Created
November 18, 2017 08:29
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make fastq; align; make expression table;
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| # usage: | |
| # python 3reads.py /batch/dir1/ /batch/dir2/ # run all steps on two batches | |
| # python 3reads.py -2 -3 -loadAndKeep /batch/dir # run steps 2 and 3 and use STAR --loadAndKeep | |
| # python 3reads.py /batch/dir1 /batch/dir2/ -13 # run steps 1 and 3 on two batches | |
| import sys, os | |
| base_dir = '/home/sxv/code/s7s/' | |
| MAKE_FASTQ = '%s/make_fastq.sh' % base_dir | |
| ALIGN = '%s/align_smart-3seq.sh' % base_dir | |
| MAKE_EXPRESSION_TABLE = '%s/make_expression_table.R' % base_dir | |
| steps = '123' | |
| batch_dirs = [] | |
| for arg in sys.argv[1:]: | |
| if arg[0] == '-': | |
| if arg == '-loadAndKeep' or arg == '-keep': | |
| ALIGN = '%s/align_smart-3seq.loadAndKeep.sh' % base_dir | |
| else: | |
| if steps == '123': | |
| steps = arg[1:] | |
| else: | |
| steps += arg[1:] | |
| else: | |
| batch_dirs.append(arg) | |
| def make_fastq(): | |
| os.system("bash -c 'cp %s %s'" % (MAKE_FASTQ, batch_dir)) | |
| os.system("bash -c 'cd %s && bash %s .'" % (batch_dir, MAKE_FASTQ)) | |
| os.system("bash -c 'cd %s && mkdir -p fastq && mv *gz fastq'" % batch_dir) | |
| def align(): | |
| os.system("bash -c 'cp %s %s/fastq/'" % (ALIGN, batch_dir)) | |
| os.system("bash -c 'cd %s/fastq && bash %s /media/stroma-common/genome/hg38/star/dbsnp147_gencode25-68/ *fastq.gz'" % (batch_dir, ALIGN)) | |
| os.system("bash -c 'cd %s && mkdir -p bam && mv fastq/*ba? fastq/*log bam/'" % batch_dir) | |
| def make_expression_table(): | |
| os.system("bash -c 'cp %s %s/bam'" % (MAKE_EXPRESSION_TABLE, batch_dir)) | |
| os.system("bash -c 'cd %s/bam && Rscript %s --no-rlog /media/stroma-common/genome/hg38/gencode.v25.annotation.gtf *bam'" % (batch_dir, MAKE_EXPRESSION_TABLE)) | |
| os.system("bash -c 'cd %s/bam && xlsx2csv -s 1 gene_expression.xlsx raw_reads.csv'" % batch_dir) | |
| project_name = batch_dir.split('/')[-1] or batch_dir.split('/')[-2] | |
| os.system("bash -c 'cd %s/bam && cp raw_reads.csv %s.raw_reads.csv && cp raw_reads.csv %sresults/%s.raw_reads.csv'" % (batch_dir, project_name, base_dir, project_name)) | |
| for batch_dir in batch_dirs: | |
| if '1' in steps: make_fastq() | |
| if '2' in steps: align() | |
| if '3' in steps: make_expression_table() | |
| # if 'o' in steps: optional_step() |
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