[med-svn] [Git][med-team/centrifuge][master] 6 commits: Use 2to3 to port to Python3
Andreas Tille
gitlab at salsa.debian.org
Tue Sep 10 07:38:00 BST 2019
Andreas Tille pushed to branch master at Debian Med / centrifuge
Commits:
7416efb0 by Andreas Tille at 2019-09-10T06:07:17Z
Use 2to3 to port to Python3
- - - - -
a8203d6d by Andreas Tille at 2019-09-10T06:07:54Z
Fix Depends
- - - - -
b96b8f0f by Andreas Tille at 2019-09-10T06:08:16Z
debhelper-compat 12
- - - - -
3f21054b by Andreas Tille at 2019-09-10T06:08:19Z
Standards-Version: 4.4.0
- - - - -
199e8685 by Andreas Tille at 2019-09-10T06:28:45Z
use dh-python
- - - - -
c8c350ba by Andreas Tille at 2019-09-10T06:31:09Z
Upload to unstable
- - - - -
6 changed files:
- debian/changelog
- − debian/compat
- debian/control
- + debian/patches/2to3.patch
- debian/patches/series
- debian/rules
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,13 @@
+centrifuge (1.0.3-3) unstable; urgency=medium
+
+ * Use 2to3 to port to Python3
+ Closes: #936281
+ * debhelper-compat 12
+ * Standards-Version: 4.4.0
+ * use dh-python
+
+ -- Andreas Tille <tille at debian.org> Tue, 10 Sep 2019 08:20:22 +0200
+
centrifuge (1.0.3-2) unstable; urgency=medium
[ Steffen Moeller ]
=====================================
debian/compat deleted
=====================================
@@ -1 +0,0 @@
-11
=====================================
debian/control
=====================================
@@ -3,10 +3,12 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.
Uploaders: Andreas Tille <tille at debian.org>
Section: science
Priority: optional
-Build-Depends: debhelper (>= 11~),
+Build-Depends: debhelper-compat (= 12),
+ dh-python,
+ dh-sequence-python3,
hisat2,
jellyfish
-Standards-Version: 4.3.0
+Standards-Version: 4.4.0
Vcs-Browser: https://salsa.debian.org/med-team/centrifuge
Vcs-Git: https://salsa.debian.org/med-team/centrifuge.git
Homepage: https://ccb.jhu.edu/software/centrifuge/
@@ -15,7 +17,8 @@ Package: centrifuge
Architecture: any
Depends: ${shlibs:Depends},
${misc:Depends},
- python,
+ ${python3:Depends},
+ python3,
hisat2,
jellyfish
Description: rapid and memory-efficient system for classification of DNA sequences
=====================================
debian/patches/2to3.patch
=====================================
@@ -0,0 +1,442 @@
+Description: Use 2to3 to port to Python3
+Bug-Debian: https://bugs.debian.org/936281
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Tue, 10 Sep 2019 08:02:24 +0200
+
+--- a/Makefile
++++ b/Makefile
+@@ -364,11 +364,11 @@ centrifuge.bat:
+
+ centrifuge-build.bat:
+ echo "@echo off" > centrifuge-build.bat
+- echo "python %~dp0/centrifuge-build %*" >> centrifuge-build.bat
++ echo "python3 %~dp0/centrifuge-build %*" >> centrifuge-build.bat
+
+ centrifuge-inspect.bat:
+ echo "@echo off" > centrifuge-inspect.bat
+- echo "python %~dp0/centrifuge-inspect %*" >> centrifuge-inspect.bat
++ echo "python3 %~dp0/centrifuge-inspect %*" >> centrifuge-inspect.bat
+
+
+ .PHONY: centrifuge-src
+--- a/centrifuge-build
++++ b/centrifuge-build
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+
+ """
+ Copyright 2014, Daehwan Kim <infphilo at gmail.com>
+--- a/centrifuge-inspect
++++ b/centrifuge-inspect
