I want to reformat one text file, so every paragraph will have approximately 150 characters.
After deleting all \n characters we have one long line.
Input:
1 Line
Output:
Every first blank after every 150 characters to be replaced with \n
Feel free to try fold:
fold -s -w 150 filename
sed 's/\(.\{128\}.\{22\}[^ ]*\) /\1\
/g' YourFile
128 than 22 due to limitation of posix sed to 128 char per repetition (GNU sed should directly accept 150)
you really should post some code of what you've tried on here rather than essentially asking other people to do it for you, but here is a snippet that should do something like what you want and break after the first fullstop:
inputline = "somelongstring"
outputline = ""
count = 0
for character in inputline: #iterate through the line
count += 1 #increment the counter on each loop
if count >= 150: #check counter
if character == ".": #if fullstop then add fullstop and newline to output
outputline += ".\n"
count = 0 #reset counter
else:
outputline += character #otherwise pass character to output
else:
outputline += character #otherwise pass character to output
Related
I have a requirement wherein I have a CSV file which has data in a wrong format. However based on the number pipes I need to add a newline character and make the data ready for Consumption.
Can we count the number pipes and add newline \ncharacter?
Example:
sadasd|asdasd|l||||0sds|sdsds|2||||0sdsd|asdasd|l||||0
Expected output:
sadasd|asdasd|l||||0
sds|sdsds|2||||0
sdsd|asdasd|l||||0 .
Something like this?
_in = "sadasd|asdasd|l||||0sds|sdsds|2||||0sdsd|asdasd|l||||0"
_out = ""
pipeCount = 0
for char in _in:
if pipeCount == 6:
_out = _out+char+"\n"
pipeCount = 0
else:
_out = _out+char
if char == "|":
pipeCount += 1
print(_out)
I am not sure I understood the criterion for adding newline (See comments on question), but my output conforms with your expectation:
sadasd|asdasd|l||||0
sds|sdsds|2||||0
sdsd|asdasd|l||||0
Output is still a string, but you can just as easily make it a list of string.
I have files looking like this:
# BJD K2SC-Flux EAPFlux Err Flag Spline
2457217.463564 5848.004 5846.670 6.764 0 0.998291
2457217.483996 6195.018 6193.685 6.781 1 0.998291
2457217.504428 6396.612 6395.278 6.790 0 0.998292
2457217.524861 6220.890 6219.556 6.782 0 0.998292
2457217.545293 5891.856 5890.523 6.766 1 0.998292
2457217.565725 5581.000 5579.667 6.749 1 0.998292
2457217.586158 5230.566 5229.232 6.733 1 0.998292
2457217.606590 4901.128 4899.795 6.718 0 0.998293
2457217.627023 4604.127 4602.793 6.700 0 0.998293
I need to find and count the lines with Flag = 1. (5th column.) This is how I have done it:
foundlines=[]
c=0
import re
with open('examplefile') as f:
for index, line in enumerate(f):
try:
found = re.findall(r' 1 ', line)[0]
foundlines.append(index)
print(line)
c+=1
except:
pass
print(c)
In Shell, I would just do grep " 1 " examplefile | wc -l, which is much shorter than the Python script above. The python script works, but I am interested in whether is there a shorter, more compact way to do the task than the script above? I prefer the shortness of Shell so I would like to have something similar in Python.
You have CSV data, you can use the csv module:
import csv
with open('your file', 'r', newline='', encoding='utf8') as fp:
rows = csv.reader(fp, delimiter=' ')
# generator comprehension
errors = (row for row in rows if row[4] == '1')
for error in errors:
print(error)
You shell implementation can be made even shorter, grep has -c option to get you a count, no need for an anonymous pipe and wc:
grep -c " 1 " examplefile
You shell code simply gets you the line counts where the pattern 1 is found, but your Python code additionally keeps a list of indexes of lines where the pattern is matched.
Only to get the line counts, you can use sum and genexp/list comprehension, also no need for Regex; simple string __contains__ check would do as strings are iterable:
with open('examplefile') as f:
count = sum(1 for line in f if ' 1 ' in line)
print(count)
If you want to keep indexes as well, you can stick to your idea with only replacing re test with str test:
count = 0
indexes = []
with open('examplefile') as f:
for idx, line in enumerate(f):
if ' 1 ' in line:
count += 1
indexes.append(idx)
Additionally, doing a bare except is almost always a bad idea (at least you should use except Exception to leave out SystemExit, KeyboardInterrupt like exceptions), catch only the exceptions you know might be raised.
