diff --git a/non-regression-tests/mimic_multi_machine/run_virome_mm.sh b/non-regression-tests/mimic_multi_machine/run_virome_mm.sh index cf79ac1376b7830949eca4860120dfde81217a9d..ab75c9de2c943ef52eec5775b66772317afc5678 100755 --- a/non-regression-tests/mimic_multi_machine/run_virome_mm.sh +++ b/non-regression-tests/mimic_multi_machine/run_virome_mm.sh @@ -4,7 +4,7 @@ DATA_PATH=../data mkdir tmp for i in 0 1 2 3 4 do - python ../../PhageTerm.py --mm --dir_cov_mm tmp -c 5 --core_id $i -f "$DATA_PATH/R1_1M_READS_EACH_PHAGE(1).fastq.4" -p "$DATA_PATH/R2_1M_READS_EACH_PHAGE(1).fastq.4" -r "$DATA_PATH/virome_6seq.fa" || exit 1$i + python ../../phagetermvirome/PhageTerm.py --mm --dir_cov_mm tmp -c 5 --core_id $i -f "$DATA_PATH/R1_1M_READS_EACH_PHAGE(1).fastq.4" -p "$DATA_PATH/R2_1M_READS_EACH_PHAGE(1).fastq.4" -r "$DATA_PATH/virome_6seq.fa" || exit 1$i done mkdir tmp2 @@ -12,8 +12,8 @@ mkdir DR for i in 0 1 2 3 4 5 do -python ../../PhageTerm.py --mm --dir_cov_mm=tmp --dir_seq_mm=tmp2 --DR_path=DR --seq_id=$i --nb_pieces=5 -f "$DATA_PATH/R1_1M_READS_EACH_PHAGE(1).fastq.4" -p "$DATA_PATH/R2_1M_READS_EACH_PHAGE(1).fastq.4" -r "$DATA_PATH/virome_6seq.fa" || exit 2$i +python ../../phagetermvirome/PhageTerm.py --mm --dir_cov_mm=tmp --dir_seq_mm=tmp2 --DR_path=DR --seq_id=$i --nb_pieces=5 -f "$DATA_PATH/R1_1M_READS_EACH_PHAGE(1).fastq.4" -p "$DATA_PATH/R2_1M_READS_EACH_PHAGE(1).fastq.4" -r "$DATA_PATH/virome_6seq.fa" || exit 2$i done -python ../../PhageTerm.py --mm -f "$DATA_PATH/R1_1M_READS_EACH_PHAGE(1).fastq.4" -p "$DATA_PATH/R2_1M_READS_EACH_PHAGE(1).fastq.4" -r "$DATA_PATH/virome_6seq.fa" --DR_path=DR --dir_seq_mm=tmp2 ||exit 3 +python ../../phagetermvirome/PhageTerm.py --mm -f "$DATA_PATH/R1_1M_READS_EACH_PHAGE(1).fastq.4" -p "$DATA_PATH/R2_1M_READS_EACH_PHAGE(1).fastq.4" -r "$DATA_PATH/virome_6seq.fa" --DR_path=DR --dir_seq_mm=tmp2 ||exit 3 python check_virome_res.py diff --git a/phagetermvirome/PhageTerm.py b/phagetermvirome/PhageTerm.py index 7aaa7648bf126320534acf96753a37ed63bc25ef..4894d27b4e8a36e5e6647bea2dfcac821db73362 100755 --- a/phagetermvirome/PhageTerm.py +++ b/phagetermvirome/PhageTerm.py @@ -120,12 +120,12 @@ def main(): f.close() exit() # Consider that if we put results in files, it is because we are processing large datasets on a cluster. if tParms.dir_cov_mm!=None and tParms.seq_id!=None and tParms.dir_seq_mm!=None and tParms.DR_path!=None: - from _modules.seq_processing import sum_readsCoverage_for_seq + from seq_processing import sum_readsCoverage_for_seq # in that case, we are processing all the results of readCoverage sequence by sequence in an embarrassingly parallel way on a cluster. sum_readsCoverage_for_seq(tParms.dir_cov_mm, tParms.seq_id, tParms.nb_pieces, inDArgs, fParms, inRawDArgs, tParms.dir_seq_mm,tParms.DR_path) exit() if tParms.dir_seq_mm!=None and tParms.dir_cov_mm==None and tParms.seq_id==None and tParms.DR_path!=None: # report generation - from _modules.generate_report import loadDR,genReport + from generate_report import loadDR,genReport loadDR(tParms.DR_path, DR) genReport(fParms, inDArgs, inRawDArgs, no_match, DR) exit() diff --git a/phagetermvirome/generate_report.py b/phagetermvirome/generate_report.py index abd73fa1f3ae631fc39b9d2b0803c562f1cc7a28..c11c92c96d45e7ecdbb55f232b1343f89966c023 100644 --- a/phagetermvirome/generate_report.py +++ b/phagetermvirome/generate_report.py @@ -3,7 +3,7 @@ import os import pickle from reportlab.platypus import SimpleDocTemplate, Paragraph, Spacer, Image, Table, TableStyle, PageBreak from reportlab.lib.pagesizes import letter, landscape -from _modules.functions_PhageTerm import SummaryReport,WorkflowReport,ExportCohesiveSeq,ExportPhageSequence,CreateReport +from functions_PhageTerm import SummaryReport,WorkflowReport,ExportCohesiveSeq,ExportPhageSequence,CreateReport def loadDR(DR_path,DR): diff --git a/phagetermvirome/seq_processing.py b/phagetermvirome/seq_processing.py index f3c66b2e474be2c34fbf5c09b8c264c65d93bc13..d188f4a3d394b73d284bb2706e710a10aebcf622 100755 --- a/phagetermvirome/seq_processing.py +++ b/phagetermvirome/seq_processing.py @@ -7,9 +7,9 @@ from __future__ import print_function from time import gmtime, strftime import os import numpy as np -from _modules.utilities import checkReportTitle -from _modules.readsCoverage_res import loadRCRes -from _modules.common_readsCoverage_processing import processCovValuesForSeq +from utilities import checkReportTitle +from readsCoverage_res import loadRCRes +from common_readsCoverage_processing import processCovValuesForSeq #from SeqStats import SeqStats def sum_readsCoverage_for_seq(dir_cov_res,idx_refseq,nb_pieces,inDArgs,fParms,inRawDArgs,dir_seq_res,DR_path): if os.path.exists(DR_path):