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+
+ """
+ Copyright 2014, Daehwan Kim <infphilo at gmail.com>
+--- a/evaluation/centrifuge_evaluate.py
++++ b/evaluation/centrifuge_evaluate.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+
+ import sys, os, subprocess, inspect
+ import platform, multiprocessing
+@@ -25,7 +25,7 @@ def read_taxonomy_tree(tax_file):
+ """
+ def compare_scm(centrifuge_out, true_out, taxonomy_tree, rank):
+ ancestors = set()
+- for tax_id in taxonomy_tree.keys():
++ for tax_id in list(taxonomy_tree.keys()):
+ if tax_id in ancestors:
+ continue
+ while True:
+@@ -106,7 +106,7 @@ def compare_scm(centrifuge_out, true_out
+ unclassified += 1
+
+ raw_unique_classified = 0
+- for value in db_dic.values():
++ for value in list(db_dic.values()):
+ if len(value) == 1:
+ raw_unique_classified += 1
+ return classified, unique_classified, unclassified, len(db_dic), raw_unique_classified
+@@ -152,7 +152,7 @@ def compare_abundance(centrifuge_out, tr
+ if tax_id in db_dic:
+ SSR += (abundance - db_dic[tax_id]) ** 2;
+ if debug:
+- print >> sys.stderr, "\t\t\t\t{:<10}: {:.6} vs. {:.6} (truth vs. centrifuge)".format(tax_id, abundance, db_dic[tax_id])
++ print("\t\t\t\t{:<10}: {:.6} vs. {:.6} (truth vs. centrifuge)".format(tax_id, abundance, db_dic[tax_id]), file=sys.stderr)
+ else:
+ SSR += (abundance) ** 2
+
+@@ -179,7 +179,7 @@ def sql_execute(sql_db, sql_query):
+ """
+ def create_sql_db(sql_db):
+ if os.path.exists(sql_db):
+- print >> sys.stderr, sql_db, "already exists!"
++ print(sql_db, "already exists!", file=sys.stderr)
+ return
+
+ columns = [
+@@ -316,7 +316,7 @@ def evaluate(index_base,
+ os.mkdir(index_path)
+ index_fnames = ["%s/%s.%d.cf" % (index_path, index_base, i+1) for i in range(3)]
+ if not check_files(index_fnames):
+- print >> sys.stderr, "Downloading indexes: %s" % ("index")
++ print("Downloading indexes: %s" % ("index"), file=sys.stderr)
+ os.system("cd %s; wget ftp://ftp.ccb.jhu.edu/pub/infphilo/centrifuge/data/%s.tar.gz; tar xvzf %s.tar.gz; rm %s.tar.gz; ln -s %s/%s* .; cd -" % \
+ (index_path, index_base, index_base, index_base, index_base, index_base))
+ assert check_files(index_fnames)
+@@ -356,7 +356,7 @@ def evaluate(index_base,
+ scm_fname = "%s/%s.scm" % (read_path, read_base)
+ read_fnames = [read1_fname, read2_fname, truth_fname, scm_fname]
+ if not check_files(read_fnames):
+- print >> sys.stderr, "Simulating reads %s_1.fq %s_2.fq ..." % (read_base, read_base)
++ print("Simulating reads %s_1.fq %s_2.fq ..." % (read_base, read_base), file=sys.stderr)
+ centrifuge_simulate = os.path.join(path_base, "centrifuge_simulate_reads.py")
+ simulate_cmd = [centrifuge_simulate,
+ "--num-fragment", str(num_fragment)]
+@@ -377,11 +377,11 @@ def evaluate(index_base,
+ else:
+ base_fname = read_base + "_single"
+
+- print >> sys.stderr, "Database: %s" % (index_base)
++ print("Database: %s" % (index_base), file=sys.stderr)
+ if paired:
+- print >> sys.stderr, "\t%d million pairs" % (num_fragment / 1000000)
++ print("\t%d million pairs" % (num_fragment / 1000000), file=sys.stderr)
+ else:
+- print >> sys.stderr, "\t%d million reads" % (num_fragment / 1000000)
++ print("\t%d million reads" % (num_fragment / 1000000), file=sys.stderr)
