Mercurial > repos > johnheap > vapper
comparison Tryp_V_T.py @ 27:92c5ecb025b6 draft
Uploaded
| 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): |