Add script to check update.

check/check.py

@@ -0,0 +1,127 @@
+#!/usr/local/bin/python3
+# coding: utf-8
+
+############################
+# Import
+############################
+import os
+import sys
+import argparse
+import subprocess
+from subprocess import Popen, PIPE
+import shutil
+
+############################
+# Global Variables
+############################
+
+############################
+# Functions
+############################
+
+
+def check_file(file):
+    """
+    Check if a file exist and is readable
+    """
+    if not os.path.isfile(file) or not os.access(file, os.R_OK):
+        print("the file " + file + " is missing or not readable.\n")
+        PARSER.print_help()
+        sys.exit(1)
+
+def List_to_dic(filename):
+    """
+    Send a file (three columns : sample, phylogroup and mashgroup with header) to a list
+    """
+
+    dico={}
+    with open(filename, "r") as f:
+        f.readline()
+        for line in f:
+            try:
+                sample, phylo, mash=line.strip().split("\t")
+                dico[sample]={}
+                dico[sample]['phylo']=phylo
+                dico[sample]['mash']=mash
+            except ValueError:
+                pass
+
+    return dico
+
+def Html_to_dic(filename):
+    """
+    Send a file (three columns : sample, phylogroup and mashgroup with header) to a list
+    """
+
+    dico={}
+    with open(filename, "r", encoding="utf-8") as f:
+        for line in f:
+            if '<tr class="odd">' in line or '<tr class="even">' in line:
+                sample=f.readline().strip()
+                sample_tmp=sample.replace('<td align="left">', '')
+                sample=sample_tmp.replace('</td>', '')
+                f.readline()
+                f.readline()
+                phylo=f.readline().strip()
+                phylo_tmp=phylo.replace('<td align="left">', '')
+                phylo=phylo_tmp.replace('</td>', '')
+                mash=f.readline().strip()
+                mash_tmp=mash.replace('<td align="left">', '')
+                mash=mash_tmp.replace('</td>', '')
+                dico[sample]={}
+                dico[sample]['phylo']=phylo
+                dico[sample]['mash']=mash
+
+    return dico
+
+def comparaison(dico_old, dico_new):
+
+    with open('check.log', "w") as w:
+
+        for sample in dico_old.keys():
+            if dico_old[sample]['phylo'] != dico_new[sample]['phylo'] or dico_old[sample]['mash'] != dico_new[sample]['mash']:
+                sentence='Error with '+ sample 
+                sentence+="\tWaited :" + dico_old[sample]['phylo'] + '/' + dico_old[sample]['mash']
+                sentence+="\tNew : " + dico_new[sample]['phylo'] + '/' + dico_new[sample]['mash']
+
+                print(sentence)
+                w.write(sentence+"\n")
+
+
+
+
+############################
+# Main
+############################
+if __name__ == "__main__":
+
+    fastafile='fastafile'
+
+    # Clermontyping
+    if os.path.isdir('res_check'):
+        abso_dir = os.path.abspath('res_check')
+        shutil.rmtree(abso_dir)
+    cmd = ["../clermonTyping.sh", "--fastafile", fastafile, "--name", "res_check"]
+    subprocess.call(cmd)
+
+    ## 
+    inputList='ref_resultat'
+    check_file(inputList)
+    res_waited=List_to_dic(inputList)
+
+    inputHtml='res_check/res_check.html'
+    check_file(inputHtml)
+    res_new=Html_to_dic(inputHtml)
+
+    print('%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%')
+    comparaison(res_waited, res_new)
+    if os.stat('check.log').st_size == 0:
+        print("Congratulation! Database is updated succesfull.")
+    else:
+        print("ERROR!!! Look at the check.log file.")
+
+
+
+
+
+

