I want remove the long unaligned gap from the files with position wise. I have input life this files
>f1
--------------------------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------------GTTYGVC
SKAFKFLGTPADTGHGTVVLELQYTGTDGPCKVPISSVASLNDLTPVGRLVTVNPFVSVA
>f2
--------------------------------------------------------------------------------------------------------------------
-----------------------------MVHRQWFFDLPLPWA-----------------------------------------GTTYGMC
TEKFSFAKNPADTGHGTVVIELSYSGSDGPCKIPIVSVASLNDMTPVGRLVTVNPFVATS
>f3
MRCVGVGNRDFVEGLSGATWVDVVLEHGGCVTTMAKNKPTLDIELQKTEATQLATLRKLC
IEGKITNITTDSRCPTQGEAVLPEEQDQNYVCKHTYVDRGWGNGCGLFGKGSLVTCAKFQ
CLEPIEGKVVQYENLKYTVIITVHTGDQHQVGNETQGVTAEITPQASTTEAILPEYGTLGGG
And I want the output like this
>f1
------------------------------------------------------------------------------------------------------GTTYGVC
SKAFKFLGTPADTGHGTVVLELQYTGTDGPCKVPISSVASLNDLTPVGRLVTVNPFVSVA
>f2
-----------------------------MVHRQWFFDLPLPWA-----------------------------------------GTTYGMC
TEKFSFAKNPADTGHGTVVIELSYSGSDGPCKIPIVSVASLNDMTPVGRLVTVNPFVATS
>f3
IEGKITNITTDSRCPTQGEAVLPEEQDQNYVCKHTYVDRGWGNGCGLFGKGSLVTCAKFQ
CLEPIEGKVVQYENLKYTVIITVHTGDQHQVGNETQGVTAEITPQASTTEAILPEYGTLGGG
So equal number of gaps are removed from f1 and f2 gaps as well as from f3 remove the one line on the basis of position removed from f1 and f2.
Thanks in advance
•
written
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skjobs1234 •
code:
import sys
inp=sys.argv[1]
output=sys.argv[2]
count=0
tempcount=0
with open(inp, 'r') as file:
for line in file:
if line[0]=='>':
if count<tempcount:
count=tempcount
tempcount=0
elif set(line)=={'-','\n'}:
tempcount=tempcount+1
if count<tempcount:
count=tempcount
with open(inp, 'r') as file2:
lines=file2.read().split('>')[1:]
list=[]
i=count+1
for fa in lines:
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'm getting this error on Terminal
**Traceback (most recent call last):
File "biostar.py", line 3, in <module>
inp=sys.argv[1]
IndexError: list index out of range**
did you provide the input and output file's absolute path in the command line? or could you copy the command you run here?
Yes.. It's working.. Thank for your valuable suggestion and time
Dear Shoujun your script is running well. But the out is not coming which i want. Please see once more this problem. Thanking for helping me
Actually your script is not removing gap properly, I want to remove only unaligned (gap) region from > files. I want to give a brief example with output
tem1------------------------------------------------------FHLTTR GGEPHMIVSKQERGKSLLFKTSAGVNMCTLIAMDLGELCEDTMTYKCPRITETEPDDVDC
tem2------------------------------------------------------------ --------------------------TPVECFEPSMLKKKQLTVLDLHPG-G-KTRRVLP
query MNNQRKKTGKPSINMLKRVRNRVSTGSQLAKRFSKGLLNGQGPMKLVMAFIAFLRFLAIP PTAGVLARWGTFKKSGAIKVLKGFKKEISNMLSIINQRKKTSLCLMMILPAALAFHLTSR
I want output like this
tem1 FHLTTRGGEPHMIVSKQERGKSLLFKTSAGVNMCTLIAMDLGELCEDTMTYKCPRITETEPDDVDC tem2-------------------------------------TPVECFEPSMLKKKQLTVLDLHPG-G-KTRRVLP query MNNQRPTAGVLARWGTFKKSGAIKVLKGFKKEISNMLSIINQRKKTSLCLMMILPAALAFHLTSR
Condition 1 So you can see here, if the gaps are found at same position in both tem1 & tem2 then remove gaps and also remove query (it doesn't matter gap or not but it should be remove equal number of sequences with same position)
Condition 2 if the if gaps found more than 20 residues in all >tem at the same position then it should remove.