Also, while parsing structured data, you should use specific tool e.g. here csv.reader with space as the separator (line.split(' ') should do in this case as well) and checking against index-4 would be safest (see Tomalak's answer). With the ' 1 ' in line test, there would be misleading results if any other column contains 1.
Considering the above, here's the shell way using awk to match against the 5-th field:
awk '$5 == "1" {count+=1}; END{print count}' examplefile
Shortest code
This is a very short version under some specific preconditions:
You just want to count occurrences like your grep invocation
There is guaranteed to be only one " 1 " per line
That " 1 " can only occur in the desired column
Your file fits easily into memory
Note that if these preconditions are not met, this may cause issues with memory or return false positives.
print(open("examplefile").read().count(" 1 "))
Easy and versatile, slightly longer
Of course, if you're interested in actually doing something with these lines later on, I recommend Pandas:
df = pandas.read_table('test.txt', delimiter=" ",
comment="#",
names=['BJD', 'K2SC-Flux', 'EAPFlux', 'Err', 'Flag', 'Spline'])
To get all the rows where Flag is 1:
flaggedrows = df[df.Flag == 1]
returns:
BJD K2SC-Flux EAPFlux Err Flag Spline
1 2.457217e+06 6195.018 6193.685 6.781 1 0.998291
4 2.457218e+06 5891.856 5890.523 6.766 1 0.998292
5 2.457218e+06 5581.000 5579.667 6.749 1 0.998292
6 2.457218e+06 5230.566 5229.232 6.733 1 0.998292
To count them:
print(len(flaggedrows))
returns 4
I'm trying to count a line 8 characters or less at a time and have it count how many times lower case "f" shows up. The value for how many times f shows up keeps showing zero. Text1.txt has lower case f"" one time on line 1 and 4 times on line 2.
with open("text1.txt","r+") as r:
while True:
cCount = r.readlines(1)
charSet = cCount.count("f")
print charSet
if not cCount:
break
if charSet == 1:
print("hello")
Where has my python logic failed.
Try this:
with open("text1.txt","r") as r:
for line in r:
print(line.count("f"))
this is the proper way to iterate over a file
EDIT: to change " fghfghf" to "3ghgh"
with open("text1.txt","r") as r:
for line in r:
if line.count("f")==3:
print("3"+line.replace("f",""))
this is a continuation of Generator not working to split string by particular identifier . Python 2 . however, i modified the code completely and it's not the same format at all. this is about edge cases
Edge Cases:
. when sequence length is different than number of quality values
. when there's an empty sequence or entry
. when the number of lines with quality values is more than one
