Removing gap using array
#/usr/bin/python
import sys
inp=sys.argv[1]
output=sys.argv[2]
count=0
tempcount=0
with open(inp, 'r') as file:
for word in file:
if word[0]=='>':
if count<tempcount:
count=tempcount
tempcount=0
elif set(word)=={'-','\n'}:
tempcount=tempcount+1
if count<tempcount:
count=tempcount
with open(inp, 'r') as file2:
words=file2.read().split('>')[1:]
list=[ ]
i=count+1
for fa in words:
fasta=fa.split('\n')
list=list+['>'+fasta[0]]+fasta[i:]
list=[i+'\n' for i in list if i]
with open(output, 'w') as out:
out.writelines(list)
I would like to remove the gap one by one. while this script is removing line by line. My objective is to remove the gap if found more than 20 gap (-) in template sequences.
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updated
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Biostar
•
written
by
skjobs1234 •
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written
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skjobs1234 •
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I added code markup to your post for increased readability. You can do this by selecting the text and clicking the 101010 button. When you compose or edit a post that button is in your toolbar, see image below:
Hello skjobs1234!
It appears that your post has been cross-posted to another site: https://stackoverflow.com/questions/47508097/
This is typically not recommended as it runs the risk of annoying people in both communities.
Because this code : 'for word in file' treat file as a list of lines. Thus, you are counting lines.
Maybe you could try this way:
Please can u modify this script?
I have tried.. But not getting solution.