The format of your given example is messed up. I cannot really understand how you want to remove the gap.
Could you just upload as fig?
Yes I can
please give me email ID?
You can ping on my email id
redacted (see below)
•
written
by
skjobs1234 •
You can upload to the forum. Or send to my email: redacted
•
written
by
shoujun.gu
I want to remove All Positions Containing A Gap In A Multiple Alignment by perl, python or any other scripting language
This script is working well, but I want to remove gap one by one, not directly line by line. Can you modify this program into one by one if the gap is continue more than 20-25
Please can you modify this script?
This script is removing gap line by line. But I would like to remove the gap one by one string.
This script is removing line by line gap. But I want to remove the gap if the gap is more than 20. It can be possible by the array. Take every gap into in a array and match to the other file. If found the gap in all files then remove otherwise skip if found in any one.
import sys
inp=sys.argv[1]
output=sys.argv[2]
count=0
tempcount=0
with open(inp, 'r') as file:
for line in file:
if line[0]=='>':
if count<tempcount:
count=tempcount
tempcount=0
elif set(line)=={'-','\n'}:
tempcount=tempcount+1
if count<tempcount:< p="">
count=tempcount
with open(inp, 'r') as file2:
lines=file2.read().split('>')[1:]
list=[]
i=count+1
for fa in lines:
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)
This script is removing line by line gap (-). But I would like to remove the gap one string by string. if more than 20 continuous string found in all input template file then remove the gap, otherwise if not found any gap at same position in any template the skip. Example of Input
f1 ------------------------------------------------------------------------------------------------------GTTYGVCSKAFKFLGTPADTGHGTVVLELQYTGTDGPCKVPISSVASLNDLTPVGRLVTVNPFVSVA
f2 -----------------------------MVHRQWFFDLPLPWA-----------------------------------------GTTYGMCTEKFSFAKNPADTGHGTVVIELSYSGSDGPCKIPIVSVASLNDMTPVGRLVTVNPFVATS
Query IEGKITNITTDSRCPTAVLPEEQDQNYVCKHTYVDRGWGNGCGLFGKGSLVTCAKFQCLEPIEGKVVQYENLKYTVIITVHTGDQHQVGNETQGVTAEITPQASTTEAILPEYGTLGGG
Output should be like
f1 --------------------------------GTTYGVCSKAFKFLGTPADTGHGTVVLELQYTGTDGPCKVPISSVASLNDLTPVGRLVTVNPFVSVA
f2 MVHRQWFFDLPLPWAGTTYGMCTEKFSFAKNPADTGHGTVVIELSYSGSDGPCKIPIVSVASLNDMTPVGRLVTVNPFVATS
f3 AVLPEEQDQNYVCKHTCAKFQCLEPIEGKVVQYENLKYTVIITVHTGDQHQVGNETQGVTAEITPQASTTEAILPEYGTLGGG
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Do you know the positions of the gaps to remove? Are they based on the blast result?
No. Please guide Yes.. On the based on blast result. I have got the aligned file PROMAL3D to get aligned file.. yes the position is known.
provide examples of the positions in which to remove gaps
Example Input file
>f1
------------------------------------------------------------------------------------------------------GTTYGVC SKAFKFLGTPADTGHGTVVLELQYTGTDGPCKVPISSVASLNDLTPVGRLVTVNPFVSVA
>f2
-----------------------------MVHRQWFFDLPLPWA-----------------------------------------GTTYGMC TEKFSFAKNPADTGHGTVVIELSYSGSDGPCKIPIVSVASLNDMTPVGRLVTVNPFVATS
Outpur file example
why you keep the gaps at the beginning of f1 and f2 output? how many gaps do you want to keep?
This does not look like you want to remove gaps but just remove the new line characters on the fasta header line.
why ? sounds like http://xyproblem.info/
How about Gblocks: http://molevol.cmima.csic.es/castresana/Gblocks/Gblocks_documentation.html
I have used this Gblocks and trimal but both are not suitable for your data set. Please help how to write the perl or python script
This question is unrelated to Perl or Blast so I removed those tags.
Hello skjobs1234!
It appears that your post has been cross-posted to another site: https://bioinformatics.stackexchange.com/questions/2524/r
This is typically not recommended as it runs the risk of annoying people in both communities.