Mercurial > repos > rakesh4osdd > asist

changeset 4:3ea72fb2eaac draft

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Deleted selected files test files
author rakesh4osdd
date Wed, 30 Jun 2021 05:48:04 +0000
parents 734777d3c253
children de75544681e0
files asist_dynamic.ipynb test-data/clsi.csv test-data/input.csv test-data/input2.csv test-data/output.csv
diffstat 5 files changed, 23 insertions(+), 114 deletions(-) [+]
line wrap: on
line diff
--- a/asist_dynamic.ipynb	Wed Jun 30 05:35:56 2021 +0000
+++ b/asist_dynamic.ipynb	Wed Jun 30 05:48:04 2021 +0000
@@ -27,20 +27,22 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 176,
+   "execution_count": 162,
    "id": "d66ec0d2",
    "metadata": {},
    "outputs": [],
    "source": [
-    "input_file=sys.argv[1]\n",
-    "output_file=sys.argv[2]\n",
-    "#input_file='test-data/asist_input.csv'\n",
-    "#output_file='test-data/asist_output.csv'"
+    "#input_file=sys.argv[1]\n",
+    "#output_file=sys.argv[2]\n",
+    "input_file='test-data/strains_788_input_16k.csv'\n",
+    "output_file='/mnt/d/PhD_Work/Tina_Work/ASIST_Galaxy/ASIST/strains_788_output_16k.csv'\n",
+    "#input_file='/mnt/d/PhD_Work/Tina_Work/ASIST_Galaxy/ASIST/asist_example15.csv'\n",
+    "#output_file='/mnt/d/PhD_Work/Tina_Work/ASIST_Galaxy/ASIST/asist_example15_output.csv'"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 177,
+   "execution_count": 163,
    "id": "bf24c946",
    "metadata": {},
    "outputs": [],
@@ -77,7 +79,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 178,
+   "execution_count": 164,
    "id": "8bad7d9d",
    "metadata": {},
    "outputs": [],
@@ -152,7 +154,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 179,
+   "execution_count": 165,
    "id": "7629fc10",
    "metadata": {},
    "outputs": [],
@@ -164,7 +166,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 180,
+   "execution_count": 166,
    "id": "bed1abba",
    "metadata": {},
    "outputs": [],
@@ -175,7 +177,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 181,
+   "execution_count": 167,
    "id": "a64b5022",
    "metadata": {},
    "outputs": [],
@@ -189,7 +191,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 182,
+   "execution_count": 168,
    "id": "caac57d7",
    "metadata": {},
    "outputs": [],
@@ -201,7 +203,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 183,
+   "execution_count": 169,
    "id": "eb4b0c4d",
    "metadata": {
     "scrolled": true
@@ -213,7 +215,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 184,
+   "execution_count": 170,
    "id": "86441c0f",
    "metadata": {},
    "outputs": [],
@@ -223,7 +225,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 185,
+   "execution_count": 171,
    "id": "75698be5",
    "metadata": {},
    "outputs": [],
@@ -234,7 +236,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 186,
+   "execution_count": 172,
    "id": "c14a13eb",
    "metadata": {
     "scrolled": true
@@ -246,8 +248,8 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 187,
-   "id": "ff484767",
+   "execution_count": 173,
+   "id": "1b113050",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -256,7 +258,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 188,
+   "execution_count": 174,
    "id": "5ab72211",
    "metadata": {},
    "outputs": [],
@@ -266,8 +268,8 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 189,
-   "id": "020dbe85",
+   "execution_count": 175,
+   "id": "c17c84c4",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -280,7 +282,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "9c17e66a",
+   "id": "7e8e1fa8",
    "metadata": {},
    "outputs": [],
    "source": []
--- a/test-data/clsi.csv	Wed Jun 30 05:35:56 2021 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,23 +0,0 @@
