Mercurial > repos > cpt > cpt_find_spanins

comparison findSpanin.py @ 4:673d1776d3b9 draft

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planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc
author cpt
date Fri, 05 Jan 2024 05:51:06 +0000
parents fd70980a516b
children 46b252c89e9e
comparison
equal deleted inserted replaced
3:fd70980a516b 4:673d1776d3b9
16 ) 16 )
17 17
18 ### Requirement Inputs 18 ### Requirement Inputs
19 #### INPUT : putative_isp.fa & putative_osp.fa (in that order) 19 #### INPUT : putative_isp.fa & putative_osp.fa (in that order)
20 #### PARAMETERS : 20 #### PARAMETERS :
21
21 22
22 ############################################################################### 23 ###############################################################################
23 def write_output(candidates): 24 def write_output(candidates):
24 """output file function...maybe not needed""" 25 """output file function...maybe not needed"""
25 pass 26 pass
130 # pair_dict['pairs']['locations'].extend(pos_uniques) 131 # pair_dict['pairs']['locations'].extend(pos_uniques)
131 else: 132 else:
132 spanin_data["positive"]["amt_positive"] = 0 133 spanin_data["positive"]["amt_positive"] = 0
133 spanin_data["positive"]["pos_amt_unique"] = 0 134 spanin_data["positive"]["pos_amt_unique"] = 0
134 if spanin_data["negative"]["coords"]: 135 if spanin_data["negative"]["coords"]:
135
136 # do something else... 136 # do something else...
137 # print('in other function') 137 # print('in other function')
138 # print(spanin_data['negative']['coords']) 138 # print(spanin_data['negative']['coords'])
139 for each_hit in spanin_data["negative"]["coords"]: 139 for each_hit in spanin_data["negative"]["coords"]:
140 neg_check.append(each_hit[1]) 140 neg_check.append(each_hit[1])
194 # spanins['total_unique'] = len(pair_dict['pairs']['pair_number']) 194 # spanins['total_unique'] = len(pair_dict['pairs']['pair_number'])
195 return spanins, pair_dict 195 return spanins, pair_dict
196 196
197 197
198 if __name__ == "__main__": 198 if __name__ == "__main__":
199
200 # Common parameters for both ISP / OSP portion of script 199 # Common parameters for both ISP / OSP portion of script
201 200
202 parser = argparse.ArgumentParser( 201 parser = argparse.ArgumentParser(
203 description="Trim the putative protein candidates and find potential i-spanin / o-spanin pairs" 202 description="Trim the putative protein candidates and find potential i-spanin / o-spanin pairs"
204 ) 203 )
328 ) 327 )
329 if each_spanin_type == "EMBEDDED": 328 if each_spanin_type == "EMBEDDED":
330 for k, v in SPANIN_TYPES["EMBEDDED"].items(): 329 for k, v in SPANIN_TYPES["EMBEDDED"].items():
331 # print(k) 330 # print(k)
332 f.writelines( 331 f.writelines(
333 "" 332 +str(k)
334 + str(k)
335 + " ==> Amount of corresponding candidate o-spanins(s): " 333 + " ==> Amount of corresponding candidate o-spanins(s): "
336 + str(len(v)) 334 + str(len(v))
337 + "\n" 335 + "\n"
338 ) 336 )
339 if each_spanin_type == "SEPARATED": 337 if each_spanin_type == "SEPARATED":
340 for k, v in SPANIN_TYPES["SEPARATED"].items(): 338 for k, v in SPANIN_TYPES["SEPARATED"].items():
341 f.writelines( 339 f.writelines(
342 "" 340 +str(k)
343 + str(k)
