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Update 21.03 #35

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Empty file modified LICENSE
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17 changes: 11 additions & 6 deletions bin/clermont.py
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Original file line number Diff line number Diff line change
@@ -1,6 +1,11 @@
#!/usr/bin/env python3
"""
Current Version - 1.4.0: Fév. 2019
Current Version - 21.03: Mar 2021
21.03:
- Adding an essential primer for F group
- Change the mash database
21.02:
- Change arpAgpE primers by fdm primers for E group
1.4.0:
- Adding an essential primer for G group
1.3.0:
Expand Down Expand Up @@ -57,7 +62,7 @@
#Definition of Primers names and size of PCR product (bp)
class Primers:
def __init__(self):
self.names = {"trpA": 783, "trpBA": 489, "chuAalbertii": 136, "citPferg": 300, "chuA": 288, "yjaA": 211, "TspE4.C2": 152, "arpA": 400, "ArpAgpE": 301, "trpAgpC": 219, "aesI": 315, "aesII": 125, "chuIII": 183, "chuIV": 461, "chuV": 600, "ybgD": 177}
self.names = {"trpA": 783, "trpBA": 489, "chuAalbertii": 136, "citPferg": 300, "chuA": 288, "yjaA": 211, "TspE4.C2": 152, "arpA": 400, "fdm": 265, "trpAgpC": 219, "aesI": 315, "aesII": 125, "chuIII": 183, "chuIV": 461, "chuV": 600, "ybgD": 177, "cfaB" : 314}

###############################################################################
############# FUNCTIONS #############
Expand Down Expand Up @@ -203,7 +208,7 @@ def pcr_parser_groups(quadruplex):
quadruplex.append('-')
#return the specific primers (grp E or C disambiguity)
specific = []
specific_names = ["chuAalbertii", "citPferg", "aesI", "aesII", "chuIII", "chuIV", "chuV", 'ArpAgpE', 'trpAgpC']
specific_names = ["chuAalbertii", "citPferg", "aesI", "aesII", "chuIII", "chuIV", "chuV", 'fdm', 'trpAgpC', 'cfaB', 'ybgD']
for name in specific_names:
if name in pcr_products:
specific.append(name)
Expand All @@ -229,18 +234,18 @@ def find_phylo_group(markers):
return("cladeI")
else:
#Double check for clade E
if "ArpAgpE" in markers:
if "fdm" in markers:
return("E")
else:
return("E or cladeI")
else:
if "TspE4.C2" in markers:
if "ArpAgpE" in markers:
if "fdm" in markers:
return("E")
else:
return("D")
else:
if "ArpAgpE" in markers:
if "fdm" in markers:
return("E")
else:
return("D")
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4 changes: 2 additions & 2 deletions clermonTyping.sh → clermonTyping
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Expand Up @@ -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 : 21.03 (Mar. 2021)
version="Clermont Typing Current version : 21.03 (Mar. 2021)"

# Contact: antoine.bridier-nahmias@inserm.fr

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Binary file modified data/mash/mash_reference.msh
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12 changes: 8 additions & 4 deletions data/primers.fasta
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Original file line number Diff line number Diff line change
@@ -1,3 +1,7 @@
>cfaB_R
AGATATCACTGTTACTGCTAACG
>cfaB_F
TTAACGCATCGGAAGCAAAG
>ybgD_R
TATGCGGCTGATGAAGGATC
>ybgD_F
Expand Down Expand Up @@ -34,10 +38,10 @@ AGTTTATCGCTGCGGGTCGC
AACGCTATTCGCCAGCTTGC
>arpA_R
TCTCCCCATACCGTACGCTA
>ArpAgpE_F
GATTCCATCTTGTCAAAATATGCC
>ArpAgpE_R
GAAAAGAAAAAGAATTCCCAAGAG
>fdm_F
TGGCGGCATTGTTAGCGTAC
>fdm_R
GGGTACCAGAATCACCTTAC
>trpAgpC_F
AGTTTTATGCCCAGTGCGAG
>trpAgpC_R
Expand Down