+
+ program_bin_base = "%s/.." % path_base
+ def get_program_version(program, version):
+@@ -428,7 +428,7 @@ def evaluate(index_base,
+ if version:
+ program_name += ("_%s" % version)
+
+- print >> sys.stderr, "\t%s\t%s" % (program_name, str(datetime.now()))
++ print("\t%s\t%s" % (program_name, str(datetime.now())), file=sys.stderr)
+ if paired:
+ program_dir = program_name + "_paired"
+ else:
+@@ -449,7 +449,7 @@ def evaluate(index_base,
+ program_cmd = get_program_cmd(program, version, read1_fname, read2_fname, out_fname)
+ start_time = datetime.now()
+ if verbose:
+- print >> sys.stderr, "\t", start_time, " ".join(program_cmd)
++ print("\t", start_time, " ".join(program_cmd), file=sys.stderr)
+ if program in ["centrifuge"]:
+ proc = subprocess.Popen(program_cmd, stdout=open(out_fname, "w"), stderr=subprocess.PIPE)
+ else:
+@@ -462,7 +462,7 @@ def evaluate(index_base,
+ if duration < 0.1:
+ duration = 0.1
+ if verbose:
+- print >> sys.stderr, "\t", finish_time, "finished:", duration
++ print("\t", finish_time, "finished:", duration, file=sys.stderr)
+
+ results = {"strain" : [0, 0, 0],
+ "species" : [0, 0, 0],
+@@ -484,21 +484,21 @@ def evaluate(index_base,
+ # if rank == "strain":
+ # assert num_cases == num_fragment
+
+- print >> sys.stderr, "\t\t%s" % rank
+- print >> sys.stderr, "\t\t\tsensitivity: {:,} / {:,} ({:.2%})".format(classified, num_cases, float(classified) / num_cases)
+- print >> sys.stderr, "\t\t\tprecision : {:,} / {:,} ({:.2%})".format(classified, raw_classified, float(classified) / raw_classified)
+- print >> sys.stderr, "\n\t\t\tfor uniquely classified ",
++ print("\t\t%s" % rank, file=sys.stderr)
++ print("\t\t\tsensitivity: {:,} / {:,} ({:.2%})".format(classified, num_cases, float(classified) / num_cases), file=sys.stderr)
++ print("\t\t\tprecision : {:,} / {:,} ({:.2%})".format(classified, raw_classified, float(classified) / raw_classified), file=sys.stderr)
++ print("\n\t\t\tfor uniquely classified ", end=' ', file=sys.stderr)
+ if paired:
+- print >> sys.stderr, "pairs"
++ print("pairs", file=sys.stderr)
+ else:
+- print >> sys.stderr, "reads"
+- print >> sys.stderr, "\t\t\t\t\tsensitivity: {:,} / {:,} ({:.2%})".format(unique_classified, num_cases, float(unique_classified) / num_cases)
+- print >> sys.stderr, "\t\t\t\t\tprecision : {:,} / {:,} ({:.2%})".format(unique_classified, raw_unique_classified, float(unique_classified) / raw_unique_classified)
++ print("reads", file=sys.stderr)
++ print("\t\t\t\t\tsensitivity: {:,} / {:,} ({:.2%})".format(unique_classified, num_cases, float(unique_classified) / num_cases), file=sys.stderr)
++ print("\t\t\t\t\tprecision : {:,} / {:,} ({:.2%})".format(unique_classified, raw_unique_classified, float(unique_classified) / raw_unique_classified), file=sys.stderr)
+
+ # Calculate sum of squared residuals in abundance
+ if rank == "strain":
+ abundance_SSR = compare_abundance("centrifuge_report.tsv", truth_fname, taxonomy_tree, debug)
+- print >> sys.stderr, "\t\t\tsum of squared residuals in abundance: {}".format(abundance_SSR)
++ print("\t\t\tsum of squared residuals in abundance: {}".format(abundance_SSR), file=sys.stderr)
+
+ if runtime_only:
+ os.chdir("..")
