Mercurial > repos > cpt > cpt_find_spanins
comparison findSpanin.py @ 4:673d1776d3b9 draft default tip
planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc
| author | cpt |
|---|---|
| date | Fri, 05 Jan 2024 05:51:06 +0000 |
| parents | fd70980a516b |
| children |
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| 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 |