GPatch 0.3.5__tar.gz → 0.3.8__tar.gz

{GPatch-0.3.5/src/GPatch.egg-info → GPatch-0.3.8}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: GPatch
-Version: 0.3.5
+Version: 0.3.8
 Summary: Assemble contigs into a chromosome-scalse pseudo-assembly using alignments to a reference sequence.
 Home-page: https://github.com/adadiehl/GPatch
 Author: Adam Diehl
@@ -40,8 +40,8 @@ Description: # GPatch
         
         ## Usage
         ```
-        usage: GPatch [-h] -q SAM/BAM -r FASTA [-x BED] [-b FILENAME] [-m N]
-                               [-d N] [-f FLOAT] [-e FLOAT]
+        usage: GPatch.py [-h] -q SAM/BAM -r FASTA [-x STR] [-b FILENAME] [-m N]
+                         [-w PATH] [-d]
         ```
         
         Starting with alignments of contigs to a reference genome, produce a chromosome-scale pseudoassembly by patching gaps between mapped contigs with sequences from the reference. Reference chromosomes with no mapped contigs are printed to output unchanged.
@@ -59,7 +59,9 @@ Description: # GPatch
         | __-x STR, --prefix STR__ | Prefix to add to output file names. Default=None |
         | __-b FILENAME, --store_final_bam FILENAME__ | Store the final set of primary contig alignments to the given file name. Default: Do not store the final BAM. |
         | __-m N, --min_qual_score N__ | Minimum mapping quality score to retain an alignment. Default=30 |
-        
+        | __-w PATH, --whitelist PATH__ | Path to BED file containing whitelist regions: i.e., the inverse of blacklist regions. Supplying this will have the effect of excluding alignments that fall entirely within blacklist regions. Default=None |
+        | __-d, --drop_missing__ | Omit unpatched reference chromosome records from the output if no contigs map to them. Default: Unpatched chromosomes are printed to output unchanged. |
+        | __-t, --no_trim__ | Do not trim the 5-prime end of contigs whose mappings overlap the previously-placed contig. Default: Overlapping contig sequence will be trimmed at the previous 3-prime contig breakpoint. |
         
         ## Output
         
@@ -74,7 +76,10 @@ Description: # GPatch
         ## Citing GPatch
         Please use the following citation if you use this software in your work:
         
-        CITATION_HERE
+        Fast and Accurate Draft Genome Patching with GPatch
+        Adam Diehl, Alan Boyle
+        bioRxiv 2025.05.22.655567; doi: https://doi.org/10.1101/2025.05.22.655567
+        
 Keywords: genomics,genome assembly
 Platform: UNKNOWN
 Classifier: Development Status :: 4 - Beta

{GPatch-0.3.5 → GPatch-0.3.8}/README.md

@@ -32,8 +32,8 @@ Installation from the github repository is not recommended. However, if you must
 
 ## Usage
 ```
-usage: GPatch [-h] -q SAM/BAM -r FASTA [-x BED] [-b FILENAME] [-m N]
-                       [-d N] [-f FLOAT] [-e FLOAT]
+usage: GPatch.py [-h] -q SAM/BAM -r FASTA [-x STR] [-b FILENAME] [-m N]
+                 [-w PATH] [-d]
 ```
 
 Starting with alignments of contigs to a reference genome, produce a chromosome-scale pseudoassembly by patching gaps between mapped contigs with sequences from the reference. Reference chromosomes with no mapped contigs are printed to output unchanged.
@@ -51,7 +51,9 @@ Starting with alignments of contigs to a reference genome, produce a chromosome-
 | __-x STR, --prefix STR__ | Prefix to add to output file names. Default=None |
 | __-b FILENAME, --store_final_bam FILENAME__ | Store the final set of primary contig alignments to the given file name. Default: Do not store the final BAM. |
 | __-m N, --min_qual_score N__ | Minimum mapping quality score to retain an alignment. Default=30 |
-
+| __-w PATH, --whitelist PATH__ | Path to BED file containing whitelist regions: i.e., the inverse of blacklist regions. Supplying this will have the effect of excluding alignments that fall entirely within blacklist regions. Default=None |
+| __-d, --drop_missing__ | Omit unpatched reference chromosome records from the output if no contigs map to them. Default: Unpatched chromosomes are printed to output unchanged. |
+| __-t, --no_trim__ | Do not trim the 5-prime end of contigs whose mappings overlap the previously-placed contig. Default: Overlapping contig sequence will be trimmed at the previous 3-prime contig breakpoint. |
 
 ## Output
 
@@ -66,4 +68,6 @@ GPatch produces three output files:
 ## Citing GPatch
 Please use the following citation if you use this software in your work:
 