+--- a/evaluation/centrifuge_simulate_reads.py
++++ b/evaluation/centrifuge_simulate_reads.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+
+ #
+ # Copyright 2015, Daehwan Kim <infphilo at gmail.com>
+@@ -156,7 +156,7 @@ def read_transcript(genomes_seq, gtf_fil
+ transcripts[transcript_id][2].append([left, right])
+
+ # Sort exons and merge where separating introns are <=5 bps
+- for tran, [chr, strand, exons] in transcripts.items():
++ for tran, [chr, strand, exons] in list(transcripts.items()):
+ exons.sort()
+ tmp_exons = [exons[0]]
+ for i in range(1, len(exons)):
+@@ -167,7 +167,7 @@ def read_transcript(genomes_seq, gtf_fil
+ transcripts[tran] = [chr, strand, tmp_exons]
+
+ tmp_transcripts = {}
+- for tran, [chr, strand, exons] in transcripts.items():
++ for tran, [chr, strand, exons] in list(transcripts.items()):
+ exon_lens = [e[1] - e[0] + 1 for e in exons]
+ transcript_len = sum(exon_lens)
+ if transcript_len >= frag_len:
+@@ -444,8 +444,8 @@ def getSamAlignment(dna, exons, genome_s
+ MD += ("{}".format(MD_match_len))
+
+ if len(read_seq) != read_len:
+- print >> sys.stderr, "read length differs:", len(read_seq), "vs.", read_len
+- print >> sys.stderr, pos, "".join(cigars), cigar_descs, MD, XM, NM, Zs
++ print("read length differs:", len(read_seq), "vs.", read_len, file=sys.stderr)
++ print(pos, "".join(cigars), cigar_descs, MD, XM, NM, Zs, file=sys.stderr)
+ assert False
+
+ return pos, cigars, cigar_descs, MD, XM, NM, Zs, read_seq
+@@ -575,8 +575,8 @@ def samRepOk(genome_seq, read_seq, chr,
+ tMD += ("{}".format(match_len))
+
+ if tMD != MD or tXM != XM or tNM != NM or XM > max_mismatch or XM != NM:
+- print >> sys.stderr, chr, pos, cigar, MD, XM, NM, Zs
+- print >> sys.stderr, tMD, tXM, tNM
++ print(chr, pos, cigar, MD, XM, NM, Zs, file=sys.stderr)
++ print(tMD, tXM, tNM, file=sys.stderr)
+ assert False
+
+
+@@ -631,7 +631,7 @@ def simulate_reads(index_fname, base_fna
+ # Read genome sequences into memory
+ genomes_fname = index_fname + ".fa"
+ if not os.path.exists(genomes_fname):
+- print >> sys.stderr, "Extracting genomes from Centrifuge index to %s, which may take a few hours ..." % (genomes_fname)
++ print("Extracting genomes from Centrifuge index to %s, which may take a few hours ..." % (genomes_fname), file=sys.stderr)
+ extract_cmd = [centrifuge_inspect,
+ index_fname]
+ extract_proc = subprocess.Popen(extract_cmd, stdout=open(genomes_fname, 'w'))
+@@ -660,15 +660,15 @@ def simulate_reads(index_fname, base_fna
+ assert num_frag == sum(expr_profile)
+
+ if dna:
+- genome_ids = genome_seqs.keys()
++ genome_ids = list(genome_seqs.keys())
+ else:
+- transcript_ids = transcripts.keys()
++ transcript_ids = list(transcripts.keys())
+ random.shuffle(transcript_ids)
+ assert len(transcript_ids) >= len(expr_profile)
+
+ # Truth table
