diff cpt_related_genome_prot/relatedness_prot.py @ 0:ebcc87a27f9c draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cpt_related_genome_prot/relatedness_prot.py	Fri Jun 10 08:46:28 2022 +0000
@@ -0,0 +1,254 @@
+#!/usr/bin/env python
+import sys
+import argparse
+import json
+import logging
+from Bio.Blast import NCBIXML
+
+logging.basicConfig(level=logging.DEBUG)
+log = logging.getLogger()
+
+def parse_blast(blast, isXML = False):
+    res = []
+    finalRes = []
+    if isXML:
+      for iter_num, blast_record in enumerate(NCBIXML.parse(blast), 1):
+        for alignment in blast_record.alignments:
+            tempID = alignment.hit_id[alignment.hit_id.find("gb|") + 3:]
+            tempID = tempID[:tempID.find("|")]
+            tempDesc = alignment.title
+            while tempDesc.find("|") >= 0:
+              tempDesc = tempDesc[tempDesc.find("|") + 1:]
+            tempDesc = tempDesc.strip()
+            tempID = tempID.strip()
+            #for hsp in alignment.hsps:
+            line = [str(blast_record.query)[:str(blast_record.query).find("[")].strip()]
+            line.append(alignment.hit_id)
+            line.append(tempDesc)
+            line.append(alignment.accession)
+            res.append(line)
+      blast.seek(0)
+      resInd = -1
+      taxLine = blast.readline()
+      while taxLine: 
+        if "<Hit>" in taxLine:
+          resInd += 1
+          taxSlice = ""
+        elif "<taxid>" in taxLine:
+          taxSlice = taxLine[taxLine.find("<taxid>") + 7:taxLine.find("</taxid>")]
+          finalRes.append(res[resInd])
+          finalRes[-1].append(taxSlice)
+        taxLine = blast.readline()
+      return finalRes
+    else:
+      for line in blast:
+        finalRes.append(line.strip("\n").split("\t"))
+    return finalRes
+
+def with_dice(blast):
+    for data in blast:
+        dice = 2 * int(data[14]) / (float(data[22]) + float(data[23]))
+        yield data + [dice]
+
+
+def filter_dice(blast, threshold=0.5):
+    for data in blast:
+        if data[-1] > threshold:
+            yield data
+
+
+def split_identifiers_nucl(_, ident):
+    if "<>" in ident:
+        idents = ident.split("<>")
+    else:
+        idents = [ident]
+    return idents
+
+
+def split_identifiers_prot(_, ident):
+    if "<>" in ident:
+        idents = ident.split("<>")
+    else:
+        idents = [ident]
+    return [
+        x[x.index("[") + 1 : x.rindex("]")]
+        for x in idents
+        # MULTISPECIES: recombination-associated protein RdgC [Enterobacteriaceae]<>RecName: Full=Recombination-associated protein RdgC<>putative exonuclease, RdgC [Enterobacter sp. 638]
+        if "[" in x and "]" in x
+    ]
+
+
+def split_identifiers_phage(par, ident):
+    par = par.replace("lcl|", "")
+    par = par[0 : par.index("_prot_")]
+    return [par]
+
+
+def important_only(blast, split_identifiers):
+    for data in blast:
+        yield [
+            data[0],  # 01 Query Seq-id (ID of your sequence)
+            data[1],  # 13 All subject Seq-id(s), separated by a ';'
+            split_identifiers(
+                data[1], data[2]
+            ),  # 25 All subject title(s), separated by a '<>'
+            data[3].split(";"),  # Extra: All Subject Accessions
+            data[4].split(";"),  # Extra: All TaxIDs
+        ]
+
+
+def deform_scores(blast):
+    for data in blast:
+        for org in data[2]:
+            yield [data[0], data[1], org, data[3], data[4]]
+
+
+def expand_fields(blast):
+    for data in blast:
+        for x in range(0, len(data[4])):
+            yield [data[0], data[1], data[2][x], data[3], int(data[4][x])]
+
+def expand_taxIDs(blast, taxFilter):
+    for data in blast:
+        # if(len(data[4]) > 0):
+        #  print(data[0])
+        for ID in data[4]:
+            if ID != "N/A":
+              filterOut = False
+              for tax in taxFilter:
+                if str(ID).strip() == tax:
+                  filterOut = True
+              if not filterOut:
+                yield [data[0], data[1], data[2], data[3], int(ID)]
+
+
+def expand_titles(blast):
+    for data in blast:
