair[0]])
):
# print(zip(matches[indexNames1[0]], matches[indexNames1[1]]))
# print(([pair[1]], [pair[0]]))
for i in range(len(indexNames1)):
Expand All @@ -193,26 +248,26 @@ def matchLists(cols1, cols2, indexName1, indexName2):
matches[indexNames1[i]][index4] += [col1[indexNames1[i]][index1]]
del col1[indexNames1[i]][index1]


return matches, col1, col2


# Option of additional formatting to shorten lists. Not used. Not complete.
# 'EJ' maps to 'GapJunction'.
# 'R', 'Rp', 'S', 'Sp' map to 'Send'.
# 'NMJ' does not map.
def typeMapping(cols1, cols2, indexName1, indexName2):
list1 = ['GapJunction','Send']
list2 = ['EJ','NMJ','R','Rp','S','Sp']
list1 = ["GapJunction", "Send"]
list2 = ["EJ", "NMJ", "R", "Rp", "S", "Sp"]
type1 = cols1[indexName1[2]]
type2 = cols2[indexName2[2]]


if __name__ == '__main__':
if __name__ == "__main__":
fName1 = "CElegansNeuronTables.xls"
fName2 = "NeuronConnectFormatted.xlsx"

# file1 = "C:\\Users\\Ari\\Documents\\Projects\\OpenWorm\\book1.txt"
# file2 = "C:\\Users\\Ari\\Documents\\Projects\\OpenWorm\\book2.txt"
# xfile1 = "C:\\Users\\Ari\\Documents\\Projects\\OpenWorm\\CElegansNeuroML\\CElegansNeuronTables.xls"
# xfile2 = "C:\\Users\\Ari\\Documents\\Projects\\OpenWorm\\CElegansNeuroML\\NeuronConnectFormatted.xlsx"
comparitor(fName1,fName2)
comparitor(fName1, fName2)
Loading