+ truth_file = open(base_fname + ".truth", "w")
+- print >> truth_file, "taxID\tgenomeLen\tnumReads\tabundance\tname"
++ print("taxID\tgenomeLen\tnumReads\tabundance\tname", file=truth_file)
+ truth_list = []
+ normalized_sum = 0.0
+ debug_num_frag = 0
+@@ -695,19 +695,19 @@ def simulate_reads(index_fname, base_fna
+ if can_tax_id in names:
+ name = names[can_tax_id]
+ abundance = raw_abundance / genome_len / normalized_sum
+- print >> truth_file, "{}\t{}\t{}\t{:.6}\t{}".format(tax_id, genome_len, t_num_frags, abundance, name)
++ print("{}\t{}\t{}\t{:.6}\t{}".format(tax_id, genome_len, t_num_frags, abundance, name), file=truth_file)
+ truth_file.close()
+
+ # Sequence Classification Map (SCM) - something I made up ;-)
+ scm_file = open(base_fname + ".scm", "w")
+
+ # Write SCM header
+- print >> scm_file, "@HD\tVN:1.0\tSO:unsorted"
+- for tax_id in genome_seqs.keys():
++ print("@HD\tVN:1.0\tSO:unsorted", file=scm_file)
++ for tax_id in list(genome_seqs.keys()):
+ name = ""
+ if tax_id in names:
+ name = names[tax_id]
+- print >> scm_file, "@SQ\tTID:%s\tSN:%s\tLN:%d" % (tax_id, name, len(genome_seqs[tax_id]))
++ print("@SQ\tTID:%s\tSN:%s\tLN:%d" % (tax_id, name, len(genome_seqs[tax_id])), file=scm_file)
+
+ read_file = open(base_fname + "_1.fa", "w")
+ if paired_end:
+@@ -718,11 +718,11 @@ def simulate_reads(index_fname, base_fna
+ t_num_frags = expr_profile[t]
+ if dna:
+ tax_id = genome_ids[t]
+- print >> sys.stderr, "TaxID: %s, num fragments: %d" % (tax_id, t_num_frags)
++ print("TaxID: %s, num fragments: %d" % (tax_id, t_num_frags), file=sys.stderr)
+ else:
+ transcript_id = transcript_ids[t]
+ chr, strand, transcript_len, exons = transcripts[transcript_id]
+- print >> sys.stderr, transcript_id, t_num_frags
++ print(transcript_id, t_num_frags, file=sys.stderr)
+
+ genome_seq = genome_seqs[tax_id]
+ genome_len = len(genome_seq)
+@@ -763,14 +763,14 @@ def simulate_reads(index_fname, base_fna
+ XS = "\tXS:A:{}".format(strand)
+ TI = "\tTI:Z:{}".format(transcript_id)
+
+- print >> read_file, ">{}".format(cur_read_id)
+- print >> read_file, read_seq
++ print(">{}".format(cur_read_id), file=read_file)
++ print(read_seq, file=read_file)
+ output = "{}\t{}\t{}\t{}\tNM:i:{}\tMD:Z:{}".format(cur_read_id, tax_id, pos + 1, cigar_str, NM, MD)
+ if paired_end:
+- print >> read2_file, ">{}".format(cur_read_id)
+- print >> read2_file, reverse_complement(read2_seq)
++ print(">{}".format(cur_read_id), file=read2_file)
++ print(reverse_complement(read2_seq), file=read2_file)
+ output += "\t{}\t{}\tNM2:i:{}\tMD2:Z:{}".format(pos2 + 1, cigar2_str, NM2, MD2)
+- print >> scm_file, output
++ print(output, file=scm_file)
+
+ cur_read_id += 1
+
+@@ -865,7 +865,7 @@ if __name__ == '__main__':
+ parser.print_help()
+ exit(1)
+ if not args.dna:
+- print >> sys.stderr, "Error: --rna is not implemented."