-CITATION_HERE
+Fast and Accurate Draft Genome Patching with GPatch
+Adam Diehl, Alan Boyle
+bioRxiv 2025.05.22.655567; doi: https://doi.org/10.1101/2025.05.22.655567

{GPatch-0.3.5 → GPatch-0.3.8}/setup.py

@@ -29,7 +29,7 @@ def main():
 
     metadata = dict(
         name="GPatch",
-        version="0.3.5",
+        version="0.3.8",
         author="Adam Diehl",
         author_email="adadiehl@umich.edu",
         description="Assemble contigs into a chromosome-scalse pseudo-assembly using alignments to a reference sequence.",

{GPatch-0.3.5 → GPatch-0.3.8}/src/GPatch/GPatch.py

@@ -7,7 +7,7 @@ from Bio.Seq import Seq
 import pysam
 import random
 
-__version__ = "0.3.5"
+__version__ = "0.3.8"
 
 """
 Given a name-sorted BAM file, cluster mapped reads by name and
@@ -21,16 +21,25 @@ def create_primary_alignments_list(query_bam, min_qual_score):
     Extract all primary alignments from the BAM file and return
     as a list.
     """
+    #i = 0
+    #j = 0
+    #k = 0
+    #l = 0
     ret = []
     for aln in query_bam:
+        #i += 1
         if aln.is_unmapped:
             # Skip unmapped contigs
+            #j += 1
             continue
         if aln.mapping_quality < min_qual_score:
             # Skip low-quality mappings
+            #k += 1
             continue
         if not (aln.is_supplementary or aln.is_secondary):
+            #l += 1
             ret.append(aln)
+    #sys.stderr.write("%d\t%d\t%d\t%d\t%d\n" % (i, j, k, l, len(ret)))
     return ret
 
 
@@ -45,7 +54,9 @@ def contig_breakpoints_from_cigar(primary_alignments):
         chrom = contig.reference_name
         start = contig.reference_start
         end = contig.reference_end
+        #sys.stderr.write("%s\t%s\t%s\n" % (chrom, start, end))
         # Check for left and right soft-clips
+        #sys.stderr.write("%s\n%s\n" % (contig.cigartuples[0], contig.cigartuples[-1]))
         if contig.cigartuples[0][0] == 4:
             # left soft-clip
             start -= contig.cigartuples[0][1]
@@ -53,6 +64,7 @@ def contig_breakpoints_from_cigar(primary_alignments):
             # right soft-clip
             end += contig.cigartuples[-1][1]
         contig_breakpoints[contig.query_name] = [chrom, start, end, contig.query_name]
+        #sys.stderr.write("%s\n" % (contig_breakpoints))
 
     return contig_breakpoints
     
@@ -168,6 +180,9 @@ def main():
     parser.add_argument('-d', '--drop_missing',
                         required=False, default=False, action="store_true",
                         help='Omit unpatched reference chromosome records from the output if no contigs map to them. Default: Unpatched chromosomes are printed to output unchanged.')
+    parser.add_argument('-t', '--no_trim',
+                        required=False, default=False, action="store_true",
+                        help='Do not trim the 5-prime end of contigs whose mappings overlap the previously-placed contig. Default: Overlapping contig sequence will be trimmed at the previous 3-prime contig breakpoint.')
     
     args = parser.parse_args()
 
@@ -204,6 +219,7 @@ def main():
     for ref_seq in SeqIO.parse(args.reference_fasta, "fasta"):
         # Select all contigs mapped to this sequence.
         contigs = list(sorted_primary_alignments.fetch(ref_seq.id))
+        #sys.stderr.write("%s\t%s\n" % (ref_seq.id, contigs))
 
         # Convert the list of contigs into a list of tuples: (start, end, name),
         # representing the inferred contig breakpoints, sorted by start, then end position.
@@ -265,11 +281,16 @@ def main():
         patched_seq = ""
         for contig in contigs:
             rstart = contig_breakpoints[contig.query_name][1]
+            """
+            # This introduced a one-off error! We don't need to do this
+            # because all coordinates are already in proper zero-based form.
             if rstart > 0:
                 rstart -= 1
+            """
 
