extract postion motif from fasta file

Question

[Jason]

Use shell command or python

Suppose I have two files. The first file has more than 100 list of fasta file. The second file has list of motifs. I want to extract the postion of each string in the motifs and save that in txt file 3.

Forexample:

File 1:

>sp|P26140|3BHS2_MOUSE 3 beta-hydroxysteroid dehydrogenase/Delta 5-->4-isomerase type 2 OS=Mus musculus GN=Hsd3b2 PE=1 SV=4

MPGWSCLVTGAGGFLGQRIIQLLVQEEDLEEIRVLDKVFRPETRKEFFNLETSIKVTVLE

GDILDTQYLRRACQGISVVIHTAAIIDVTGVIPRQTILDVNLKGTQNLLEACIQASVPAF

IFSSSVDVAGPNSYKEIVLNGHEEECHESTWSDPYPYSKKMAEKAVLAANGSMLKNGGTL

QTCALRPMCIYGERSPLISNIIIMALKHKGILRSFGKFNTANPVYVGNVAWAHILAARGL

RDPKKSPNIQGEFYYISDDTPHQSFDDISYTLSKEWGFCLDSSWSLPVPLLYWLAFLLET

VSFLLSPIYRYIPPFNRHLVTLSGSTFTFSYKKAQRDLGYEPLVSWEEAKQKTSEWIGTL

VEQHRETLDTKSQ

>sp|P35730|ODBB_RAT 2-oxoisovalerate dehydrogenase subunit beta, mitochondrial OS=Rattus norvegicus GN=Bckdhb PE=1 SV=3

MAAVAARAGGLLRLGAAGAERRRRGLRCAALVQGFLQPAVDDASQKRRVAHFTFQPDPES

LQYGQTQKMNLFQSITSALDNSLAKDPTAVIFGEDVAFGGVFRCTVGLRDKYGKDRVFNT

PLCEQGIVGFGIGIAVTGATAIAEIQFADYIFPAFDQIVNEAAKYRYRSGDLFNCGSLTI

RAPWGCVGHGALYHSQSPEAFFAHCPGIKVVIPRSPFQAKGLLLSCIEDKNPCIFFEPKI

LYRAAVEQVPVEPYKIPLSQAEVIQEGSDVTLVAWGTQVHVIREVASMAQEKLGVSCEVI

DLRTIVPWDVDTVCKSVIKTGRLLISHEAPLTGGFASEISSTVQEECFLNLEAPISRVCG

YDTPFPHIFEPFYIPDKWKCYDALRKMINY

File 2:

Motif

P26140      MPGWSC

P35730     AERRRRGLRCAAL

File 3

Result:

P26140       1,2,3,4,5

P35730      19,20,21,22,23,24,25,27,28,29,30,31

[GenoMax]

If this is not an assignment then you can use fuzzpro from EMBOSS. Second example from above.

########################################
# Program: fuzzpro
# Rundate: Tue 13 Mar 2018 00:02:50
# Commandline: fuzzpro
#    -auto
#    -sequence /var/lib/emboss-explorer/output/289888/.sequence
#    -pattern AERRRRGLRCAAL
#    -outfile outfile
#    -rformat2 seqtable
# Report_format: seqtable
# Report_file: outfile
########################################

#=======================================
#
# Sequence: ODBB_RAT     from: 1   to: 390
# HitCount: 1
#
# Pattern_name Mismatch Pattern
# pattern             0 AERRRRGLRCAAL
#
#=======================================

  Start     End Pattern               Mismatch Sequence
     19      31 pattern:AERRRRGLRCAAL        . AERRRRGLRCAAL

#---------------------------------------
#---------------------------------------

#---------------------------------------
# Total_sequences: 1
# Total_length: 390
# Reported_sequences: 1
# Reported_hitcount: 1
#---------------------------------------

[Jason]

I want to read many patterns with list of sequences. This software will only read one pattern for each run.

thank you

[st.ph.n]

If you want python, look into regex.findall()

[abbey]

This may be a good time to learn regex, my friend. If this is for an assignment then I think you will learn the most that way: https://regexr.com/

Answer 1

[cpad0112]

Motifs (tab separated):

$ cat pat.txt 
P26140  MPGWSC
P35730  AERRRRGLRCAAL

output using seqkit and csvtk (csvtk for formatting the output):

$ seqkit tab2fx pat.txt | seqkit locate -f - test.fa | csvtk -t pretty
seqID                   patternName   pattern         strand   start   end   matched
sp|P26140|3BHS2_MOUSE   P26140        MPGWSC          +        1       6     MPGWSC
sp|P35730|ODBB_RAT      P35730        AERRRRGLRCAAL   +        19      31    AERRRRGLRCAAL

Input:

$ cat test.fa 
>sp|P26140|3BHS2_MOUSE 3 beta-hydroxysteroid dehydrogenase/Delta 5-->4-isomerase type 2 OS=Mus musculus GN=Hsd3b2 PE=1 SV=4
MPGWSCLVTGAGGFLGQRIIQLLVQEEDLEEIRVLDKVFRPETRKEFFNLETSIKVTVLE
GDILDTQYLRRACQGISVVIHTAAIIDVTGVIPRQTILDVNLKGTQNLLEACIQASVPAF
IFSSSVDVAGPNSYKEIVLNGHEEECHESTWSDPYPYSKKMAEKAVLAANGSMLKNGGTL
QTCALRPMCIYGERSPLISNIIIMALKHKGILRSFGKFNTANPVYVGNVAWAHILAARGL
RDPKKSPNIQGEFYYISDDTPHQSFDDISYTLSKEWGFCLDSSWSLPVPLLYWLAFLLET
VSFLLSPIYRYIPPFNRHLVTLSGSTFTFSYKKAQRDLGYEPLVSWEEAKQKTSEWIGTL
VEQHRETLDTKSQ
>sp|P35730|ODBB_RAT 2-oxoisovalerate dehydrogenase subunit beta, mitochondrial OS=Rattus norvegicus GN=Bckdhb PE=1 SV=3
MAAVAARAGGLLRLGAAGAERRRRGLRCAALVQGFLQPAVDDASQKRRVAHFTFQPDPES
LQYGQTQKMNLFQSITSALDNSLAKDPTAVIFGEDVAFGGVFRCTVGLRDKYGKDRVFNT
PLCEQGIVGFGIGIAVTGATAIAEIQFADYIFPAFDQIVNEAAKYRYRSGDLFNCGSLTI
RAPWGCVGHGALYHSQSPEAFFAHCPGIKVVIPRSPFQAKGLLLSCIEDKNPCIFFEPKI
LYRAAVEQVPVEPYKIPLSQAEVIQEGSDVTLVAWGTQVHVIREVASMAQEKLGVSCEVI
DLRTIVPWDVDTVCKSVIKTGRLLISHEAPLTGGFASEISSTVQEECFLNLEAPISRVCG
YDTPFPHIFEPFYIPDKWKCYDALRKMINY