From 1c3f2809e9f54c3bee95b62ea15e2bcef91cb582 Mon Sep 17 00:00:00 2001 From: arivers Date: Fri, 6 Jul 2018 08:21:44 -0500 Subject: [PATCH] Corrected spelling errors in main.py --- itsxpress/main.py | 26 +++++++++++++------------- 1 file changed, 13 insertions(+), 13 deletions(-) diff --git a/itsxpress/main.py b/itsxpress/main.py index 7ae398a..f4976aa 100755 --- a/itsxpress/main.py +++ b/itsxpress/main.py @@ -247,7 +247,7 @@ def __init__(self, uc_file, rep_file, seq_file): def _get_trimmed_seq_generator(self, seqgen, itspos): """This function takes a Biopython SeqIO sequence generator of sequences, and - returns a generator of trimmed sequecnes. Sequences where the ITS ends could + returns a generator of trimmed sequences. Sequences where the ITS ends could not be determined are ommited. Args: @@ -282,7 +282,7 @@ def _filterfunc(record): return False def map_func(record): - """Trims the record down to to correct region + """Trims the record down to correct region Args: record (obj): a Biopython SeqRecord object @@ -340,7 +340,7 @@ class SeqSample: tempdir (obj): A temporary directory object fastq (str): The path to the input fastq file uc_file (str): The path to the Vsearch uc mapping file - rep_file: (str) the path to the representitive seequences fasta file created by Vsearch + rep_file: (str) the path to the representative sequences fasta file created by Vsearch seq_file (str): the location of the fastq or fastq.gz sequence file used for analysis """ @@ -367,7 +367,7 @@ def _deduplicate(self, threads=1): """Runs Vsearch dereplication to create a fasta file of nonredundant sequences. Args: - threads (int or str):the number of prosessor threads to use + threads (int or str):the number of processor threads to use """ try: @@ -387,7 +387,7 @@ def _deduplicate(self, threads=1): logging.exception("Could not perform dereplication with Vsearch. Error from Vsearch was:\n {}".format(p2.stderr.decode('utf-8'))) raise e except FileNotFoundError as f: - logging.error("Vsearch was not found, make sure Vsearch is installed and executible") + logging.error("Vsearch was not found, make sure Vsearch is installed and executable") raise f def _search(self, hmmfile, threads=1): @@ -408,10 +408,10 @@ def _search(self, hmmfile, threads=1): p4 = subprocess.run(parameters,stderr=subprocess.PIPE, stdout=subprocess.DEVNULL) p4.check_returncode() except subprocess.CalledProcessError as e : - logging.exception("Could not perform ITS identificaton with hmmserach. The error was:\n {}".format(p4.stderr.decode('utf-8'))) + logging.exception("Could not perform ITS identification with hmmserach. The error was:\n {}".format(p4.stderr.decode('utf-8'))) raise e except FileNotFoundError as f: - logging.error("hmmsearch was not found, make sure HMMER3 is installed and executible") + logging.error("hmmsearch was not found, make sure HMMER3 is installed and executable") raise f class SeqSamplePairedInterleaved(SeqSample): @@ -436,7 +436,7 @@ def _merge_reads(self, threads): logging.exception("could not perform read merging with BBmerge. Error from BBmerge was: \n {}".format(p1.stderr.decode('utf-8'))) raise e except FileNotFoundError as f: - logging.error("BBmerge was not found, make sure BBmerge is executible") + logging.error("BBmerge was not found, make sure BBmerge is executable") raise f class SeqSamplePairedNotInterleaved(SeqSample): @@ -463,7 +463,7 @@ def _merge_reads(self, threads): logging.exception("Could not perform read merging with BBmerge. Error from BBmerge was: \n {}".format(p1.stderr.decode('utf-8'))) raise e except FileNotFoundError as f: - logging.error("BBmerge was not found, make sure BBmerge is executible") + logging.error("BBmerge was not found, make sure BBmerge is executable") raise f class SeqSampleNotPaired(SeqSample): @@ -478,7 +478,7 @@ def __init__(self, fastq, tempdir): def _is_paired(fastq, fastq2, single_end): - """Dertermines workflow based on file inputs. + """Determines the workflow based on file inputs. Args: @@ -526,7 +526,7 @@ def _check_fastqs(fastq, fastq2=None): Args: fastq (str): The path to a fastq or fastq.gz file - fastq2 (str): The path to a fastq or fastq.gz file for the reverese sequences + fastq2 (str): The path to a fastq or fastq.gz file for the reverse sequences Raises: SystemExit if invalid input sequences are found. @@ -541,7 +541,7 @@ def _check_fastqs(fastq, fastq2=None): logging.error("There appears to be an issue with your input fastq or fastq.gz file(s).") raise e except FileNotFoundError as e: - logging.error("BBtools was not found. check that the BBtools reformat.sh package is executible") + logging.error("BBtools was not found. check that the BBtools reformat.sh package is executable") raise e @@ -557,7 +557,7 @@ def main(args=None): _logger_setup(args.log) try: - logging.info("Verifing the input sequecnes.") + logging.info("Verifing the input sequences.") _check_fastqs(args.fastq, args.fastq2) # Parse input types paired_end, interleaved = _is_paired(args.fastq,args.fastq2, args.single_end)