Add N7-G data channel compatibility

Added --concat flag allowing Ringmapper to concatenate and process
N1/3 and N7-G modifications simultaneously and generate N1/3-N1/3,
N13-N7G, and N7G-N7G RINGs.

Additionally, added a new statistic allowing for determination of
effect size of a given RING.

README.md

@@ -1,4 +1,4 @@
-# RingMapper v1.2
+# RingMapper v1.3
 
 Code for performing RING-MaP and PAIR-MaP analysis
 (RingMapper & PairMapper)
@@ -31,6 +31,11 @@ by ShapeMapper2 using the --output-parsed flag.
 See the ShapeMapper2 documentation for further information regarding
 alignment and processing options.
 
+Following the release of ShapeMapper2.3 RingMapper may now be used to compute
+N1/3-N7 and N7-N7 RINGs in addition to traditional N1/3-N1/3 RINGs. See the
+section titled "RingMapper Usage for N7" below. Note - PairMapper not currently
+tested for compatibility with N7 functionality.
+
 RING and PAIR-MaP data can be visualized using the arcPlot plotting tool,
 available at https://github.com/Weeks-UNC/arcPlot
 
@@ -104,6 +109,41 @@ Ringfile        List of correlations. See docs/ringfile-format.txt
 
 --------------------------------------------------------------------------
 
+RingMapper Usage for N7
+-----------------
+```
+ringmapper.py <optional args> --parsedMutga parsed.mutga --fasta fasta.fa inputfile outputfile | --help
+```
+
+### Required inputs
+```
+inputfile       Parsed mutation file of modified sample
+--parsedMutga   Parsed mutation file of modified sample containing N7 modifications
+--fasta         Path to fasta sequence file
+outputpath      Path where output Ringfiles will be written
+```
+
+### Optional arguments
+```
+--untreatedMutga   Path to mutation file for untreated sample containing N7 modifications.
+                   Nts with high mutation rates or correlations in the untreated sample
+                   are ignored (Required --untreated)
+
+--keepconcat       Keep the concatenated mutation string files for use in other analyses
+
+A full list of optional arguments/parameters can be accessed by running with --help flag
+```
+
+### Outputs
+```
+Ringfile_concatrings   List of N1/3-N1/3, N1/3-N7, and N7-N7 correlations. See docs/ringfile-format.txt
+Ringfile_N1            List of N1/3-N1/3 correlations. See docs/ringfile-format.txt
+Ringfile_N1N7          List of N1/3-N7 correlations. See docs/ringfile-format.txt
+Ringfile_N7            List of N7-N7 correlations. See docs/ringfile-format.txt
+```
+
+--------------------------------------------------------------------------
+
 PairMapper Usage
 -----------------
 ```

changelog.txt

@@ -1,3 +1,24 @@
+Version 1.3
+August 30, 2024
+Thomas Miller <[email protected]>, Lucas Kearns <[email protected]>,
+David Mitchell <[email protected]>
+***********************************************************************
+
+ADDED:
+
+Added ShapeMapper_MMS0_Mut_Filter.py. Filters SM runs performed with min mut
+separation set to 0. Enables optimal base pair detection by PairMapper. See README for details.
+
+Added --concat flag. This flag allows RingMapper to concatenate N1/3 and N7-G mut files and
+generate N1/3-N1/3, N1/3-N7G, and N7G-N7G RINGs. 
+
+Added alpha statistic calculation. Equivalent to 
+(comutations / Depth) / 
+((i mutations and no j mutations / Depth) * (j mutations and no i mutations / Depth))
+(See 2024 N7 publication for a more in depth explanation / cleaner
+formula). Allows for determination of effect size of a given RING.
+
+
 Version 1.2
 August 25, 2022
 Anthony Mustoe <[email protected]>
@@ -80,5 +101,3 @@ than matrix format
 write pairmapper files despite failure of one on more quality checks
 
 -added significantDifference function for computing differences between contigency tables
-
-

docs/ringfile-format.txt

@@ -33,6 +33,11 @@ Mod_Depth   Number of times windows i,j were read together in the Modified sampl
 
 Mod_Comuts  Number of times windows i,j were mutated together in the Modified sample
 
+Alpha       Statistic quantifying the coupling strength between nucleotides. Equivalent
+            to   pij / (pi*pj)   where pij is the joint probability of both nucleotides
+            i and j being mutated and pi and pj are the marginal mutation probabilities
+            of i and j.
+
 Unt_Depth   Number of times windows i,j were read together in the Untreated sample
 
 Unt_Comuts  Number of times windows i,j were mutated together in the Untreated sample

pairmapper.py

@@ -234,7 +234,7 @@ def isComplement(seq1, seq2, maxGU, maxNC):
             if isComplement(self.parent.sequence[i:i+self.parent.window], 
                     self.parent.sequence[j:j+self.parent.window], maxGU=maxGU, maxNC=maxNC):
                 compcorrs.append((i,j))
-
+        print(compcorrs)
         return compcorrs
 
 

readMutStrings.pyx

@@ -21,7 +21,8 @@
 from libc.stdio cimport FILE, fopen, fclose, getline
 from libc.stdlib cimport atoi, free
 from libc.string cimport strsep, strtok, strcmp, strdup
-
+import warnings
+warnings.filterwarnings("ignore", message="numpy.dtype size changed")
 import numpy as np
 cimport numpy as np