Description: Use 2to3 to port to Python3 Bug-Debian: https://bugs.debian.org/938565 Author: Andreas Tille Last-Update: Wed, 04 Sep 2019 16:44:45 +0200 --- a/tools/TQS.py +++ b/tools/TQS.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/python3 __doc__ = """ TQS @@ -53,18 +53,18 @@ def main(): f = open(opts.seqfile) seq = f.readlines() f.close() - except Exception, e: - print "ERROR: Could not read from %s: %s" % (opts.seqfile, e) - print usage % (sys.argv[0:]) + except Exception as e: + print("ERROR: Could not read from %s: %s" % (opts.seqfile, e)) + print(usage % (sys.argv[0:])) sys.exit() try: f = open(opts.qualfile) qual = f.readlines() f.close() - except Exception, e: - print "ERROR: Could not read from %s: %s" % (opts.qualfile, e) - print usage % (sys.argv[0:]) + except Exception as e: + print("ERROR: Could not read from %s: %s" % (opts.qualfile, e)) + print(usage % (sys.argv[0:])) sys.exit() @@ -75,22 +75,22 @@ def main(): try: FASTA = open(fasta, 'w') except: - print "ERROR: Can not write to %s" % fasta + print("ERROR: Can not write to %s" % fasta) sys.exit() try: LOG = open(log, 'w') except: - print "ERROR: Can not write to %s" % log + print("ERROR: Can not write to %s" % log) sys.exit() if opts.mer < 15 or opts.mer > 200: - print "ERROR: -l must be a number between 15 and 200." + print("ERROR: -l must be a number between 15 and 200.") sys.exit() if opts.consec < 16 or opts.consec > opts.mer: - print "ERROR: -c must be a number between 16 and -l." + print("ERROR: -c must be a number between 16 and -l.") sys.exit() LOG.write(""" @@ -130,7 +130,7 @@ def parseQualFile(threshold, difference, read_number = 0 if verbose: - print "Printing trimming pattern for all reads passing the set threshold values...\n" + print("Printing trimming pattern for all reads passing the set threshold values...\n") for line in qual: read_number += 1 ### this keeps track of the read order, respected between the prb and seq files @@ -156,7 +156,7 @@ def parseQualFile(threshold, difference, if head_match != None: ok_read += 1 col = head_match.span() - if not trim_info.has_key(read_number): + if read_number not in trim_info: trim_info[read_number] = {} start = int(col[0]) @@ -167,7 +167,7 @@ def parseQualFile(threshold, difference, if verbose: sub = concat[trim_info[read_number]['start']:trim_info[read_number]['end']] - print "passed seqs:%i line#%i %s (start trim:%i,length:%i) %s\n" % (ok_read, read_number, concat, start, end, sub) + print("passed seqs:%i line#%i %s (start trim:%i,length:%i) %s\n" % (ok_read, read_number, concat, start, end, sub)) LOG.write("%i out of %i sequences passed your filter (I >= %i and D >= %i and L >= %i)\n" % (ok_read, read_number, threshold, difference, consecutive)) @@ -191,7 +191,7 @@ def readNTrim(trim_info, seq, verbose, F gDNAlinker2_field = re.compile('^ATCTAACAG') if verbose: - print "Printing trimmed sequences for all reads passing the set threshold values minus, excluding sequence containing linkers...\n" + print("Printing trimmed sequences for all reads passing the set threshold values minus, excluding sequence containing linkers...\n") for line in seq: read_number += 1 ### tracks read number / will match order in prb file @@ -199,7 +199,7 @@ def readNTrim(trim_info, seq, verbose, F info = line.split("\t") ### split line, the seq file lists: lane tile xcoord y coord DNAseq dna_string = info[4] - if trim_info.has_key(read_number): + if read_number in trim_info: trim_seq = dna_string[trim_info[read_number]['start']:trim_info[read_number]['end']] if re.match(dna_sequence_field, trim_seq): ### no ambiguous bases? if re.match(gDNAlinker1_field, trim_seq) or re.match(gDNAlinker2_field,trim_seq): ### matches gDNA linker? @@ -208,7 +208,7 @@ def readNTrim(trim_info, seq, verbose, F usable_reads += 1 FASTA.write(">%s-%s-%s-%s\n%s\n" % (info[0],info[1],info[2],info[3],trim_seq)) if verbose: - print "line#%i %s (start trim:%i,length:%i) %s" % (read_number,info[4],trim_info[read_number]['start'],trim_info[read_number]['end'],trim_seq) + print("line#%i %s (start trim:%i,length:%i) %s" % (read_number,info[4],trim_info[read_number]['start'],trim_info[read_number]['end'],trim_seq)) LOG.write("%i out of %i sequences appear to be usable, after filtering out sequences hard-coded in this program * %i gDNA linker sequences*\n" % (usable_reads, read_number,gDNAlinker_count)) return --- a/tools/TQS.readme +++ b/tools/TQS.readme @@ -24,12 +24,12 @@ __version__ = '1.0' Execution example ================== -python TQS.py -f test_seq.txt -q test_prb.txt -l 36 -t 5 -d 5 -c 20 +python3 TQS.py -f test_seq.txt -q test_prb.txt -l 36 -t 5 -d 5 -c 20 Options ======= -python TQS.py --help +python3 TQS.py --help Usage: TQS.py [options] --- a/tools/TQSexport.py +++ b/tools/TQSexport.