fixed issues report in #8

bmds-lab · Jan 11, 2024 · cacfbfc · cacfbfc
1 parent bb50af9
commit cacfbfc
Showing 1 changed file with 22 additions and 13 deletions.
diff --git a/src/crackling/Crackling.py b/src/crackling/Crackling.py
@@ -253,7 +253,7 @@ def processSequence(sequence):
 
  duplicatePercent = round(numDuplicateGuides / numIdentifiedGuides * 100.0, 3)
  printer(f'\tIdentified {numIdentifiedGuides:,} possible target sites in this file.')
- printer(f'\tOf these, {len(duplicateGuides):,} are not unique. These sites occur a total of {numDuplicateGuides} times.')
+ printer(f'\tOf these, {len(duplicateGuides):,} are not unique. These sites occur a total of {numDuplicateGuides:,} times.')
  printer(f'\tRemoving {numDuplicateGuides:,} of {numIdentifiedGuides:,} ({duplicatePercent}%) guides.')
  printer(f'\t{len(candidateGuides):,} distinct guides have been discovered so far.')
 
@@ -277,7 +277,7 @@ def processSequence(sequence):
  for batchFile in guideBatchinator:
  batchStartTime = time.time()
 
- printer(f'Processing batch file {(batchFileId+1):,} of {len(guideBatchinator)}')
+ printer(f'Processing batch file {(batchFileId+1):,} of {len(guideBatchinator):,}')
 
  # Create new candidate guide dictionary
  candidateGuides = {}
@@ -401,14 +401,17 @@ def processSequence(sequence):
  errorCount = 0
  notFoundCount = 0
 
- pgLength = int(configMngr['rnafold']['page-length'])
+ pgLength = min(
+ int(configMngr['input']['batch-size']), 
+ int(configMngr['rnafold']['page-length'])
+ )
 
  for pgIdx, pageCandidateGuides in Paginator(
  filterCandidateGuides(candidateGuides, MODULE_MM10DB),
  pgLength
  ):
  if pgLength > 0:
- printer(f'\tProcessing page {(pgIdx+1)} ({pgLength:,} per page).')
+ printer(f'\tProcessing page {(pgIdx+1):,} (max {pgLength:,} per page).')
 
  if os.path.exists(configMngr['rnafold']['output']):
  os.remove(configMngr['rnafold']['output'])
@@ -501,10 +504,10 @@ def processSequence(sequence):
  printer(f'\t{failedCount:,} of {testedCount:,} failed here.')
 
  if errorCount > 0:
- printer(f'\t{errorCount} of {testedCount} erred here.')
+ printer(f'\t{errorCount:,} of {testedCount:,} erred here.')
 
  if notFoundCount > 0:
- printer(f'\t{notFoundCount} of {testedCount} not found in RNAfold output.')
+ printer(f'\t{notFoundCount:,} of {testedCount:,} not found in RNAfold output.')
 
  #########################################
  ## Calc mm10db result ##
@@ -529,9 +532,9 @@ def processSequence(sequence):
  candidateGuides[target23]['acceptedByMm10db'] = CODE_ACCEPTED
  acceptedCount += 1
 
- printer(f'\t{acceptedCount} accepted.')
+ printer(f'\t{acceptedCount:,} accepted.')
 
- printer(f'\t{failedCount} failed.')
+ printer(f'\t{failedCount:,} failed.')
 
  del acceptedCount
 
@@ -606,15 +609,18 @@ def processSequence(sequence):
  testedCount = 0
  failedCount = 0
 
- pgLength = int(configMngr['bowtie2']['page-length'])
+ pgLength = min(
+ int(configMngr['input']['batch-size']), 
+ int(configMngr['bowtie2']['page-length'])
+ )
 
  for pgIdx, pageCandidateGuides in Paginator(
  filterCandidateGuides(candidateGuides, MODULE_SPECIFICITY),
  pgLength
  ):
 
  if pgLength > 0:
- printer(f'\tProcessing page {(pgIdx+1)} ({pgLength:,} per page).')
+ printer(f'\tProcessing page {(pgIdx+1):,} (max {pgLength:,} per page).')
 
  if os.path.exists(configMngr['bowtie2']['output']):
  os.remove(configMngr['bowtie2']['output'])
@@ -732,15 +738,18 @@ def processSequence(sequence):
  testedCount = 0
  failedCount = 0
 
- pgLength = int(configMngr['offtargetscore']['page-length'])
+ pgLength = min(
+ int(configMngr['input']['batch-size']), 
+ int(configMngr['offtargetscore']['page-length'])
+ )
 
  for pgIdx, pageCandidateGuides in Paginator(
  filterCandidateGuides(candidateGuides, MODULE_SPECIFICITY),
  pgLength
  ):
 
  if pgLength > 0:
- printer(f'\tProcessing page {(pgIdx+1)} ({pgLength:,} per page).')
+ printer(f'\tProcessing page {(pgIdx+1):,} (max {pgLength:,} per page).')
 
  # prepare the list of candidate guides to score
  guidesInPage = 0
@@ -873,7 +882,7 @@ def processSequence(sequence):
  #########################################
  printer('Done.')
 
- printer(f'{len(candidateGuides)} guides evaluated.')
+ printer(f'{len(candidateGuides):,} guides evaluated.')
 
  printer('This batch ran in {} (dd hh:mm:ss) or {} seconds'.format(
  time.strftime('%d %H:%M:%S', time.gmtime((time.time() - batchStartTime))),