Author: Andreas Tille Last-Update: Wed, 10 Jul 2019 21:58:30 +0200 Description: Result of 2to3 port to Python3 --- a/scripts/count_fixed_catalog_snps.py +++ b/scripts/count_fixed_catalog_snps.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/python3 import optparse import sys @@ -39,7 +39,7 @@ batch_id = int(opts.batch_id) if len(path) == 0 or os.path.exists(path) == False: - print >> sys.stderr, "You must specify a valid path to Stacks input files." + print("You must specify a valid path to Stacks input files.", file=sys.stderr) p.print_help() sys.exit() @@ -62,10 +62,10 @@ pos = entry.find(".matches.tsv") if (pos != -1): files.append(entry[0:pos]) - print >> sys.stderr, "Found", len(files), "Stacks samples." + print("Found", len(files), "Stacks samples.", file=sys.stderr) except: - print >> sys.stderr, "Unable to read files from Stacks directory, '" + path + "'" + print("Unable to read files from Stacks directory, '" + path + "'", file=sys.stderr) def parse_cigar(cigar, components): @@ -143,14 +143,14 @@ matches[sample_locus] = cat_locus else: if cat_locus != matches[sample_locus]: - print >> sys.stderr, "Error: sample locus", sample_locus, "matches more than one catalog locus." + print("Error: sample locus", sample_locus, "matches more than one catalog locus.", file=sys.stderr) if len(cigar) > 0: if sample_locus not in cigars: cigars[sample_locus] = cigar else: if cigar != cigars[sample_locus]: - print >> sys.stderr, "Error: sample locus", sample_locus, "has multiple cigar alignments." + print("Error: sample locus", sample_locus, "has multiple cigar alignments.", file=sys.stderr) fh.close() @@ -279,23 +279,23 @@ # i = 1 for file in files: - print >> sys.stderr, "Processing file", str(i), "of", len(files), "['" + file + "']" + print("Processing file", str(i), "of", len(files), "['" + file + "']", file=sys.stderr) cnt = count_sample_snps(path, file, sample_snps) - print >> sys.stderr, " Found", cnt, "heterozygous SNPs in sample." + print(" Found", cnt, "heterozygous SNPs in sample.", file=sys.stderr) i += 1 total_snps = 0 for locus in sample_snps: for col in sample_snps[locus]: total_snps += 1 -print >> sys.stderr, "Found", total_snps, "variable sites across the population." +print("Found", total_snps, "variable sites across the population.", file=sys.stderr) # # Count all the SNPs found in the catalog. # -print >> sys.stderr, "Processing the catalog" +print("Processing the catalog", file=sys.stderr) cnt = count_catalog_snps(path, batch_id, catalog_snps) -print >> sys.stderr, " Found", cnt, "heterozygous SNPs in the catalog." +print(" Found", cnt, "heterozygous SNPs in the catalog.", file=sys.stderr) # # Count all the SNPs in the catalog but not in any sample: these are the fixed differences cstacks identified. @@ -315,7 +315,7 @@ fixed_snps += 1 for col in sample_snps[locus]: if col not in c: - print "Locus:", locus, "col:", col, "Catalog SNPs:", catalog_snps[locus], "Sample SNPs:", sample_snps[locus] + print("Locus:", locus, "col:", col, "Catalog SNPs:", catalog_snps[locus], "Sample SNPs:", sample_snps[locus]) -print >> sys.stderr, "Found", total_snps, "SNPs across all samples and in the catalog." -print >> sys.stderr, "Found", fixed_snps, "fixed SNPs only in the catalog." +print("Found", total_snps, "SNPs across all samples and in the catalog.", file=sys.stderr) +print("Found", fixed_snps, "fixed SNPs only in the catalog.", file=sys.stderr) --- a/scripts/integrate_alignments.py +++ b/scripts/integrate_alignments.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/python3 import optparse import sys @@ -49,7 +49,7 @@ batch_id = int(opts.batch_id) if len(out_path) == 0 or os.path.exists(out_path) == False: - print >> sys.stderr, "You must specify a valid path to write files to." + print("You must specify a valid path to write files to.", file=sys.stderr) p.print_help() sys.exit() @@ -57,12 +57,12 @@ out_path += "/" if len(aln_path) == 0 or os.path.exists(aln_path) == False: - print >> sys.stderr, "You must specify a valid path to a SAM file containing catalog locus alignments." + print("You must specify a valid path to a SAM file containing catalog locus alignments.", file=sys.stderr) p.print_help() sys.exit() if len(path) == 0 or os.path.exists(path) == False: - print >> sys.stderr, "You must specify a valid path to Stacks input files." + print("You must specify a valid path to Stacks input files.", file=sys.stderr) p.print_help() sys.exit() @@ -85,10 +85,10 @@ pos = entry.find(".matches.tsv") if (pos != -1): files.append(entry[0:pos]) - print >> sys.stderr, "Found", len(files), "Stacks samples." + print("Found", len(files), "Stacks samples.", file=sys.stderr) except: - print >> sys.stderr, "Unable to read files from Stacks directory, '", path, "'" + print("Unable to read files from Stacks directory, '", path, "'", file=sys.stderr) def parse_catalog_alignments(aln_path, alns): @@ -115,7 +115,7 @@ alns[locus] = (chr, bp, "+"); fh.close() - print >> sys.stderr, "Loaded", len(alns), "catalog locus alignments from '", aln_path, "'." + print("Loaded", len(alns), "catalog locus alignments from '", aln_path, "'.", file=sys.stderr) def convert_sample(path, file, out_path, alns): @@ -414,14 +414,14 @@ i = 1 for file in files: - print >> sys.stderr, "Processing file", str(i), "of", len(files), "['" + file + "']" + print("Processing file", str(i), "of", len(files), "['" + file + "']", file=sys.stderr) cnt = convert_sample(path, file, out_path, alns) - print >> sys.stderr, " Added alignments for", cnt, "loci." + print(" Added alignments for", cnt, "loci.", file=sys.stderr) i += 1 # # Now process the catalog. # -print >> sys.stderr, "Processing the catalog" +print("Processing the catalog", file=sys.stderr) cnt = convert_catalog(path, batch_id, out_path, alns) -print >> sys.stderr, " Added alignments for", cnt, "catalog loci." +print(" Added alignments for", cnt, "catalog loci.", file=sys.stderr)