check/fastafile

@@ -0,0 +1,49 @@
+db/042.fasta
+db/101-1.fasta
+db/327-20.fasta
+db/536.fasta
+db/53638.fasta
+db/55989.fasta
+db/APECO78.fasta
+db/ATCC35469T.fasta
+db/B1147.fasta
+db/B156.fasta
+db/B253.fasta
+db/B49.fasta
+db/B646.fasta
+db/B691.fasta
+db/B7A.fasta
+db/CFT073.fasta
+db/E1118.fasta
+db/E1426.fasta
+db/E1492.fasta
+db/E2348-69.fasta
+db/E24377A.fasta
+db/ECOR01.fasta
+db/ECOR31.fasta
+db/ECOR37.fasta
+db/ECOR42.fasta
+db/ECOR44.fasta
+db/ECOR46.fasta
+db/ECOR47.fasta
+db/ESC_BA9053AA_AS.fasta
+db/ESC_CA3818AA_AS.fasta
+db/ESC_FA7277AA_AS.fasta
+db/ESC_GA0630AA_AS.fasta
+db/ESC_GA5165AA_AS.fasta
+db/ESC_NA3019AA_AS.fasta
+db/ESC_NA8746AA_AS.fasta
+db/ESC_OA1838AA_AS.fasta
+db/H442.fasta
+db/H605.fasta
+db/H95.fasta
+db/IAI17.fasta
+db/IAI18.fasta
+db/IAI24.fasta
+db/IAI32.fasta
+db/IAI39.fasta
+db/IAI41.fasta
+db/IAI42.fasta
+db/ROAR8.fasta
+db/SMS35.fasta
+db/TA004.fasta

check/ref_resultat

@@ -0,0 +1,51 @@
+sample	Clermontyping	Mash
+E1492.fasta	cladeI	cladeI
+H442.fasta	cladeI	cladeI
+IAI32.fasta	cladeI	cladeI
+B1147.fasta	cladeII	cladeII
+ESC_NA3019AA_AS.fasta	cladeII	cladeII
+ESC_OA1838AA_AS.fasta	cladeII	cladeII
+ESC_GA5165AA_AS.fasta	cladeIII	cladeIII
+TA004.fasta	cladeIII	cladeIII
+ESC_BA9053AA_AS.fasta	cladeIII	cladeIII
+B49.fasta	cladeIV	cladeIV
+ESC_FA7277AA_AS.fasta	cladeIV	cladeIV
+H605.fasta	cladeIV	cladeIV
+B646.fasta	cladeV	cladeV
+E1118.fasta	cladeV	cladeV
+ESC_CA3818AA_AS.fasta	cladeV	cladeV
+53638.fasta	A	A
+101-1.fasta	A	A
+ECOR01.fasta	A	A
+B156.fasta	albertii	albertii
+ESC_GA0630AA_AS.fasta	albertii	albertii
+ESC_NA8746AA_AS.fasta	albertii	albertii
+55989.fasta	B1	B1
+B7A.fasta	B1	B1
+E24377A.fasta	B1	B1
+536.fasta	B2	B2
+CFT073.fasta	B2	B2
+E2348-69.fasta	B2	B2
+APECO78.fasta	C	C
+IAI18.fasta	C	C
+IAI41.fasta	C	C
+042.fasta	D	D
+ECOR46.fasta	D	D
+ECOR47.fasta	D	D
+IAI17.fasta	D	A
+ECOR31.fasta	E	E
+ECOR37.fasta	E	E
+ECOR42.fasta	E	E
+ECOR44.fasta	E	D
+IAI24.fasta	E	D
+IAI39.fasta	F	F
+SMS35.fasta	F	F
+ROAR8.fasta	F	F
+ATCC35469T.fasta	fergusonii	fergusonii
+B253.fasta	fergusonii	fergusonii
+B691.fasta	fergusonii	fergusonii
+327-20.fasta	G	G
+E1426.fasta	G	G
+H95.fasta	G	G
+IAI42.fasta	Unknown	C
+

clermonTyping.sh

@@ -10,8 +10,8 @@
 # 4] Launch in silicco PCR for getting phylogroup
 # 5] Reportings tools
 #
-# Current version : 20.03 (Mar. 2020)
-version="Clermont Typing  Current version : 20.03 (Mar. 2020)"
+# Current version : 20.08 (Aug. 2020)
+version="Clermont Typing  Current version : 20.08 (Aug. 2020)"
 
 # Contact: antoine.bridier-nahmias@inserm.fr