Mercurial > repos > johnheap > vapper

comparison Tryp_V_T.py @ 27:92c5ecb025b6 draft

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author johnheap
date Wed, 05 Jun 2019 16:17:30 -0400
parents 7983a9305b53
children be77587bdfda
comparison
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26:7983a9305b53 27:92c5ecb025b6
236 def getPhyloNumber(sac): 236 def getPhyloNumber(sac):
237 i = sac.find('_') 237 i = sac.find('_')
238 return int(sac[1:i]) 238 return int(sac[1:i])
239 239
240 def combineFPMK(tdict): 240 def combineFPMK(tdict):
241 dir_path = os.path.dirname(os.path.realpath(__file__))+'/' 241 # dir_path = os.path.dirname(os.path.realpath(__file__))+'/'
242 242 cur_path = os.getcwd()+'/'
243 fpkm_df = pd.read_csv(dir_path+tdict['name']+'.cuff/genes.fpkm_tracking', sep='\t') 243 fpkm_df = pd.read_csv(cur_path+tdict['name']+'.cuff/genes.fpkm_tracking', sep='\t')
244 244
245 #fpkm_df = pd.read_csv('genes.fpkm_tracking',sep='\t') 245 #fpkm_df = pd.read_csv('genes.fpkm_tracking',sep='\t')
246 #print(fpkm_df.head()) 246 #print(fpkm_df.head())
247 fpkm_df['locus'] = fpkm_df['locus'].apply(lambda names: names[:names.find(':')]) 247 fpkm_df['locus'] = fpkm_df['locus'].apply(lambda names: names[:names.find(':')])
248 #print(fpkm_df.head()) 248 #print(fpkm_df.head())
249 249
250 reducedBlast_df = pd.read_csv(dir_path + tdict['name']+'_transcript.csv') 250 reducedBlast_df = pd.read_csv(cur_path + tdict['name']+'_transcript.csv')
251 # reducedBlast_df = pd.read_csv('TrinityVT_transcript.csv') 251 # reducedBlast_df = pd.read_csv('TrinityVT_transcript.csv')
252 saccverSet = set(reducedBlast_df['saccver']) 252 saccverSet = set(reducedBlast_df['saccver'])
253 saccverList = list(saccverSet) 253 saccverList = list(saccverSet)
254 saccverList.sort() 254 saccverList.sort()
255 # print(saccverList[:5]) 255 # print(saccverList[:5])
357 ax.set_title(title, x=0, wrap='True',ha='left',) 357 ax.set_title(title, x=0, wrap='True',ha='left',)
358 358
359 plt.savefig(tdict['html_resource'] + tdict['name']+"_phylotypes.png") 359 plt.savefig(tdict['html_resource'] + tdict['name']+"_phylotypes.png")
360 if tdict['pdf'] == 'PDF_Yes': 360 if tdict['pdf'] == 'PDF_Yes':
361 plt.savefig(tdict['html_resource'] + tdict['name']+"phylotypes.pdf") 361 plt.savefig(tdict['html_resource'] + tdict['name']+"phylotypes.pdf")
362 plt.show() 362 # plt.show()
363 pass 363 pass
364 364
365 365
366 366
367 def doBarChart(tdict, sum2_df): 367 def doBarChart(tdict, sum2_df):