Nsite_parser

Rim Gubaev, 2018

Nsite is a program that allows to search regulatory elements within promoter sequences of the genes. The Nsite output represents HTML page with text which is quite uncomfortable to use for subsequent analysis. This script takes Nsite output as text copied from HTML page and converts it to a tab-delimited text file.

Usage

python3 Nsite_parser.py Nsite_output.txt Nsite_table.txt

• 1^st argument is text copied from HTML page (Nsite output)
• 2^nd argument is a tab-delimited text file (Nsite_parser.py output)

Sample input

Program   Nsite | Version 6.2014
   Search for motifs of   3032 Transcription Factor Binding Sites (TFBS)
   SET of TFBSs: REGSITE DB: 3032 Plant Transcription Factor Binding Sites [Last update: 13.07.2016]; Softberry Inc.

 Search PARAMETRS:
     Expected  Mean  Number                      :  0.0100000
     Statistical Siginicance Level               :  0.9500000
     Level of homology between known TFBS and motif:   80%
     Variation of Distance between TFBS Blocks     :   20%

 NOTE: Mism. - Mismatches   | Mean. Exp. Number - Mean Expected Number   | Up.Conf.Int. - Upper Confidence Interval
       Mismatches are given in Lower case
____________________________________________________________

 QUERY: 1466315
 Length of Query Sequence:       1000 bp     | Nucleotide Frequencies:  A -  0.35   G -  0.20   T -  0.30   C -  0.14


 TFBS AC: RSP00039//OS: tomato (Lycopersicon esculentum), Lycopersicon esculentum /GENE: LAT56; LAT59;/TFBS: 56/59 box /BF: GT-1 related transcription factors
 Motifs on "+" Strand: Mean Exp. Number   0.00202     Up.Conf.Int.  1     Found   1
     324  TGAAATTGTGA      334 (Mism.= 0)

 TFBS AC: RSP00314//OS: arabidopsis (Arabidopsis thaliana) /GENE: GA3/TFBS: rbe /BF: RSG, a bZIP transcriptional activator;
 Motifs on "+" Strand: Mean Exp. Number   0.00554     Up.Conf.Int.  1     Found   1
     906  TCCAAaTTGGA      916 (Mism.= 1)

 Motifs on "-" Strand: Mean Exp. Number   0.00754     Up.Conf.Int.  1     Found   1
     916  TCCAAtTTGGA      906 (Mism.= 1)
     
      Totally       7 motifs of     6 different TFBSs have been found
____________________________________________________________

 QUERY: 3205204
 Length of Query Sequence:       1000 bp     | Nucleotide Frequencies:  A -  0.28   G -  0.22   T -  0.28   C -  0.22


 TFBS AC: RSP00130//OS: soybean (Glycine max) /GENE: GmAux28/TFBS: C2 /BF: unknown nuclear factor
 Motifs on "+" Strand: Mean Exp. Number   0.00236     Up.Conf.Int.  1     Found   1
     569  tATtATtATAATAATAAAaA      588 (Mism.= 4)

 Motifs on "-" Strand: Mean Exp. Number   0.00208     Up.Conf.Int.  1     Found   1
     584  tATtATtATAATAATAtATA      565 (Mism.= 4)

 TFBS AC: RSP00157//OS: soybean (Glycine max) /GENE: GmAux28/TFBS: D2 /BF: unknown nuclear factor
 Motifs on "+" Strand: Mean Exp. Number   0.00789     Up.Conf.Int.  1     Found   1
     558  ATTTATATAtAT      569 (Mism.= 1)

 Motifs on "-" Strand: Mean Exp. Number   0.00789     Up.Conf.Int.  1     Found   1
     569  ATaTATATAAAT      558 (Mism.= 1)

 TFBS AC: RSP00802//OS: potato (Solanum tuberosum) /GENE: patatin 21/TFBS: Box A-1 /BF: BABF
 Motifs on "+" Strand: Mean Exp. Number   0.00222     Up.Conf.Int.  1     Found   2
     545  tTATATATATATTATtTAta      564 (Mism.= 4)
     558  ATtTATATATATatTATtAT      577 (Mism.= 4)

 Motifs on "-" Strand: Mean Exp. Number   0.00222     Up.Conf.Int.  1     Found   2
     569  ATATATATAaATaATATAta      550 (Mism.= 4)
     567  ATATATAaATAaTATATAta      548 (Mism.= 4)

 TFBS AC: RSP01712//OS: tomato (Solanum lycopersicum) /GENE: LeACS2/TFBS: RIN BS /BF: RIN
 Motifs on "+" Strand: Mean Exp. Number   0.00201     Up.Conf.Int.  1     Found   1
     520  CTAAAAAAAG      529 (Mism.= 0)

 TFBS AC: RSP01897//OS: Arabidopsis (Arabidopsis thaliana) /GENE: MYB44 (At5g67300)/TFBS: VRE1 /BF: VIP1
 Motifs on "-" Strand: Mean Exp. Number   0.00395     Up.Conf.Int.  1     Found   1
     921  ACAGCTGTA      913 (Mism.= 0)

 TFBS AC: RSP02013//OS: rice (Oryza sativa) /GENE: BRI1/TFBS: E-box (BRI1, P1_3) /BF: RAVL1
 Motifs on "+" Strand: Mean Exp. Number   0.00110     Up.Conf.Int.  1     Found   1
     913  TACAGCTGTT      922 (Mism.= 0)

 Totally      20 motifs of    13 different TFBSs have been found
____________________________________________________________
etc...

Sample output

GeneID	Length	FactorID	Strand	Mean_exp_value	Found
1466315	1000 bp	RSP00039	+	0.00202	1
1466315	1000 bp	RSP00314	+	0.00554	1
1466315	1000 bp	RSP02003	-	0.00783	1
3205204	1000 bp	RSP00130	+	0.00236	1
3205204	1000 bp	RSP00130	-	0.00208	1
107816122	1000 bp	RSP00492	+	0.00000	5
107816122	1000 bp	RSP01644	+	0.00376	1

• GeneID corresponds to QUERY: row which in turn is automatically picked up from sequence header of input fasta file.
• Length reflects the lenght (Length of Query Sequence: row) of input promoter sequence.
• FactorID corresponds to TFBS AC: row from regulatory elements database.
• Strand indicates whether regulatory element located on '+' or '-' strand.
• Mean_exp_value is expected value.
• Found is a number of regulatory elements which are found within promoter sequence.

Email:rimgubaev@gmail.com