-Antibiotics,Susceptible,Resistant,Intermediate
-Amikacin,≤ 16,≥ 64,32
-Tobramycin,≤ 4,≥ 16,8
-Gentamicin,≤ 4,≥ 16,8
-Netilmicin,≤ 8,≥ 32,16
-Imipenem,≤ 2,≥ 8,4
-Meropenem,≤ 2,≥ 8,4
-Doripenem,≤ 2,≥ 8,4
-Ciprofloxacin,≤ 1,≥ 4,2
-Levofloxacin,≤ 2,≥ 8,4
-Piperacillin/ tazobactam,≤ 16/4,≥ 128/4,32/4-64/4
-Ticarcillin/ clavulanic acid,≤ 16/2,≥ 128/2,32/2-64/2
-Cefotaxime,≤ 8,≥ 64,16-32
-Ceftriaxone,≤ 8,≥ 64,16-32
-Ceftazidime,≤ 8,≥ 32,16
-Cefepime,≤ 8,≥ 32,16
-Trimethoprim/ sulfamethoxazole,≤ 2/38,≥ 4/76,-
-Ampicillin/ sulbactam,≤ 8/4,≥ 32/16,16/8
-Colistin,-,≥ 4,≤ 2
-Polymyxin B,-,≥ 4,≤ 2
-Tetracycline,≤ 4,≥ 16,8
-Doxycycline,≤ 4,≥ 16,8
-Minocycline,≤ 4,≥ 16,8
\ No newline at end of file
--- a/test-data/input.csv	Wed Jun 30 05:35:56 2021 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,31 +0,0 @@
-id,Strain name,Antibiotics,Resistance_profile,sign,MIC,unit
-470,Acinetobacter baumannii A85,Colistin,Susceptible ,NA,0.1,mg/L
-470,Acinetobacter baumannii A85,Colistin,Susceptible ,NA,1,mg/L
-470,Acinetobacter baumannii A85,Colistin,Susceptible ,NA,2,mg/L
-470,Acinetobacter baumannii AB307-0294,Ampicillin,resistant,>=,0,mg/L
-470,Acinetobacter baumannii AB307-0294,Ampicillin/sulbactam,susceptible,<=,mg/L,mg/L
-470,Acinetobacter baumannii AB307-0294,piperacillin/tazobactam,susceptible,<=,0,mg/L
-470,Acinetobacter baumannii AB307-0294,Cefazolin,resistant,>=,64,mg/L
-470,Acinetobacter baumannii AB307-0294,Ceftriaxone,susceptible,==,16,mg/L
-470,Acinetobacter baumannii AB307-0294,Cefepime,susceptible,==,8,mg/L
-470,Acinetobacter baumannii AB307-0294,Meropenem,susceptible,<=,0.25,mg/L
-470,Acinetobacter baumannii AB307-0294,Imipenem,susceptible,<=,1,mg/L
-470,Acinetobacter baumannii AB307-0294,Tigecycline,susceptible,<=,0.5,mg/L
-470,Acinetobacter baumannii AB5075-UW,Ceftazidime,Resistant,NA,>128,mg/L
-470,Acinetobacter baumannii AB5075-UW,Cefepime,Resistant,NA,>256,mg/L
-470,Acinetobacter baumannii AB5075-UW,Ciprofloxacin,Resistant,NA,>32,mg/L
-470,Acinetobacter baumannii DU202,colistin ,Susceptible,NA,,mg/L
-470,Acinetobacter baumannii DU202,trimethoprim/sulfamethoxazole,Resistant,NA,8/152,mg/L
-470,Acinetobacter baumannii DU202,Ampicillin/sulbactam,Resistant,NA,>=0.3 mg/L,mg/L
-470,Acinetobacter baumannii DU202,ticarcillin/clavulanic acid,Resistant,NA,>=128/2,mg/L
-470,Acinetobacter baumannii DU202,piperacillin/tazobactam ,Resistant,NA,NA,mg/L
-470,Acinetobacter baumannii DU202,trimethoprim/sulfamethoxazole,Resistant,NA,8/152,mg/L
-470,Acinetobacter baumannii ORAB01,piperacillin/tazobactam,Resistant,NA,>64/4,mg/L
-470,Acinetobacter baumannii strain MRSN7100,amoxicillin/clavulanic acid,Resistant,>, 16/8,mg/L
-470,Acinetobacter baumannii strain MRSN7168,amoxicillin/clavulanic acid,Resistant,>, 16/8,mg/L
-470,Acinetobacter baumannii strain MRSN7336,amoxicillin/clavulanic acid,Resistant,>, 16/8,mg/L
-470,Acinetobacter baumannii strain MRSN7834,amoxicillin/clavulanic acid,Resistant,>, 16/8,mg/L
-470,Acinetobacter baumannii strain FDA-CDC-AR_0305,polymyxin B,Susceptible,==,1,mg/L
-470,Acinetobacter baumannii strain FDA-CDC-AR_0306,polymyxin B,Susceptible,==,1,mg/L
-470,Acinetobacter baumannii strain FDA-CDC-AR_0307,polymyxin B,Resistant,==,8,mg/L
-470,Acinetobacter baumannii strain FDA-CDC-AR_0308,polymyxin B,Resistant,==,4,mg/L
--- a/test-data/input2.csv	Wed Jun 30 05:35:56 2021 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,29 +0,0 @@
-id,genome Ids,Strain name,Antibiotics,Resistance_profile,sign,MIC,unit
-470,CP021782.1,Acinetobacter baumannii A85,Colistin,Susceptible ,NA,0.1,mg/L
-470,CP021782.1,Acinetobacter baumannii A85,Netilmicin,Susceptible ,NA,1,mg/L
-470,CP001172.2,Acinetobacter baumannii AB307-0294,Ampicillin,resistant,>=,0,mg/L