i cannot figure out how to work with the edge cases above. If its an empty data file, then I still want to output empty strings. i'm trying with these sequences right here for my input file: (Just a little background, IDs are set by # at beginning of line, sequence characters are followed by the lines after until a line with + is reached. the next lines are going to have quality values (value ~= chr(char) ) this format is terrible and poorly thought out.
#m120204_092117_richard_c100250832550000001523001204251233_s1_p0/422/ccs
CTGTTGCGGATTGTTTGGCTATGGCTAAAACCGATGAAGAAAAAGGAAATGCCAAAACCGTTTATAGCGATTGATCCAAGAAATCCAAAATAAAAGGACACAAAACAAACAAAATCAATTGAGTAAAACAGAAAGGCCATCAAGCAAGCGAGTGCTTGATAACTTAGATGACCCTACTGATCAAGAGGCCATAGAGCAATGTTTAGAGGGCTTGAGCGATAGTGAAAGGGCGCTAATTCTAGGAATTCAAACGACAAGCTGATGAAGTGGATCTGATTTATAGCGATCTAAGAAACCGTAAAACCTTTGATAACATGGCGGCTAAAGGTTATCCGTTGTTACCAATGGATTTCAAAAATGGCGGCGATATTGCCACTATTAACCGCTACTAATGTTGATGCGGACAAATAGCTAGCAGATAATCCTATTTATGCTTCCATAGAGCCTGATATTACCAAGCATACGAAACAGAAAAAACCATTAAGGATAAGAATTTAGAAGCTAAATTGGCTAAGGCTTTAGGTGGCAATAAACAAATGACGATAAAGAAAAAAGTAAAAAACCCACAGCAGAAACTAAAGCAGAAAGCAATAAGATAGACAAAGATGTCGCAGAAACTGCCAAAAATATCAGCGAAATCGCTCTTAAGAACAAAAAAGAAAAGAGTGGGATTTTGTAGATGAAAATGGTAATCCCATTGATGATAAAAAGAAAGAAGAAAAACAAGATGAAACAAGCCCTGTCAAACAGGCCTTTATAGGCAAGAGTGATCCCACATTTGTTTTTAGCGCAATACACCCCCATTGAAATCACTCTGACTTCTAAAGTAGATGCCACTCTCACAGGTATAGTGAGTGGGGTTGTAGCCAAAGATGTATGGAACATGAACGGCACTATGATCTTATTAAGACAAACGGCCACTAAGGTGTATGGGAATTATCAAAGCGTGAAAGGTGGCCACGCCTATTATGACTCGTTTAATGATAGTCTTTACTAAAGCCATTACGCCTGATGGGGTGGTGATACCTCTAGCAAACGCTCAAGCAGCAGGCATGCTGGGTGAAGCAGGCGGTAGATGGCTATGTGAATAATCACTTCATGAAGCGTATAGGCTTTGCTGTGATAGCAAGCGTGGTTAATAGCTTCTTGCAAACTGCACCTATCATAGCTCTAGATAAACTCATAGGCCTTGGCAAAGGCAGAAGTGAAAGGACACCTGAATTTAATTACGCTTTGGGTCAAGCTATCAATGGTAGTATGCAAAGTTCAGCTCAGATGTCTAATCAAATTCTAGGGCAACTGATGAATATCCCCCAAGTTTTTACAAAAATGAGGGCGATAGTATTAAGATTCTCACCATGGACGATATTGATTTTAGTGGTGTGTATGATGTTAAAATTGACCAACAAATCTGTGGTAGATGAAATTATCAAACAAAGCACCAAAAACTTTGTCTAGAGAACATGAAGAAATCACCACAGCCCCAAAGGTGGCAATTGATTCAAGAGAAAGGATAAAATATATTCATGTTATTAAACTCGGTTCTTTACAAAATAAAAAGACAAACCAACCTAGGCTCTTCTAGAGGA
+
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
#m120204_092117_richard_c100250832550000001523001204251233_s1_p0/904/ccs
CTCTCTCATCACACACGAGGAGTGAAGAGAGAACCTCCTCTCCACACGTGGAGTGAGGAGATCCTCTCACACACGTGAGGTGTTGAGAGAGATACTCTCTCATCACCTCACGTGAGGAGTGAGAGAGAT
+
{~~~~~sXNL>>||~~fVM~jtu~&&(uxy~f8YHh=<gA5
''<O1A44N'`oK57(((G&&Q*Q66;"$$Df66E~Z\ZMO>^;%L}~~~~~Q.~~~~x~#-LF9>~MMqbV~ABBV=99mhIwGRR~
#different_number_of_seq_qual
ATCG
+
**!
#this_should_work
GGGG
+
****
The ones with an error, I'm trying to replace the seq and qual strings with empty strings
seq,qual = '',''
Here's my code so far. These edge cases are so difficult for me to figure out please help . . .
def read_fastq(input, offset):
"""
Inputs a fastq file and reads each line at a time. 'offset' parameter can be set to 33 (phred+33 encoding
fastq), and 64. Yields a tuple in the format (ID, comments for a sequence, sequence, [integer quality values])
Capable of reading empty sequences and empty files.
