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Merge pull request #128 from broadinstitute/dp-fix
pylint/landscape inspired code fixes
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -7,11 +7,11 @@ | |
| "[email protected], [email protected]" | ||
| __commands__ = [] | ||
|
|
||
| import argparse, logging, itertools, re, shutil, tempfile, os | ||
| import argparse, logging, itertools, re, shutil, os | ||
| import Bio.AlignIO, Bio.SeqIO, Bio.Data.IUPACData | ||
| import pysam | ||
| import util.cmd, util.file, util.vcf, util.misc | ||
| from util.stats import mean, median, fisher_exact, chi2_contingency | ||
| from util.stats import median, fisher_exact, chi2_contingency | ||
| from interhost import CoordMapper | ||
| from tools.vphaser2 import Vphaser2Tool | ||
| from tools.samtools import SamtoolsTool | ||
|
|
@@ -117,7 +117,7 @@ def filter_strand_bias(isnvs, minReadsEach = None, maxBias = None) : | |
| if maxBias == None : | ||
| maxBias = defaultMaxBias | ||
| for row in isnvs: | ||
| front = row[:alleleCol] | ||
| #front = row[:alleleCol] | ||
| for fieldInd in range(len(row) - 1, alleleCol - 1, -1) : | ||
| f, r = AlleleFieldParser(row[fieldInd]).strand_counts() | ||
| if (int(f)<minReadsEach or int(r)<minReadsEach | ||
|
|
@@ -179,8 +179,8 @@ def compute_library_bias(isnvs, inBam, inConsFasta) : | |
| libBam = rgBams[0] | ||
| samtoolsTool.index(libBam) | ||
| n_reads = samtoolsTool.count(libBam) | ||
| log.debug("LB:{} has {} reads in {} read groups ({})".format( | ||
| lib, n_reads, len(rgs), ', '.join(rgs))) | ||
| log.debug("LB:%s has %s reads in %s read groups (%s)", | ||
| lib, n_reads, len(rgs), ', '.join(rgs)) | ||
| libBams.append(libBam) | ||
|
|
||
| for row in isnvs : | ||
|
|
@@ -454,8 +454,8 @@ def merge_to_vcf(refFasta, outVcf, samples, isnvs, assemblies, strip_chr_version | |
| if tot_n>0 and float(n)/tot_n >= 0.005) | ||
| # drop this position:sample if no variation left | ||
| if len(row['allele_counts']) < 2: | ||
| log.info("dropping iSNV at %s:%s (%s) because no variation remains after simple filtering" % ( | ||
| row['s_chrom'], row['s_pos'], row['sample'])) | ||
| log.info("dropping iSNV at %s:%s (%s) because no variation remains after simple filtering", | ||
| row['s_chrom'], row['s_pos'], row['sample']) | ||
| continue | ||
| # reposition vphaser deletions minus one to be consistent with | ||
| # VCF conventions | ||
|
|
@@ -512,7 +512,7 @@ def merge_to_vcf(refFasta, outVcf, samples, isnvs, assemblies, strip_chr_version | |
| cons_stop = samp_to_cmap[s].mapBtoA(ref_sequence.id, end, side = 1)[1] | ||
| if cons_start == None or cons_stop == None : | ||
| log.info("variant is outside consensus assembly " | ||
| "for %s at %s:%s-%s." % (s, ref_sequence.id, pos, end)) | ||
| "for %s at %s:%s-%s.", s, ref_sequence.id, pos, end) | ||
| continue | ||
| cons = samp_to_seqIndex[s][samp_to_cmap[s].mapBtoA(ref_sequence.id)] | ||
| allele = str(cons[cons_start-1:cons_stop].seq).upper() | ||
|
|
@@ -521,7 +521,7 @@ def merge_to_vcf(refFasta, outVcf, samples, isnvs, assemblies, strip_chr_version | |
| if all(a in set(('A','C','T','G')) for a in allele): | ||
| consAlleles[s] = allele | ||
| else: | ||
| log.warning("dropping ambiguous consensus for %s at %s:%s-%s: %s" % (s, ref_sequence.id, pos, end, allele)) | ||
| log.warning("dropping ambiguous consensus for %s at %s:%s-%s: %s", s, ref_sequence.id, pos, end, allele) | ||
|
|
||
| # define genotypes and fractions | ||
| iSNVs = {} # {sample : {allele : fraction, ...}, ...} | ||
|
|
@@ -575,8 +575,8 @@ def merge_to_vcf(refFasta, outVcf, samples, isnvs, assemblies, strip_chr_version | |
| raise Exception() | ||
| if f>0.5 and a!=consAllele[samp_offsets[s]]: | ||
| log.warning("vPhaser and assembly pipelines mismatch at " | ||
| "%s:%d (%s) - consensus %s, vPhaser %s" % | ||
| (ref_sequence.id, pos, s, consAllele[samp_offsets[s]], a)) | ||
| "%s:%d (%s) - consensus %s, vPhaser %s", | ||
| ref_sequence.id, pos, s, consAllele[samp_offsets[s]], a) | ||
| new_allele = list(consAllele) | ||
| new_allele[samp_offsets[s]] = a | ||
| a = ''.join(new_allele) | ||
|
|
@@ -612,7 +612,7 @@ def merge_to_vcf(refFasta, outVcf, samples, isnvs, assemblies, strip_chr_version | |
| # if we filtered any alleles above, make sure to omit absent alleles | ||
| alleles_isnv2.append((len(counts),sum(counts),a)) | ||
| else: | ||
| log.info("dropped allele {} at position {}:{}".format(a, ref_sequence.id, pos)) | ||
| log.info("dropped allele %s at position %s:%s", a, ref_sequence.id, pos) | ||