344 + " ==> Amount of corresponding candidate o-spanins(s): " 341 + " ==> Amount of corresponding candidate o-spanins(s): "
345 + str(len(v)) 342 + str(len(v))
346 + "\n" 343 + "\n"
347 ) 344 )
348 if each_spanin_type == "OVERLAPPED": 345 if each_spanin_type == "OVERLAPPED":
349 for k, v in SPANIN_TYPES["OVERLAPPED"].items(): 346 for k, v in SPANIN_TYPES["OVERLAPPED"].items():
350 f.writelines( 347 f.writelines(
351 "" 348 +str(k)
352 + str(k)
353 + " ==> Amount of corresponding candidate o-spanins(s): " 349 + " ==> Amount of corresponding candidate o-spanins(s): "
354 + str(len(v)) 350 + str(len(v))
355 + "\n" 351 + "\n"
356 ) 352 )
357 except TypeError: 353 except TypeError:
412 ) 408 )
413 ) 409 )
414 if each_posp[6] == "+": 410 if each_posp[6] == "+":
415 if each_posp[2] in pair_dict["pairs"]["pair_number"].keys(): 411 if each_posp[2] in pair_dict["pairs"]["pair_number"].keys():
416 f.write( 412 f.write(
417 "" 413 +str(pair_dict["pairs"]["pair_number"][each_posp[2]])
418 + str(pair_dict["pairs"]["pair_number"][each_posp[2]])
419 + "\n" 414 + "\n"
420 ) 415 )
421 elif each_posp[6] == "-": 416 elif each_posp[6] == "-":
422 if each_posp[1] in pair_dict["pairs"]["pair_number"].keys(): 417 if each_posp[1] in pair_dict["pairs"]["pair_number"].keys():
423 f.write( 418 f.write(
424 "" 419 +str(pair_dict["pairs"]["pair_number"][each_posp[1]])
425 + str(pair_dict["pairs"]["pair_number"][each_posp[1]])
426 + "\n" 420 + "\n"
427 ) 421 )
428 else: 422 else:
429 f.write("nothing found") 423 f.write("nothing found")
430 424
489 ) 483 )
490 if each_posp[6] == "+": 484 if each_posp[6] == "+":
491 if each_posp[2] in pair_dict["pairs"]["pair_number"].keys(): 485 if each_posp[2] in pair_dict["pairs"]["pair_number"].keys():
492 # print('ovl ; +') 486 # print('ovl ; +')
493 f.write( 487 f.write(
494 "" 488 +str(pair_dict["pairs"]["pair_number"][each_posp[2]])
495 + str(pair_dict["pairs"]["pair_number"][each_posp[2]])
496 + "\n" 489 + "\n"
497 ) 490 )
498 elif each_posp[6] == "-": 491 elif each_posp[6] == "-":
499 if each_posp[1] in pair_dict["pairs"]["pair_number"].keys(): 492 if each_posp[1] in pair_dict["pairs"]["pair_number"].keys():
500 f.write( 493 f.write(
501 "" 494 +str(pair_dict["pairs"]["pair_number"][each_posp[1]])
502 + str(pair_dict["pairs"]["pair_number"][each_posp[1]])
503 + "\n" 495 + "\n"
504 ) 496 )
505 else: 497 else:
506 f.write("nothing found") 498 f.write("nothing found")
507 499
563 ) 555 )
564 ) 556 )
565 if each_posp[6] == "+": 557 if each_posp[6] == "+":
566 if each_posp[2] in pair_dict["pairs"]["pair_number"].keys(): 558 if each_posp[2] in pair_dict["pairs"]["pair_number"].keys():
567 f.write( 559 f.write(
568 "" 560 +str(pair_dict["pairs"]["pair_number"][each_posp[2]])
569 + str(pair_dict["pairs"]["pair_number"][each_posp[2]])
570 + "\n" 561 + "\n"
571 ) 562 )
572 elif each_posp[6] == "-": 563 elif each_posp[6] == "-":
573 if each_posp[1] in pair_dict["pairs"]["pair_number"].keys(): 564 if each_posp[1] in pair_dict["pairs"]["pair_number"].keys():
574 f.write( 565 f.write(
575 "" 566 +str(pair_dict["pairs"]["pair_number"][each_posp[1]])
576 + str(pair_dict["pairs"]["pair_number"][each_posp[1]])
577 + "\n" 567 + "\n"
578 ) 568 )
579 else: 569 else:
580 f.write("nothing found") 570 f.write("nothing found")
581 571