Merge branch 'master' of https://github.com/mnshgl0110/hometools

Author: mnshgl0110

hometools/hometools.py

@@ -1773,6 +1773,46 @@ def pbamrc(args):
 # END
 
 
+def bamrc2af(args):
+    """
+    Reads the output of pbamrc and a corresponding VCF file and returns the allele frequencies of the alt alleles.
+    Currently, working for SNPs only
+    """
+    from gzip import open as gzopen
+    logger = mylogger("bamrc2af")
+    rcfin = args.bamrc.name
+    vcffin = args.vcf.name
+    outfin = 'bamrc_af.txt' if args.out is None else args.out.name
+
+    logger.info('Reading VCF')
+    posdict = dict()
+    op = gzopen if isgzip(vcffin) else open
+    with op(vcffin, 'r') as vcf:
+        for line in vcf:
+            # break
+            if line[0] == 35: continue
+            line = line.decode()
+            line = line.strip().split()
+            if line[4].upper() not in 'ACGT' : continue
+            posdict[tuple(line[:2])] = line[3], line[4]
+
+    logger.info('Reading bamrc')
+    # Get AF from bam readcount
+    basedict = dict(zip('ACGT', range(4, 8)))
+    with open(rcfin, 'r') as rc, open(outfin, 'w') as out:
+        for line in rc:
+            line = line.strip().split()
+            try:
+                ref, alt = posdict[(line[0], line[1])]
+            except KeyError:
+                logger.warning(f'Position {line[0]}:{line[1]} not found in VCF. Skipping it.')
+            refi = basedict[ref]
+            alti = basedict[alt]
+            out.write(f'{line[0]}\t{line[1]}\t{ref}\t{alt}\t{round(int(line[refi])/int(line[3]) , 2)}\t{round(int(line[alti])/int(line[3]), 2)}\n')
+    logger.info('Finishe')
+# END
+
+
 def run_ppileup(locs, out, bam, pars):
     from subprocess import Popen, PIPE
     with open(out, 'w') as fout:
@@ -2569,22 +2609,29 @@ def main(cmd):
     # <editor-fold desc="BAM Commands">
     parser_bamcov = subparsers.add_parser("bamcov", help="BAM: Get mean read-depth for chromosomes from a BAM file", formatter_class=argparse.ArgumentDefaultsHelpFormatter)
     parser_pbamrc = subparsers.add_parser("pbamrc", help="BAM: Run bam-readcount in a parallel manner by dividing the input bed file.", formatter_class=argparse.ArgumentDefaultsHelpFormatter)
+    parser_bamrc2af = subparsers.add_parser("bamrc2af", help="BAM: Reads the output of pbamrc and a corresponding VCF file and saves the allele frequencies of the ref/alt alleles.", formatter_class=argparse.ArgumentDefaultsHelpFormatter)
     parser_splitbam = subparsers.add_parser("splitbam", help="BAM: Split a BAM files based on TAG value. BAM file must be sorted using the TAG.", formatter_class=argparse.ArgumentDefaultsHelpFormatter)
     parser_mapbp = subparsers.add_parser("mapbp", help="BAM: For a given reference coordinate get the corresponding base and position in the reads/segments mapping the reference position", formatter_class=argparse.ArgumentDefaultsHelpFormatter)
     parser_bam2coords = subparsers.add_parser("bam2coords", help="BAM: Convert BAM/SAM file to alignment coords", formatter_class=argparse.ArgumentDefaultsHelpFormatter)
     parser_ppileup = subparsers.add_parser("ppileup", help="BAM: Currently it is slower than just running mpileup on 1 CPU. Might be possible to optimize later. Run samtools mpileup in parallel when pileup is required for specific positions by dividing the input bed file.", formatter_class=argparse.ArgumentDefaultsHelpFormatter)
     # </editor-fold>
 
+    # <editor-fold desc="syri CLI">
+    parser_runsyri = subparsers.add_parser("runsyri", help=hyellow("syri: Parser to align and run syri on two genomes"),
+                                           formatter_class=argparse.ArgumentDefaultsHelpFormatter)
+    parser_syriidx = subparsers.add_parser("syriidx", help=hyellow(
+        "syri: Generates index for syri.out. Filters non-SR annotations, then bgzip, then tabix index"),
+                                           formatter_class=argparse.ArgumentDefaultsHelpFormatter)
+    parser_syri2bed = subparsers.add_parser("syri2bed", help=hyellow("syri: Converts syri output to bedpe format"),
+                                            formatter_class=argparse.ArgumentDefaultsHelpFormatter)
+    # </editor-fold>
 
-    ## syri
-    parser_runsyri = subparsers.add_parser("runsyri", help=hyellow("syri: Parser to align and run syri on two genomes"), formatter_class=argparse.ArgumentDefaultsHelpFormatter)
-    parser_syriidx = subparsers.add_parser("syriidx", help=hyellow("syri: Generates index for syri.out. Filters non-SR annotations, then bgzip, then tabix index"), formatter_class=argparse.ArgumentDefaultsHelpFormatter)
-    parser_syri2bed = subparsers.add_parser("syri2bed", help=hyellow("syri: Converts syri output to bedpe format"), formatter_class=argparse.ArgumentDefaultsHelpFormatter)
-
-    ## Plotting
+    # <editor-fold desc="Plotting">
     parser_plthist = subparsers.add_parser("plthist", help="Plot: Takes frequency output (like from uniq -c) and generates a histogram plot", formatter_class=argparse.ArgumentDefaultsHelpFormatter)
     parser_plotal = subparsers.add_parser("plotal", help="Plot: Visualise pairwise-whole genome alignments between multiple genomes", formatter_class=argparse.ArgumentDefaultsHelpFormatter)
     parser_plotbar = subparsers.add_parser("pltbar", help="Plot: Generate barplot. Input: a two column file with first column as features and second column as values", formatter_class=argparse.ArgumentDefaultsHelpFormatter)
+    # </editor-fold>
+
 
     ## Assembly graphs
     parser_asmreads = subparsers.add_parser("asmreads", help=hyellow("GFA: For a given genomic region, get reads that constitute the corresponding assembly graph"), formatter_class=argparse.ArgumentDefaultsHelpFormatter)
@@ -2607,6 +2654,12 @@ def main(cmd):
         parser.print_help()
         sys.exit()
 
+    # bamrc2af
+    parser_bamrc2af.set_defaults(func=bamrc2af)
+    parser_bamrc2af.add_argument("bamrc", help="BAM readcount file generated using bamrc", type=argparse.FileType('r'))
+    parser_bamrc2af.add_argument("vcf", help="VCF file", type=argparse.FileType('r'))
+    parser_bamrc2af.add_argument("out", help="Output file", type=argparse.FileType('w'))
+
     # xls2csv
     parser_xls2tsv.set_defaults(func=xls2csv)
     parser_xls2tsv.add_argument("xls", help="Input excel file", type=argparse.FileType('r'))