--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/pytools/lib/readSeq.py	Tue Mar 18 16:23:26 2025 -0400
@@ -0,0 +1,157 @@
+#!/usr/bin/env python
+
+import sys
+import math
+import random
+import fileinput
+import re
+#import os
+import copy
+
+class readSeq:
+
+    def __init__(self, fileName, paired = False, fileType = 'fastq', compression = 'auto', sampleRate = None):
+        self.fileName = fileName
+        self.fileType = fileType
+        self.fileType = self.__detectFileFormat()
+        self.compression = compression
+        self.__readObj = self.readFile()
+        self.paired = paired
+        self.sampleRate = sampleRate
+        
+    def __iter__(self):
+        return self
+
+    def next(self):
+        record = self.__readObj.next()
+        self.header = record['header']
+        self.seq = record['seq']
+        self.seqNum = record['seqNum']
+        if self.fileType == 'fastq':
+            self.qual = record['qual']
+
+        if self.paired is True:
+            self2 = copy.copy(self)
+            record = self.__readObj.next()
+            self2.header = record['header']
+            self2.seq = record['seq']
+            self2.seqNum = record['seqNum']
+            if self.fileType == 'fastq':
+                self2.qual = record['qual']
+            return self, self2
+        else:
+            return self
+
+    def __detectFileFormat(self):
+        if self.fileType != 'auto':
+            return self.fileType
+         
+        if ( re.search('fasta$', self.fileName) or 
+             re.search('fa$', self.fileName)    or
+             re.search('fna$', self.fileName) ):
+            self.fileType = 'fasta'
+
+        elif ( re.search('fastq$', self.fileName) or
+               re.search('fq$', self.fileName) ) :
+            self.fileType = 'fastq'
+
+        return self.fileType
+
+    def readFile(self):
+
+        record = dict()       
+ 
+        # allow user to specify if compression should be auto detected using file names
+        # specified by fileinput documentation
+        if self.compression == 'auto':
+            inFH = fileinput.FileInput(self.fileName, openhook=fileinput.hook_compressed)    
+        else:
+            inFH = fileinput.FileInput(self.fileName)
+  
+        #TODO RAISE exception if file doesn't exist
+  
+        # read fastq
+        if self.fileType == 'fastq':
+            self.seqNum = 0
+            for record['header'] in inFH:
+
+                record['seqNum'] = int(math.ceil(inFH.lineno()/8.0))
+                record['seq'] = inFH.readline().strip()
+                record['r1Plus'] = inFH.readline()
+                record['qual'] = inFH.readline().strip()
+                     
+                if not re.search('^@', record['header'], flags=0):
+                    pass
+                    #TODO add exception for not being a fastq
+                          
+                record['header'] = re.sub('^@', '', record['header'].strip())
+                yield record
+
+        elif self.fileType == 'fasta':
+            record['header'] = None
+            record['seq'] = None
+            record['seqNum'] = 0
+            
+            for line in inFH:
+ 
+                line = line.strip()
+                if re.search('^>', line):
+                    line = re.sub('^>', '', line)
+                    if record['header'] is None:
+                        record['header'] = line
+                        if not re.search('>', record['header']):
+                            pass
+                            # TODO add exception for not being fasta   
+ 
+                    if record['seq'] is not None:
+                        record['seqNum'] = record['seqNum'] + 1
+                        
+                        if self.sampleRate:
+                        #subsampling of reads is desired
+                            if random.random() < self.sampleRate:
+                                yield record
+                        else:
+                            yield record
+                        record['seq'] = None
+
+                    record['header'] = line                
+                else:
+                    if record['seq'] is not None:
+                        record['seq'] += line
+                    else:
+                        record['seq'] = line
+                        
+            record['seqNum'] = record['seqNum'] + 1
+            
+            if self.sampleRate:
+                #subsampling of reads is desired
+                if random.random() < self.sampleRate:
+                    yield record
+            else:
+                yield record
+
+        try:
+            inFH = fileinput.close()
+        except:
+            pass
+
+    #except:
+        sys.exc_info()[0]
+
+    def printRecord(self):
+        if self.fileType == 'fastq':
+            print("@%s" % self.header)
+            print(self.seq)
+            print("+") 
+            print(self.qual)
+        elif self.fileType == 'fasta':
+            print(">%s" % self.header)
+            print(self.seq)
+    
+if __name__ == '__main__':
+
+    for inputfile in sys.argv[1:]:
+        #get a pair of reads
+        for r1, r2 in readSeq(inputfile, paired=True):
+            print r1.header
+            print r2.header