-470,CP001172.2,Acinetobacter baumannii AB307-0294,Ampicillin/sulbactam,susceptible,<=,mg/L,mg/L
-470,CP001172.2,Acinetobacter baumannii AB307-0294,piperacillin/tazobactam,susceptible,<=,0,mg/L
-470,CP001172.2,Acinetobacter baumannii AB307-0294,Cefazolin,resistant,>=,64,mg/L
-470,CP001172.2,Acinetobacter baumannii AB307-0294,Ceftriaxone,susceptible,==,16,mg/L
-470,CP001172.2,Acinetobacter baumannii AB307-0294,Cefepime,susceptible,==,8,mg/L
-470,CP001172.2,Acinetobacter baumannii AB307-0294,Meropenem,susceptible,<=,0.25,mg/L
-470,CP001172.2,Acinetobacter baumannii AB307-0294,Imipenem,susceptible,<=,1,mg/L
-470,CP001172.2,Acinetobacter baumannii AB307-0294,Tigecycline,susceptible,<=,0.5,mg/L
-470,CP008706.1,Acinetobacter baumannii AB5075-UW,Ceftazidime,Resistant,NA,>128,mg/L
-470,CP008706.1,Acinetobacter baumannii AB5075-UW,Cefepime,Resistant,NA,>256,mg/L
-470,CP008706.1,Acinetobacter baumannii AB5075-UW,Ciprofloxacin,Resistant,NA,>32,mg/L
-470,CP017152.1,Acinetobacter baumannii DU202,colistin ,Susceptible,NA,,mg/L
-470,CP017152.1,Acinetobacter baumannii DU202,Ampicillin/sulbactam,Resistant,NA,>=0.3 mg/L,mg/L
-470,CP017152.1,Acinetobacter baumannii DU202,ticarcillin/clavulanic acid,Resistant,NA,>=128/2,mg/L
-470,CP017152.1,Acinetobacter baumannii DU202,piperacillin/tazobactam ,Resistant,NA,NA,mg/L
-470,CP017152.1,Acinetobacter baumannii DU202,trimethoprim/sulfamethoxazole,Resistant,NA,8/152,mg/L
-470,CP015483.1,Acinetobacter baumannii ORAB01,piperacillin/tazobactam,Resistant,NA,>64/4,mg/L
-470,470.7601,Acinetobacter baumannii strain MRSN7100,amoxicillin/clavulanic acid,Resistant,>, 16/8,mg/L
-470,470.7651,Acinetobacter baumannii strain MRSN7168,amoxicillin/clavulanic acid,Resistant,>, 16/8,mg/L
-470,470.7764,Acinetobacter baumannii strain MRSN7336,amoxicillin/clavulanic acid,Resistant,>, 16/8,mg/L
-470,470.8071,Acinetobacter baumannii strain MRSN7834,amoxicillin/clavulanic acid,Resistant,>, 16/8,mg/L
-470,470.7405,Acinetobacter baumannii strain FDA-CDC-AR_0305,polymyxin B,Susceptible,==,1,mg/L
-470,470.7406,Acinetobacter baumannii strain FDA-CDC-AR_0306,polymyxin B,Susceptible,==,1,mg/L
-470,470.7407,Acinetobacter baumannii strain FDA-CDC-AR_0307,polymyxin B,Resistant,==,8,mg/L
-470,470.7408,Acinetobacter baumannii strain FDA-CDC-AR_0308,polymyxin B,Resistant,==,4,mg/L
--- a/test-data/output.csv	Wed Jun 30 05:35:56 2021 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,10 +0,0 @@
-Strain name,Resistance_phenotype,Imipenem,Meropenem,Ciprofloxacin,Piperacillin/tazobactam,Ticarcillin/clavulanicacid,Ceftriaxone,Ceftazidime,Cefepime,Trimethoprim/sulfamethoxazole,Ampicillin/sulbactam,Colistin,Polymyxinb
-Acinetobacter baumannii A85,,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Susceptible,NA
-Acinetobacter baumannii AB307-0294,,Susceptible,Susceptible,NA,Strain could not classified,NA,Intermediate,NA,Susceptible,NA,Strain could not classified,NA,NA
-Acinetobacter baumannii AB5075-UW,,NA,NA,Resistant,NA,NA,NA,Resistant,Resistant,NA,NA,NA,NA
-Acinetobacter baumannii DU202,,NA,NA,NA,Strain could not classified,Resistant,NA,NA,NA,Resistant,Strain could not classified,Strain could not classified,NA
-Acinetobacter baumannii ORAB01,,NA,NA,NA,Intermediate,NA,NA,NA,NA,NA,NA,NA,NA
-Acinetobacter baumannii strain FDA-CDC-AR_0305,,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Susceptible
-Acinetobacter baumannii strain FDA-CDC-AR_0306,,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Susceptible
-Acinetobacter baumannii strain FDA-CDC-AR_0307,,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Resistant
-Acinetobacter baumannii strain FDA-CDC-AR_0308,,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,Resistant