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/python3 __doc__ = """ TQS @@ -47,9 +47,9 @@ def main(): f = open(opts.exportfile) seq = f.readlines() f.close() - except Exception, e: - print "ERROR: Could not read from %s: %s" % (opts.exportfile, e) - print usage % (sys.argv[0:]) + except Exception as e: + print("ERROR: Could not read from %s: %s" % (opts.exportfile, e)) + print(usage % (sys.argv[0:])) sys.exit() @@ -61,17 +61,17 @@ def main(): try: FASTA = open(fasta, 'w') except: - print "ERROR: Can not write to %s" % fasta + print("ERROR: Can not write to %s" % fasta) sys.exit() try: LOG = open(log, 'w') except: - print "ERROR: Can not write to %s" % log + print("ERROR: Can not write to %s" % log) sys.exit() if opts.consec < minimum_length: - print "ERROR: -c must be a number larger than %i." % (minimum_length) + print("ERROR: -c must be a number larger than %i." % (minimum_length)) sys.exit() LOG.write(""" @@ -106,7 +106,7 @@ YYYYRYYYYYYYYYYYTTTTTOOOMOOOMMOOOOOG chr read_number = 0 if verbose: - print "Printing trimming pattern for all reads passing the set threshold values...\n" + print("Printing trimming pattern for all reads passing the set threshold values...\n") for line in export: read_number += 1 @@ -134,7 +134,7 @@ YYYYRYYYYYYYYYYYTTTTTOOOMOOOMMOOOOOG chr if head_match != None: ok_read += 1 col = head_match.span() - if not trim_info.has_key(read_number): + if read_number not in trim_info: trim_info[read_number] = {} start = int(col[0]) @@ -150,7 +150,7 @@ YYYYRYYYYYYYYYYYTTTTTOOOMOOOMMOOOOOG chr FASTA.write(">%s-%s-%s-%s%s\n%s\n" % (info[1],info[2],info[3],info[4],pair,trim_seq)) if verbose: - print "passed seqs:%i line#%i %s (start trim:%i,end trim:%i) %s\n" % (ok_read, read_number, concat, start, end, trim_seq) + print("passed seqs:%i line#%i %s (start trim:%i,end trim:%i) %s\n" % (ok_read, read_number, concat, start, end, trim_seq)) LOG.write("%i out of %i sequences passed your filter (-t >= %i and -c >= %i)\n" % (ok_read, read_number, threshold, consecutive)) --- a/tools/TQSfastq.py +++ b/tools/TQSfastq.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/python3 __doc__ = """ TQS @@ -52,9 +52,9 @@ def main(): f = open(opts.fastqfile) seq = f.readlines() f.close() - except Exception, e: - print "ERROR: Could not read from %s: %s" % (opts.fastqfile, e) - print usage % (sys.argv[0:]) + except Exception as e: + print("ERROR: Could not read from %s: %s" % (opts.fastqfile, e)) + print(usage % (sys.argv[0:])) sys.exit() @@ -66,21 +66,21 @@ def main(): try: FASTA = open(fasta, 'w') except: - print "ERROR: Can not write to %s" % fasta + print("ERROR: Can not write to %s" % fasta) sys.exit() try: LOG = open(log, 'w') except: - print "ERROR: Can not write to %s" % log + print("ERROR: Can not write to %s" % log) sys.exit() if opts.consec < minimum_length: - print "ERROR: -c must be a number larger than %i." % (minimum_length) + print("ERROR: -c must be a number larger than %i." % (minimum_length)) sys.exit() if opts.encoding != 33 and opts.encoding != 64: - print "ERROR: -e must be either 33 or 64." + print("ERROR: -e must be either 33 or 64.") sys.exit() LOG.write(""" @@ -114,7 +114,7 @@ def readNtrim(fastq, threshold, consecut record_line = 0 if verbose: - print "Printing trimming pattern for all reads passing the set threshold values...\n" + print("Printing trimming pattern for all reads passing the set threshold values...\n") for line in fastq: record_line += 1 @@ -150,7 +150,7 @@ def readNtrim(fastq, threshold, consecut if head_match != None: ok_read += 1 col = head_match.span() - if not trim_info.has_key(read_number): + if read_number not in trim_info: trim_info[read_number] = {} start = int(col[0]) @@ -160,7 +160,7 @@ def readNtrim(fastq, threshold, consecut FASTA.write(">%s\n%s\n" % (read_id, trim_seq)) if verbose: - print "%s\n%s\n%s\n passed seqs:%i line#%i %s (start trim:%i,end trim:%i) %s\n" % (read_id,seq,qual,ok_read, read_number, concat, start, end, trim_seq) + print("%s\n%s\n%s\n passed seqs:%i line#%i %s (start trim:%i,end trim:%i) %s\n" % (read_id,seq,qual,ok_read, read_number, concat, start, end, trim_seq)) LOG.write("%i out of %i sequences passed your filter (-t >= %i and -c >= %i)\n" % (ok_read, read_number, threshold, consecutive))