++ print("Error: --rna is not implemented.", file=sys.stderr)
+ exit(1)
+ # if args.dna:
+ # args.expr_profile = "constant"
+--- a/evaluation/test/centrifuge_evaluate_mason.py
++++ b/evaluation/test/centrifuge_evaluate_mason.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+
+ import sys, os, subprocess, inspect
+ import platform, multiprocessing
+@@ -27,7 +27,7 @@ def compare_scm(centrifuge_out, true_out
+ higher_ranked = {}
+
+ ancestors = set()
+- for tax_id in taxonomy_tree.keys():
++ for tax_id in list(taxonomy_tree.keys()):
+ if tax_id in ancestors:
+ continue
+ while True:
+@@ -82,7 +82,7 @@ def compare_scm(centrifuge_out, true_out
+
+ fields = line.strip().split('\t')
+ if len(fields) != 3:
+- print >> sys.stderr, "Warning: %s missing" % (line.strip())
++ print("Warning: %s missing" % (line.strip()), file=sys.stderr)
+ continue
+ read_name, tax_id = fields[1:3]
+ # Traverse up taxonomy tree to match the given rank parameter
+@@ -117,7 +117,7 @@ def compare_scm(centrifuge_out, true_out
+ # print read_name
+
+ raw_unique_classified = 0
+- for read_name, maps in db_dic.items():
++ for read_name, maps in list(db_dic.items()):
+ if len(maps) == 1 and read_name not in higher_ranked:
+ raw_unique_classified += 1
+ return classified, unique_classified, unclassified, len(db_dic), raw_unique_classified
+@@ -184,7 +184,7 @@ def evaluate(index_base,
+ read_fname]
+
+ if verbose:
+- print >> sys.stderr, ' '.join(centrifuge_cmd)
++ print(' '.join(centrifuge_cmd), file=sys.stderr)
+
+ out_fname = "centrifuge.output"
+ proc = subprocess.Popen(centrifuge_cmd, stdout=open(out_fname, "w"), stderr=subprocess.PIPE)
+@@ -208,12 +208,12 @@ def evaluate(index_base,
+ # if rank == "strain":
+ # assert num_cases == num_fragment
+
+- print >> sys.stderr, "\t\t%s" % rank
+- print >> sys.stderr, "\t\t\tsensitivity: {:,} / {:,} ({:.2%})".format(classified, num_cases, float(classified) / num_cases)
+- print >> sys.stderr, "\t\t\tprecision : {:,} / {:,} ({:.2%})".format(classified, raw_classified, float(classified) / raw_classified)
+- print >> sys.stderr, "\n\t\t\tfor uniquely classified "
+- print >> sys.stderr, "\t\t\t\t\tsensitivity: {:,} / {:,} ({:.2%})".format(unique_classified, num_cases, float(unique_classified) / num_cases)
+- print >> sys.stderr, "\t\t\t\t\tprecision : {:,} / {:,} ({:.2%})".format(unique_classified, raw_unique_classified, float(unique_classified) / raw_unique_classified)
++ print("\t\t%s" % rank, file=sys.stderr)
++ print("\t\t\tsensitivity: {:,} / {:,} ({:.2%})".format(classified, num_cases, float(classified) / num_cases), file=sys.stderr)
++ print("\t\t\tprecision : {:,} / {:,} ({:.2%})".format(classified, raw_classified, float(classified) / raw_classified), file=sys.stderr)
++ print("\n\t\t\tfor uniquely classified ", file=sys.stderr)
++ print("\t\t\t\t\tsensitivity: {:,} / {:,} ({:.2%})".format(unique_classified, num_cases, float(unique_classified) / num_cases), file=sys.stderr)
++ print("\t\t\t\t\tprecision : {:,} / {:,} ({:.2%})".format(unique_classified, raw_unique_classified, float(unique_classified) / raw_unique_classified), file=sys.stderr)
+
+ # Calculate sum of squared residuals in abundance
+ """
+@@ -252,12 +252,12 @@ def evaluate(index_base,
+ if rank_taxID not in true_abundance:
+ true_abundance[rank_taxID] = 0.0
+ true_abundance[rank_taxID] += (reads / float(genomeSize))