| alleles_isnv = list(allele for n_samples, n_reads, allele in reversed(sorted(alleles_isnv2))) | ||
| alleles = list(util.misc.unique([refAllele] + alleles_cons + alleles_isnv)) | ||
|
|
||
|
|
@@ -621,7 +621,7 @@ def merge_to_vcf(refFasta, outVcf, samples, isnvs, assemblies, strip_chr_version | |
| raise Exception() | ||
| elif len(alleles)==1: | ||
| # if we filtered any alleles above, skip this position if there is no variation left here | ||
| log.info("dropped position {}:{} due to lack of variation".format(ref_sequence.id, pos)) | ||
| log.info("dropped position %s:%s due to lack of variation", ref_sequence.id, pos) | ||
| continue | ||
| alleleMap = dict((a,i) for i,a in enumerate(alleles)) | ||
| genos = [str(alleleMap.get(consAlleles.get(s),'.')) for s in samples] | ||
|
|
@@ -690,10 +690,10 @@ def parser_merge_to_vcf(parser=argparse.ArgumentParser()): | |
| # =================================================== | ||
|
|
||
| def compute_Fws(vcfrow): | ||
| format = vcfrow[8].split(':') | ||
| if 'AF' not in format: | ||
| format_col = vcfrow[8].split(':') | ||
| if 'AF' not in format_col: | ||
| return None | ||
| af_idx = format.index('AF') | ||
| af_idx = format_col.index('AF') | ||
|
|
||
| freqs = [dat.split(':') for dat in vcfrow[9:]] | ||
| freqs = [float(dat[af_idx].split(',')[0]) for dat in freqs if len(dat)>af_idx and dat[af_idx]!='.' and dat[0]!='.' and int(dat[0])<=1] | ||
|
|
@@ -857,7 +857,7 @@ def iSNV_table(vcf_iter): | |
| out['Fws_snp'] = info['FWS'] | ||
| yield out | ||
| except: | ||
| log.error("VCF parsing error at {}:{}".format(row['CHROM'], row['POS'])) | ||
| log.error("VCF parsing error at %s:%s", row['CHROM'], row['POS']) | ||
| raise | ||
|
|
||
| def parser_iSNV_table(parser=argparse.ArgumentParser()): | ||
|
|
||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -5,7 +5,7 @@ | |
| __author__ = "[email protected]" | ||
| __commands__ = [] | ||
|
|
||
| import argparse, logging, subprocess, glob, os, os.path, time | ||
| import argparse, logging, subprocess, glob, os, time | ||
| import pysam, Bio.SeqIO | ||
| import util.cmd, util.file, util.misc | ||
| import tools.samtools | ||
|
|
||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -7,7 +7,7 @@ | |
| + "[email protected]" | ||
| __commands__ = [] | ||
|
|
||
| import argparse, logging, subprocess, os, tempfile, errno, shutil | ||
| import argparse, logging, subprocess, os, tempfile, shutil | ||
| from Bio import SeqIO | ||
| import util.cmd, util.file | ||
| import tools, tools.blast | ||
|
|
@@ -117,7 +117,6 @@ def lastal_get_hits(inFastq, db, outList): | |
| lastalPath = tools.last.Lastal().install_and_get_path() | ||
| mafSortPath = tools.last.MafSort().install_and_get_path() | ||
| mafConvertPath = tools.last.MafConvert().install_and_get_path() | ||
| prinseqPath = tools.prinseq.PrinseqTool().install_and_get_path() | ||
| noBlastLikeHitsPath = os.path.join( util.file.get_scripts_path(), | ||
| 'noBlastLikeHits.py') | ||
|
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||
|
|
@@ -560,7 +559,7 @@ def deplete_blastn(inFastq, outFastq, refDbs) : | |
| ## Run blastn using each of the databases in turn | ||
| blastOutFiles = [] | ||
| for db in refDbs : | ||
| log.info("running blastn on {} against {}".format(inFastq, db)) | ||
| log.info("running blastn on %s against %s", inFastq, db) | ||
| blastOutFiles += blastn_chunked_fasta(inFasta, db) | ||
|
|
||
| ## Combine results from different databases | ||
|
|
@@ -640,7 +639,7 @@ def deplete_blastn_bam(inBam, db, outBam, chunkSize=1000000, JVMmemory=None): | |
| read_utils.fastq_to_fasta(fastq1, fasta) | ||
| os.unlink(fastq1) | ||
| os.unlink(fastq2) | ||
| log.info("running blastn on {} pair 1 against {}".format(inBam, db)) | ||
| log.info("running blastn on %s pair 1 against %s", inBam, db) | ||
| blastOutFiles = blastn_chunked_fasta(fasta, db, chunkSize) | ||
| with open(blast_hits, 'wt') as outf: | ||
| for blastOutFile in blastOutFiles: | ||
|
|
@@ -662,7 +661,7 @@ def deplete_blastn_bam(inBam, db, outBam, chunkSize=1000000, JVMmemory=None): | |
| read_utils.fastq_to_fasta(fastq2, fasta) | ||
| os.unlink(fastq1) | ||
| os.unlink(fastq2) | ||
| log.info("running blastn on {} pair 2 against {}".format(inBam, db)) | ||
| log.info("running blastn on %s pair 2 against %s", inBam, db) | ||
| blastOutFiles = blastn_chunked_fasta(fasta, db, chunkSize) | ||
| with open(blast_hits, 'wt') as outf: | ||
| for blastOutFile in blastOutFiles: | ||
|
|
||
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