             # Check for overlapping/bookended contig mappings.
             qstart = 0  # Start of contig interval to append
+            #sys.stderr.write("%s\t%s\t%s\n" % (rstart, pos, pos-rstart))
             if rstart > pos:
                 # No overlap. Append the patch, in all lower-case
                 # for easy identification.
@@ -278,8 +299,18 @@ def main():
                 patches_bed.write("%s\t%d\t%d\n" % (ref_seq.id, pos, rstart))
             else:
                 # Handle overlapping contig ends by trimming the 5' end of
-                # this contig sequence by the length of the overlap.
-                qstart = pos - rstart
+                # this contig sequence by the length of the overlap. Note this
+                # evaluates to zero if contigs are bookended (i.e., pos and
+                # rstart are equal.)
+                if not args.no_trim:
+                    qstart = pos - rstart
+                    if qstart > len(Seq(contig.query_sequence)):
+                        # This should not happen, as it is indicative of a nested
+                        # mapping, which should be filtered out prior to sequence-
+                        # building. However, I have seen instances of nested mappings
+                        # that somehow slip through the cracks. This is a hack to fix
+                        # those instances until I can figure out why it happens.
+                        continue
                 
             # Append the contig sequence to the patched sequence string
             contig_start = len(patched_seq)
@@ -299,14 +330,17 @@ def main():
 
             # Update the current position in the reference sequence if the
             # end position of the current contig is 3' of the current pos.
+            #sys.stderr.write("%s\t%s\t%s\n" % (pos, contig_breakpoints[contig.query_name][2], len(ref_seq.seq)))
             if contig_breakpoints[contig.query_name][2] > pos:
                 # This should always evaluate true in the absence of nested contigs.
                 pos = contig_breakpoints[contig.query_name][2]
-            
+                
         # Once the above loop finishes, we need to add the terminal segment
         # from the reference genome.
-        patched_seq = patched_seq + ref_seq.seq[pos:len(ref_seq.seq)]
-        patches_bed.write("%s\t%d\t%d\n" % (ref_seq.id, pos, len(ref_seq.seq)))
+        if pos < len(ref_seq.seq):
+            #sys.stderr.write("%s\n" % (ref_seq.seq[pos:len(ref_seq.seq)]))
+            patched_seq = patched_seq + ref_seq.seq[pos:len(ref_seq.seq)]
+            patches_bed.write("%s\t%d\t%d\n" % (ref_seq.id, pos, len(ref_seq.seq)))
 
         # Swap in the patched sequence for the reference sequence and print the result 
         ref_seq.seq = patched_seq

{GPatch-0.3.5 → GPatch-0.3.8/src/GPatch.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: GPatch
-Version: 0.3.5
+Version: 0.3.8
 Summary: Assemble contigs into a chromosome-scalse pseudo-assembly using alignments to a reference sequence.
 Home-page: https://github.com/adadiehl/GPatch
 Author: Adam Diehl
@@ -40,8 +40,8 @@ Description: # GPatch
         
         ## Usage
         ```
-        usage: GPatch [-h] -q SAM/BAM -r FASTA [-x BED] [-b FILENAME] [-m N]
-                               [-d N] [-f FLOAT] [-e FLOAT]
+        usage: GPatch.py [-h] -q SAM/BAM -r FASTA [-x STR] [-b FILENAME] [-m N]
+                         [-w PATH] [-d]
         ```
         
         Starting with alignments of contigs to a reference genome, produce a chromosome-scale pseudoassembly by patching gaps between mapped contigs with sequences from the reference. Reference chromosomes with no mapped contigs are printed to output unchanged.
@@ -59,7 +59,9 @@ Description: # GPatch
         | __-x STR, --prefix STR__ | Prefix to add to output file names. Default=None |
         | __-b FILENAME, --store_final_bam FILENAME__ | Store the final set of primary contig alignments to the given file name. Default: Do not store the final BAM. |
         | __-m N, --min_qual_score N__ | Minimum mapping quality score to retain an alignment. Default=30 |
-        
+        | __-w PATH, --whitelist PATH__ | Path to BED file containing whitelist regions: i.e., the inverse of blacklist regions. Supplying this will have the effect of excluding alignments that fall entirely within blacklist regions. Default=None |
+        | __-d, --drop_missing__ | Omit unpatched reference chromosome records from the output if no contigs map to them. Default: Unpatched chromosomes are printed to output unchanged. |
+        | __-t, --no_trim__ | Do not trim the 5-prime end of contigs whose mappings overlap the previously-placed contig. Default: Overlapping contig sequence will be trimmed at the previous 3-prime contig breakpoint. |
         
         ## Output
         
@@ -74,7 +76,10 @@ Description: # GPatch
         ## Citing GPatch
         Please use the following citation if you use this software in your work:
         
-        CITATION_HERE
+        Fast and Accurate Draft Genome Patching with GPatch
+        Adam Diehl, Alan Boyle
+        bioRxiv 2025.05.22.655567; doi: https://doi.org/10.1101/2025.05.22.655567
+        
 Keywords: genomics,genome assembly
 Platform: UNKNOWN
 Classifier: Development Status :: 4 - Beta