| Previous changeset 24:728b1d375b41 (2019-06-04) Next changeset 26:7983a9305b53 (2019-06-05) |
|
Commit message:
Uploaded |
|
modified:
Tryp_V_T.py |
| b |
| diff -r 728b1d375b41 -r c0a6a170163e Tryp_V_T.py --- a/Tryp_V_T.py Tue Jun 04 18:03:36 2019 -0400 +++ b/Tryp_V_T.py Tue Jun 04 18:11:54 2019 -0400 |
| [ |
| @@ -120,7 +120,10 @@ def blastContigs(test_name,html_resource, database): db_path = database - argString = "blastx -db "+db_path+" -query "+test_name+"_for_blast.fa -outfmt 10 -out "+test_name+"_blast.txt" + #argString = "makeblastdb - in " + db_path + #subprocess.call(argString, shell=True) + + argString = "blastx -db " + db_path + " -query "+test_name+"_for_blast.fa -outfmt 10 -out "+test_name+"_blast.txt" print(argString) returncode = subprocess.call(argString, shell=True) if returncode != 0: @@ -224,7 +227,7 @@ imgString = r"<img src = '"+ tdict['name']+"_phylotypes.png' alt='Bar chart of phylotype variation' style='max-width:100%'><br><br>" htmlString += imgString - with open(tdict['html_file'], "w") as htmlfile: + with open(tdict['html_resource']+'/'+tdict['html_file'], "w") as htmlfile: htmlfile.write(htmlString) @@ -236,7 +239,7 @@ def combineFPMK(tdict): dir_path = os.path.dirname(os.path.realpath(__file__))+'/' - fpkm_df = pd.read_csv(dir_path++tdict['name']+'.cuff/genes.fpkm_tracking', sep='\t') + fpkm_df = pd.read_csv(dir_path+tdict['name']+'.cuff/genes.fpkm_tracking', sep='\t') #fpkm_df = pd.read_csv('genes.fpkm_tracking',sep='\t') #print(fpkm_df.head()) @@ -392,9 +395,9 @@ plt.subplots_adjust(bottom=0.1, top=0.9, left=0.15, right=0.9) ax.set_title(title, x=0, wrap='True',ha='left',) - plt.savefig(tdict['html_resource'] + tdict['name']+"_phylotypes.png") + plt.savefig(tdict['html_resource'] + '/' + tdict['name']+"_phylotypes.png") if tdict['pdf'] == 'PDF_Yes': - plt.savefig(tdict['html_resource'] + tdict['name']+"phylotypes.pdf") + plt.savefig(tdict['html_resource'] + '/' + tdict['name']+"phylotypes.pdf") # plt.show() pass |