mv some files to utility

1 files changed, 107 insertions, 0 deletions

diff --git a/utility/topGene_step1_cnt_abstracts.py b/utility/topGene_step1_cnt_abstracts.py
new file mode 100755
index 0000000..420c9cf
--- /dev/null
+++ b/utility/topGene_step1_cnt_abstracts.py
@@ -0,0 +1,107 @@
+#!/bin/env python3 
+import os
+import sys
+import re
+import time
+from ratspub_keywords import *
+
+def undic(dic):
+    return "|".join(dic.values())
+
+def gene_addiction_cnt(gene):
+    time.sleep(0.2)
+    q="\'(\"" + addiction.replace("|", "\"[tiab] OR \"")  + "\") AND (\"" + drug.replace("|", "\"[tiab] OR \"", ) + "\") AND (\"" + gene + "\")\'"
+    count=os.popen('esearch -db pubmed  -query ' + q + ' | xtract -pattern ENTREZ_DIRECT -element Count ').read()
+    if (len(count)==0):
+        print("pause")
+        time.sleep(15)
+        return gene_addiction_cnt(gene)
+    else:
+        return (count)
+
+def removeStopWords(terms):
+    out=str()
+    for one in terms.upper().split("|"):
+       if one not in stopWords:
+            out+="|"+one
+    return(out[1:])
+
+def saveStopWord(w):
+    with open (stopword_f,"a") as swf:
+        swf.write(w+"\n")
+    return
+
+# either start with ncbi_gene_symb_syno_name_txid9606 for fresh new counts
+# or recount the results after adding additional stopwords
+
+if len(sys.argv)==2:
+    input_f=sys.argv[1]
+else:
+    input_f="./ncbi_gene_symb_syno_name_txid9606.txt"
+
+addiction=undic(addiction_d)
+drug=undic(drug_d)
+output_f=input_f.replace(".txt","_absCnt.txt")
+out=open(output_f, "w+")
+
+stopword_f="./stop_words_addiction_gene_search.txt"
+with open (stopword_f, "r") as swf:
+    stopWords=swf.read().upper().split("\n")
+    swf.close()
+
+with open (input_f, "r") as f:
+    for line in f:
+        do_search=0
+        inputline=line
+        line=line.replace("-","\ ")
+        # remove the annotated stopword
+        if "'" in line:
+            do_search=1
+            words=line.split("|")
+            line=str()
+            for word in words:
+                # ' is used to mark/annotate a word is a stop word in the results
+                # remove the ' mark 
+                if "'" in word:
+                    word=word.replace("'","")
+                    stopWords.append(word)
+                    saveStopWord(word)
+                line+="|"+word
+            line=line[1:]
+        line=removeStopWords(line)
+        # tab is added if there are abstracts counts
+        if "\t" in line:
+            (gene, count)=line.split("\t")
+            # rerun if count is low, these are less annotated
+        #    if int(count)<50:
+        #        do_search=1
+        else:
+            #no count, 
+            gene=line.strip()
+            do_search=1
+        if do_search==1:
+            # remove synonyms with only two letters
+            if "|" in gene:
+                synos=gene.split("|")
+                # keep the gene name regardless number of characters
+                gene=synos[0]
+                #print ("gene: "+gene + " synos -->" + str(synos[1:]))
+                for syno in synos[1:]:
+                    #synonyms must be at least 3 characters
+                    if len(syno)>3:
+                        gene+="|"+syno
+            gene_q=gene.replace("|", "\"[tiab] OR \"")
+            gene_q+="[tiab]"
+            count=gene_addiction_cnt(gene_q)
+            print("original line->\t"+inputline.strip())
+            print("stopword rmed->\t"+line.strip())
+            print("final  result->\t"+gene+"\t"+count)
+            out.write(gene+"\t"+count)
+        else:
+            print("original resl->\t"+inputline.strip())
+            out.write(inputline)
+
+sorted_f=output_f.replace(".txt","_sorted.txt")
+os.system("sort -k2 -t$'\t' -rn " + output_f + " > " + sorted_f )
+
+