+- for taxID, reads in true_abundance.items():
++ for taxID, reads in list(true_abundance.items()):
+ true_abundance[taxID] /= total_sum
+
+- print >> sys.stderr, "number of genomes:", num_genomes
+- print >> sys.stderr, "number of species:", num_species
+- print >> sys.stderr, "number of uniq species:", len(true_abundance)
++ print("number of genomes:", num_genomes, file=sys.stderr)
++ print("number of species:", num_species, file=sys.stderr)
++ print("number of uniq species:", len(true_abundance), file=sys.stderr)
+
+ read_fname = "centrifuge_data/bacteria_sim10M/bacteria_sim10M.fa"
+ summary_fname = "centrifuge.summary"
+@@ -271,14 +271,14 @@ def evaluate(index_base,
+ read_fname]
+
+ if verbose:
+- print >> sys.stderr, ' '.join(centrifuge_cmd)
++ print(' '.join(centrifuge_cmd), file=sys.stderr)
+
+ out_fname = "centrifuge.output"
+ proc = subprocess.Popen(centrifuge_cmd, stdout=open(out_fname, "w"), stderr=subprocess.PIPE)
+ proc.communicate()
+
+ calc_abundance = {}
+- for taxID in true_abundance.keys():
++ for taxID in list(true_abundance.keys()):
+ calc_abundance[taxID] = 0.0
+ first = True
+ for line in open(summary_fname):
+@@ -296,12 +296,12 @@ def evaluate(index_base,
+ """
+
+ abundance_file = open("abundance.cmp", 'w')
+- print >> abundance_file, "taxID\ttrue\tcalc\trank"
++ print("taxID\ttrue\tcalc\trank", file=abundance_file)
+ for rank in ranks:
+ if rank == "strain":
+ continue
+ true_abundance_rank, calc_abundance_rank = {}, {}
+- for taxID in true_abundance.keys():
++ for taxID in list(true_abundance.keys()):
+ assert taxID in calc_abundance
+ rank_taxID = taxID
+ while True:
+@@ -322,11 +322,11 @@ def evaluate(index_base,
+ calc_abundance_rank[rank_taxID] += calc_abundance[taxID]
+
+ ssr = 0.0 # Sum of Squared Residuals
+- for taxID in true_abundance_rank.keys():
++ for taxID in list(true_abundance_rank.keys()):
+ assert taxID in calc_abundance_rank
+ ssr += (true_abundance_rank[taxID] - calc_abundance_rank[taxID]) ** 2
+- print >> abundance_file, "%s\t%.6f\t%.6f\t%s" % (taxID, true_abundance_rank[taxID], calc_abundance_rank[taxID], rank)
+- print >> sys.stderr, "%s) Sum of squared residuals: %.6f" % (rank, ssr)
++ print("%s\t%.6f\t%.6f\t%s" % (taxID, true_abundance_rank[taxID], calc_abundance_rank[taxID], rank), file=abundance_file)
++ print("%s) Sum of squared residuals: %.6f" % (rank, ssr), file=sys.stderr)
+ abundance_file.close()
+
+
=====================================
debian/patches/series
=====================================
@@ -3,3 +3,4 @@ fix_auto_ptr_usage_in_gcc-7.patch
0003-Fix-make-install-DESTDIR.patch
hardening.patch
no_msse2.patch
+2to3.patch
=====================================
debian/rules
=====================================
@@ -9,7 +9,7 @@ include /usr/share/dpkg/default.mk
export DEB_BUILD_MAINT_OPTIONS = hardening=+all
export POPCNT_CAPABILITY=0
%:
- dh $@
+ dh $@ --with python3
override_dh_auto_install:
dh_auto_install -- prefix=/usr/lib/centrifuge
View it on GitLab: https://salsa.debian.org/med-team/centrifuge/compare/3d1220dfe7fe555221b2d4d13c43eedd0ca488c2...c8c350baaea33549d4b570992524275b688a4285
--
View it on GitLab: https://salsa.debian.org/med-team/centrifuge/compare/3d1220dfe7fe555221b2d4d13c43eedd0ca488c2...c8c350baaea33549d4b570992524275b688a4285
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