Compare two files to get the position

Question

[skjobs1234]

I have two files, I want to know the starting and ending positions after the matches of the sequences. For example

File_1

VMLLVHYAIIGPGLQAKATREAQKRTAAGIMKNPTVDGITVIDLEPISYD PKFEKQLGQVMLLVLCAGQLLLMRTTWAFCEVLTLATGPILTLWEGNP FWNTTIAVSTANIFRGSYLAGAGLAFSLIKNAQTPRRGTGTTGETLGE KRQLNSLDRKEFEEYKRSGILEVDRTEAKSALKDGSKIKHAVSRGSS RWIVERGMVKPKGKVVDLGCGRGGWSYYMATLKNVTEVKGYTKGGP

File_2

FWNTTIAVSTANIFRGSYLAGAGLAFSLIKNAQTPRRGTGTTGETLGE KRQLNSLDRKEFEEYKRSGILEVDRTEAKSALKDGSKIKHAVSRGSS RWIVERGMVKPKGKVVDLGCGRGGWSYYMATLKNVTEVKGYTKGGP

So, here File_2 starting FWNTTIAVST..... sequences are matching in file_1 at at position 100 and ending YTKGGP at 250. So I want to print this starting and ending position 100-250

Script should be python or perl

Answer 1

[5heikki]

Assuming those are actually fasta formated files:

blastp -query File_2.faa -subject File_1.faa -outfmt '6 qlen length nident sstart send' \
| awk 'BEGIN{OFS=FS="\t"}{if($1==$2 && $1==$3){print $4,$5}}'

Answer 2

[finswimmer]

Hello,

you can tak pythons str.index() to find the position of a given substring. When you now the starting position, you can calculate the end position by taken the length of your sequence into account.

fin swimmer

[skjobs1234]

Hi, Fin Swimmer, I don't have to idea about the python scripting. If you can write script then it's good for me.. Otherwise please guide this str.index() in perl. I know little bit perl script

[finswimmer]

For python2:

file1 = "VMLLVHYAIIGPGLQAKATREAQKRTAAGIMKNPTVDGITVIDLEPISYDPKFEKQLGQVMLLVLCAGQLLLMRTTWAFCEVLTLATGPILTLWEGNPFWNTTIAVSTANIFRGSYLAGAGLAFSLIKNAQTPRRGTGTTGETLGEKRQLNSLDRKEFEEYKRSGILEVDRTEAKSALKDGSKIKHAVSRGSSRWIVERGMVKPKGKVVDLGCGRGGWSYYMATLKNVTEVKGYTKGGP"
file2 = "FWNTTIAVSTANIFRGSYLAGAGLAFSLIKNAQTPRRGTGTTGETLGEKRQLNSLDRKEFEEYKRSGILEVDRTEAKSALKDGSKIKHAVSRGSSRWIVERGMVKPKGKVVDLGCGRGGWSYYMATLKNVTEVKGYTKGGP"

start_index=file1.index(file2)

print start_index+1,start_index+len(file2)

Answer 3

[Pierre Lindenbaum]

a one liner using bash :-)

sdiff \
     <(echo "VMLLVHYAIIGPGLQAKATREAQKRTAAGIMKNPTVDGITVIDLEPISYD PKFEKQLGQVMLLVLCAGQLLLMRTTWAFCEVLTLATGPILTLWEGNP FWNTTIAVSTANIFRGSYLAGAGLAFSLIKNAQTPRRGTGTTGETLGE KRQLNSLDRKEFEEYKRSGILEVDRTEAKSALKDGSKIKHAVSRGSS RWIVERGMVKPKGKVVDLGCGRGGWSYYMATLKNVTEVKGYTKGGP" | tr -d ' ' | grep -o .) \
     <(echo "FWNTTIAVSTANIFRGSYLAGAGLAFSLIKNAQTPRRGTGTTGETLGE KRQLNSLDRKEFEEYKRSGILEVDRTEAKSALKDGSKIKHAVSRGSS RWIVERGMVKPKGKVVDLGCGRGGWSYYMATLKNVTEVKGYTKGGP" |   tr -d ' ' | grep -o .)  | \
   awk '($1==$2)' | cut -f1 | tr -d '\n' | fold -w 20 


FWNTTIAVSTANIFRGSYLA
GAGLAFSLIKNAQTPRRGTG
TTGETLGEKRQLNSLDRKEF
EEYKRSGILEVDRTEAKSAL
KDGSKIKHAVSRGSSRWIVE
RGMVKPKGKVVDLGCGRGGW
SYYMATLKNVTEVKGYTKGG

[skjobs1234]

I want only starting and ending position of File 1 in File_2. What is the position of same sequences of file1 in file2 . Suppose that

File_1

VMLLVHYAIIGPGLQAKATREAQKRTAAGIMKNPTVDGITVIDLEPISYD PKFEKQLGQVMLLVLCAGQLLLMRTTWAFCEVLTLATGPILTLWEGNP FWNTTIAVSTANIFRGSYLAGAGLAFSLIKNAQTPRRGTGTTGETLGE KRQLNSLDRKEFEEYKRSGILEVDRTEAKSALKDGSKIKHAVSRGSS RWIVERGMVKPKGKVVDLGCGRGGWSYYMATLKNVTEVKGYTKGGP

File_2

FWNTTIAVSTANIFRGSYLAGAGLAFSLIKNAQTPRRGTGTTGETLGE KRQLNSLDRKEFEEYKRSGILEVDRTEAKSALKDGSKIKHAVSRGSS RWIVERGMVKPKGKVVDLGCGRGGWSYYMATLKNVTEVKGYTKGGP

So, here File_2 starting FWNTTIAVST..... sequences are matching in file_1 at at position 100 and ending YTKGGP at 250. So I want to print this starting and ending position 100-250, not the sequences. Just I want position in numeric letter. like Starting 100 and ending 250