"""
ID, comment, seq, qual = None,'','',''
step = 1 #step is a variable that organizes the order fastq parsing
#step= 1 scans for ID and comment line
#step= 2 adds relevant lines to sequence string
#step= 3 adds quality values to string
for line in input:
line = line.strip()
if step == 1 and line.startswith('#'): #Step system from Nedda Saremi
if ID is not None:
qual = [ord(char)-offset for char in qual] #Converts from phred encoding to integer values
sep = None
if ' ' in ID: sep = ' '
if sep is not None:
ID, comment = ID.split(sep,1) #Separates ID and comment by ' '
yield ID, comment, seq, qual
ID,comment,seq,qual = None,'','','' #Resets variable for next sequence
ID = line[1:]
step = 2
continue
if step==2 and not line.startswith('#') and not line.startswith('+'):
seq = seq + line.strip()
continue
if step == 2 and line.startswith('+'):
step = 3
continue
while step == 3:
#process the quality data
if len(qual) == len(seq):
#once the length of the quality seq and seq are the same, end gathering data
step = 1
continue
if len(qual) < len(seq):
qual = qual + line.strip()
if len(qual) < len(seq):
step = 3
continue
if (len(qual) > len(seq)):
sys.stderr.write('\nError: ' + ID + ' sequence length not equal to quality values\n')
comment,seq,qual= '','',''
ID = line
step = 1
continue
break
if ID is not None:
#Section reserved for last entry in file
if len(qual) > 0:
qual = [ord(char)-offset for char in qual]
sep = None
if ' ' in ID: sep = ' '
if sep is not None:
ID, comment = ID.split(sep,1)
if len(seq) == 0: ID,comment,seq,qual= '','','',''
yield ID, comment, seq, qual
my output is skipping the ID #m120204_092117_richard_c100250832550000001523001204251233_s1_p0/904/ccs and adding #**! when it should not be in the output
#m120204_092117_richard_c100250832550000001523001204251233_s1_p0/422/ccs
CTGTTGCGGATTGTTTGGCTATGGCTAAAACCGATGAAGAAAAAGGAAATGCCAAAACCGTTTATAGCGATTGATCCAAGAAATCCAAAATAAAAGGACACAAAACAAACAAAATCAATTGAGTAAAACAGAAAGGCCATCAAGCAAGCGAGTGCTTGATAACTTAGATGACCCTACTGATCAAGAGGCCATAGAGCAATGTTTAGAGGGCTTGAGCGATAGTGAAAGGGCGCTAATTCTAGGAATTCAAACGACAAGCTGATGAAGTGGATCTGATTTATAGCGATCTAAGAAACCGTAAAACCTTTGATAACATGGCGGCTAAAGGTTATCCGTTGTTACCAATGGATTTCAAAAATGGCGGCGATATTGCCACTATTAACCGCTACTAATGTTGATGCGGACAAATAGCTAGCAGATAATCCTATTTATGCTTCCATAGAGCCTGATATTACCAAGCATACGAAACAGAAAAAACCATTAAGGATAAGAATTTAGAAGCTAAATTGGCTAAGGCTTTAGGTGGCAATAAACAAATGACGATAAAGAAAAAAGTAAAAAACCCACAGCAGAAACTAAAGCAGAAAGCAATAAGATAGACAAAGATGTCGCAGAAACTGCCAAAAATATCAGCGAAATCGCTCTTAAGAACAAAAAAGAAAAGAGTGGGATTTTGTAGATGAAAATGGTAATCCCATTGATGATAAAAAGAAAGAAGAAAAACAAGATGAAACAAGCCCTGTCAAACAGGCCTTTATAGGCAAGAGTGATCCCACATTTGTTTTTAGCGCAATACACCCCCATTGAAATCACTCTGACTTCTAAAGTAGATGCCACTCTCACAGGTATAGTGAGTGGGGTTGTAGCCAAAGATGTATGGAACATGAACGGCACTATGATCTTATTAAGACAAACGGCCACTAAGGTGTATGGGAATTATCAAAGCGTGAAAGGTGGCCACGCCTATTATGACTCGTTTAATGATAGTCTTTACTAAAGCCATTACGCCTGATGGGGTGGTGATACCTCTAGCAAACGCTCAAGCAGCAGGCATGCTGGGTGAAGCAGGCGGTAGATGGCTATGTGAATAATCACTTCATGAAGCGTATAGGCTTTGCTGTGATAGCAAGCGTGGTTAATAGCTTCTTGCAAACTGCACCTATCATAGCTCTAGATAAACTCATAGGCCTTGGCAAAGGCAGAAGTGAAAGGACACCTGAATTTAATTACGCTTTGGGTCAAGCTATCAATGGTAGTATGCAAAGTTCAGCTCAGATGTCTAATCAAATTCTAGGGCAACTGATGAATATCCCCCAAGTTTTTACAAAAATGAGGGCGATAGTATTAAGATTCTCACCATGGACGATATTGATTTTAGTGGTGTGTATGATGTTAAAATTGACCAACAAATCTGTGGTAGATGAAATTATCAAACAAAGCACCAAAAACTTTGTCTAGAGAACATGAAGAAATCACCACAGCCCCAAAGGTGGCAATTGATTCAAGAGAAAGGATAAAATATATTCATGTTATTAAACTCGGTTCTTTACAAAATAAAAAGACAAACCAACCTAGGCTCTTCTAGAGGA
+
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
Error: different_number_of_seq_qual sequence length not equal to quality values
#**!
