diff find_str.py @ 0:2b970db61912 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/microsatbed commit 275acb787c01484c6e435c8864090d377c3fde75
author iuc
date Sun, 21 Jul 2024 07:19:00 +0000
parents
children 5f8efb080f49
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/find_str.py	Sun Jul 21 07:19:00 2024 +0000
@@ -0,0 +1,127 @@
+import argparse
+import subprocess
+
+import pytrf  # 1.3.0
+from pyfastx import Fastx  # 0.5.2
+
+"""
+Allows all STR or those for a subset of motifs to be written to a bed file
+Designed to build some of the microsatellite tracks from https://github.com/arangrhie/T2T-Polish/tree/master/pattern for the VGP.
+"""
+
+
+def getDensity(name, bed, chrlen, winwidth):
+    """
+    pybigtools can write bigwigs and they are processed by other ucsc tools - but jb2 will not read them.
+    Swapped the conversion to use a bedgraph file processed by bedGraphToBigWig
+    """
+    nwin = int(chrlen / winwidth)
+    d = [0.0 for x in range(nwin + 1)]
+    for b in bed:
+        nt = b[5]
+        bin = int(b[1] / winwidth)
+        d[bin] += nt
+    bedg = [
+        (name, (x * winwidth), ((x + 1) * winwidth) - 1, float(d[x]))
+        for x in range(nwin + 1)
+        if (x + 1) * winwidth <= chrlen
+    ]
+    return bedg
+
+
+def write_ssrs(args):
+    """
+    The integers in the call change the minimum repeats for mono-, di-, tri-, tetra-, penta-, hexa-nucleotide repeats
+    ssrs = pytrf.STRFinder(name, seq, 10, 6, 4, 3, 3, 3)
+    NOTE: Dinucleotides GA and AG are reported separately by https://github.com/marbl/seqrequester.
+    The reversed pair STRs are about as common in the documentation sample.
+    Sequence read bias might be influenced by GC density or some other specific motif.
+    """
+    bed = []
+    wig = []
+    chrlens = {}
+    specific = None
+    if args.specific:
+        specific = args.specific.upper().split(",")
+    fa = Fastx(args.fasta, uppercase=True)
+    for name, seq in fa:
+        chrlen = len(seq)
+        chrlens[name] = chrlen
+        cbed = []
+        for ssr in pytrf.STRFinder(
+            name,
+            seq,
+            args.monomin,
+            args.dimin,
+            args.trimin,
+            args.tetramin,
+            args.pentamin,
+            args.hexamin,
+        ):
+            row = (
+                ssr.chrom,
+                ssr.start,
+                ssr.end,
+                ssr.motif,
+                ssr.repeat,
+                ssr.length,
+            )
+            if args.specific and ssr.motif in specific:
+                cbed.append(row)
+            elif args.mono and len(ssr.motif) == 1:
+                cbed.append(row)
+            elif args.di and len(ssr.motif) == 2:
+                cbed.append(row)
+            elif args.tri and len(ssr.motif) == 3:
+                cbed.append(row)
+            elif args.tetra and len(ssr.motif) == 4:
+                cbed.append(row)
+            elif args.penta and len(ssr.motif) == 5:
+                cbed.append(row)
+            elif args.hexa and len(ssr.motif) == 6:
+                cbed.append(row)
+        if args.bigwig:
+            w = getDensity(name, cbed, chrlen, args.winwidth)
+            wig += w
+        bed += cbed
+    if args.bigwig:
+        wig.sort()
+        bedg = ["%s %d %d %.2f" % x for x in wig]
+        with open("temp.bedg", "w") as bw:
+            bw.write("\n".join(bedg))
+        chroms = ["%s\t%s" % (x, chrlens[x]) for x in chrlens.keys()]
+        with open("temp.chromlen", "w") as cl:
+            cl.write("\n".join(chroms))
+        cmd = ["bedGraphToBigWig", "temp.bedg", "temp.chromlen", args.bed]
+        subprocess.run(cmd)
+    else:
+        bed.sort()
+        obed = ["%s\t%d\t%d\t%s_%d\t%d" % x for x in bed]
+        with open(args.bed, "w") as outbed:
+            outbed.write("\n".join(obed))
+            outbed.write("\n")
+
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser()
+    a = parser.add_argument
+    a("--di", action="store_true")
+    a("--tri", action="store_true")
+    a("--tetra", action="store_true")
+    a("--penta", action="store_true")
+    a("--hexa", action="store_true")
+    a("--mono", action="store_true")
+    a("--dimin", default=2, type=int)
+    a("--trimin", default=2, type=int)
+    a("--tetramin", default=2, type=int)
+    a("--pentamin", default=2, type=int)
+    a("--hexamin", default=2, type=int)
+    a("--monomin", default=2, type=int)
+    a("-f", "--fasta", default="humsamp.fa")
+    a("-b", "--bed", default="humsamp.bed")
+    a("--bigwig", action="store_true")
+    a("--winwidth", default=128, type=int)
+    a("--specific", default=None)
+    a("--minreps", default=2, type=int)
+    args = parser.parse_args()
+    write_ssrs(args)