+        for title in data[2]:
+            yield [data[0], data[1], title, data[3], data[4]]
+
+
+def filter_phage(blast, phageTaxLookup, phageSciNames):
+    for data in blast:
+        for x in range(0, len(phageTaxLookup)):
+            if (data[4]) == phageTaxLookup[x]:
+                yield [data[0], data[1], phageSciNames[x], data[3], data[4]]
+                break
+
+
+def remove_dupes(data):
+    has_seen = {}
+    for row in data:
+        # qseqid, sseqid
+        key = (row[0], row[4])
+        # If we've seen the key before, we can exit
+        if key in has_seen:
+            continue
+
+        # Otherwise, continue on
+        has_seen[key] = True
+        # Pretty simple
+        yield row
+
+def scoreMap(blast):
+    c = {}
+    m = {}
+    for (qseq, subID, subTitle, access, ID) in blast:
+        if (str(subTitle), ID) not in c:
+            m[(str(subTitle), ID)] = access
+            c[(str(subTitle), ID)] = 0
+
+        c[(str(subTitle), ID)] += 1
+    return c, m
+
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(description="Top related genomes")
+    parser.add_argument(
+        "blast", type=argparse.FileType("r"), help="Blast 25 Column Results"
+    )
+    parser.add_argument("phagedb", type=argparse.FileType("r"))
+    parser.add_argument("--access", action="store_true")
+    parser.add_argument("--protein", action="store_true")
+    parser.add_argument("--canonical", action="store_true")
+    parser.add_argument("--noFilter", action="store_true")
+    #parser.add_argument("--title", action="store_true") # Add when ready to update XML after semester
+    parser.add_argument("--hits", type=int, default=5)
+    parser.add_argument("--xmlMode", action="store_true")   
+    parser.add_argument("--taxFilter", type=str) 
+
+    args = parser.parse_args()
+
+    phageDb = args.phagedb
+    phageTaxLookup = []
+    sciName = []
+    line = phageDb.readline()
+    
+    taxList = []
+    if args.taxFilter and args.taxFilter != "" :
+      args.taxFilter = args.taxFilter.split(" ")
+      for ind in args.taxFilter:
+        taxList.append(ind.strip())
+
+    while line:
+        line = line.split("\t")
+        phageTaxLookup.append(int(line[0]))
+        line[1] = line[1].strip()
+        if (line[1] == ""):
+            line[1] = "Novel Genome"
+        sciName.append(line[1])
+        line = phageDb.readline()
+
+    if args.protein:
+        splitId = split_identifiers_prot
+        # phageNameLookup = {k['source'].rstrip('.'): k['id'] for k in phageDb}
+    elif args.canonical:
+        splitId = split_identifiers_phage
+        # phageNameLookup = {k['source'].rstrip('.'): k['id'] for k in phageDb}
+    else:
+        splitId = split_identifiers_nucl
+        # phageNameLookup = {k['desc'].rstrip('.'): k['id'] for k in phageDb}
+
+    data = parse_blast(args.blast, args.xmlMode)
+    # data = with_dice(data)
+    # data = filter_dice(data, threshold=0.0)
+    data = important_only(data, splitId)
+    
+    data = expand_taxIDs(data, taxList)
+    data = remove_dupes(data)
+    if not args.noFilter:
+        data = filter_phage(data, phageTaxLookup, sciName)
+    listify = []
+    for x in data:
+        listify.append(x)
+    #listify = greatest_taxID(listify)
+       
+    count_label = "Similar Unique Proteins"
+    
+    counts, accessions = scoreMap(listify)
+    
+    nameRec = listify[0][0]
+    sys.stdout.write(
+            "Top %d matches for BLASTp results of %s\n"
+            % (args.hits, nameRec)
+        )
+    header = "# TaxID\t"
+    #if args.title:
+    header += "Name\t"
+    if args.access:
+        header += "Accessions\t"
+    header += "Similar Unique Proteins\n"
+    sys.stdout.write(header)
+
+    for idx, ((name, ID), num) in enumerate(
+            sorted(counts.items(), key=lambda item: -item[1])
+        ):
+        if idx > args.hits - 1:
+            break
+        line = str(ID) + "\t"
+        #if args.title:
+        line += str(name) + "\t"
+        if args.access:
+          line += str(accessions[(name, ID)][0]) + "\t"
+        line += str(num) + "\n" 
+        sys.stdout.write(line)