+
#this_should_work
GGGG
+
****
You probably should use BioPython.
Your bug appears to be the read that is skipped has 129 bases in its sequence but only 128 qv. So your parser reads the next defline as a quality line which then makes it too long so it prints the error.
Then your states don't account for the situation of where you are in step 1 but dont see a defline. So you keep reading extra lines overwritting the ID variable.
but if you really want to write your own parser:
I'll address your questions one at a time.
when sequence length is different than number of quality values
This is invalid. Each record in the fastq file must have the an equal number of bases and qualities. Different records in the file can be different lengths from each other, but each record must have equal bases and qualities.
when there's an empty sequence or entry
An empty read will have blank lines for the sequence and quality lines like this:
#SOLEXA1_0007:1:9:610:1983#GATCAG/2
+SOLEXA1_0007:1:9:610:1983#GATCAG/2
#SOLEXA1_0007:2:13:163:254#GATCAG/2
CGTAGTACGATATACGCGCGTGTACTGCTACGTCTCACTTTCGCAAGATTGCTCAGCTCATTGATGCTCAATGCTGGGCCATATCTCTTTTCTTTTTTTC
+SOLEXA1_0007:2:13:163:254#GATCAG/2
HHHHGHHEHHHHHE=HAHCEGEGHAG>CHH>EG5#>5*ECE+>AEEECGG72B&A*)569B+03B72>5.A>+*A>E+7A#G<CAD?#############
when the number of lines with quality values is more than one
Due to the requirements from the first answer above. We know that the number of bases and qualities must match. Also there will never be an + character in the sequence block. So we can keep parsing the sequence block until we see a line that starts with +. Then we know we are done parsing sequence. Then we can keep parsing quality lines until we get the same number of qualities as is in the sequence. We can't rely on looking for any special characters because depending on the quality encoding, # could be a valid quality call.
Also as an aside, you appear to be splitting the sequence defline to parse out the optional comment. You have to be careful for CASAVA 1.8 format which stupidly has spaces. So you might need a regex to see if it's a CASAVA 1.8 format then don't split on whitespace etc.
Have you considered using one of the robust python packages that are available for dealing with this kind of data rather than writing a parser from scratch? In partincular I'd recommend checking out HTSeq
I'm wondering, how can I count for example all "s" characters and print their number in a text file that I'm importing? Tried few times to do it by my own but I'm still doing something wrong. If someone could give me some tips I would really appreciate that :)
Open the file, the "r" means it is opened as readonly mode.
filetoread = open("./filename.txt", "r")
With this loop, you iterate over all the lines in the file and counts the number of times the character chartosearch appears. Finally, the value is printed.
total = 0
chartosearch = 's'
for line in filetoread:
total += line.count(chartosearch)
print("Number of " + chartosearch + ": " + total)
I am assuming you want to read a file, find the number of s s and then, store the result at the end of the file.
f = open('blah.txt','r+a')
data_to_read = f.read().strip()
total_s = sum(map(lambda x: x=='s', data_to_read ))
f.write(str(total_s))
f.close()
I did it functionally just to give you another perspective.
You open the file with an open("myscript.txt", "r") with the mode as "r" because you are reading. To remove whitespaces and \n's, we do a .read().split(). Then, using a for loop, we loop over each individual character and check if it is an 'S' or an 's', and each time we find one, we add one to the scount variable (scount is supposed to mean S-count).
filetoread = open("foo.txt").read().split()
scount = 0
for k in ''.join(filetoread):
if k.lower() == 's':
scount+=1
print ("There are %d 's' characters" %(scount))
Here's a version with a reasonable time performance (~500MB/s on my machine) for ascii letters:
#!/usr/bin/env python3
import sys
from functools import partial
byte = sys.argv[1].encode('ascii') # s
print(sum(chunk.count(byte)
for chunk in iter(partial(sys.stdin.buffer.read, 1<<14), b'')))
Example:
$ echo baobab | ./count-byte b
3
It could be easily changed to support arbitrary Unicode codepoints:
#!/usr/bin/env python3
import sys
from functools import partial
char = sys.argv[1]
print(sum(chunk.count(char)
for chunk in iter(partial(sys.stdin.read, 1<<14), '')))
Example:
$ echo ⛄⛇⛄⛇⛄ | ./count-char ⛄
3
To use it with a file, you could use a redirect:
$ ./count-char < input_file