idseq流程比对结果到输出-align_output_20211217

import click
import pandas as pd
import os

@click.command()
@click.option('-i', '--input_hostfilter_file', help='input_hostfilter_file_path_name(/home/lijing/all_test/test_202112/tmp_star_trimmomatic_priceseq_dedup_lzw_bowtie2_gsnap.fasta |...)', required=True)

@click.option('-n', '--input_hostfilter_file_name', help='input_hostfilter_file_name(tmp_star_trimmomatic_priceseq_dedup_lzw_bowtie2_gsnap.fasta |...)', required=True)

@click.option('-d', '--docker', help='docker_name(823fa78ed660 |...)', required=True)
# @click.option('-i', '--inputfile', help='search_file(number_nt_virus_blastn.m8/number_nt_bacteria_blastn.m8/...)', required=True)

@click.option('-ga', '--gsnap_aligndatabase',
              help='gsnap_aligndatabase_name(/idseqflow-dockerfile-container-share/20211109/GMAP-GSNAP_data/nt_bacteria_db |...)',
              required=True)
@click.option('-gai', '--gsnap_aligndatabase_index',
              help='gsnap_aligndatabase_index_name(nt_bacteria_k16 | nt_virus_k16 | nt_standard_db |...)',
              required=True)
@click.option('-i8', '--gsnap_m8_path',
              help='gsnap_m8_path_name(/home/lijing/all_test/test_202112/K200004870_L01_60_priceseq_dedup_lzw_bowtie2_subsample_gsnapfilter_gsnap.m8 |...)',
              required=True)
@click.option('-r', '--reference', help='accession_file(nucl_gb.accession2taxid/prot.accession2taxid/...)', required=True)
@click.option('-o1', '--outfile1', help='blastn_match_taxid(number_nt_virus_blastn_match_taxid/...)',required=True)#default='result.fa' ,type=float
@click.option('-o2', '--outfile2', help='blastn_match_taxid_totaxid(number_nt_virus_blastn_match_taxid_totaxid(onlytaxid)/...)',required=True)
@click.option('-o3', '--outfile3', help='blastn_match_taxid_totaxid_lineage(number_nt_virus_blastn_match_taxid_totaxid_lineage.txt/...)',required=True)
@click.option('-o4', '--outfile4', help='number_nt_virus_blastn_match_taxid_lineage/..',required=True)
@click.option('-o5', '--outfile5', help='number_nt_virus_blastn_match_taxid_lineage_add_kgs/...',required=True)
@click.option('-o6', '--outfile6', help='number_nt_virus_blastn_match_taxid_lineage_add_kgs_delrepeat/...',required=True)
@click.option('-o7', '--outfile7', help='number_nt_virus_blastn_match_taxid_lineage_add_kgs_delrepeat1/...',required=True)
@click.option('-o8', '--outfile8', help='number_nt_virus_blastn_match_taxid_lineage_add_kgs_delrepeat1_out.txt/...',required=True)
@click.option('-o9', '--outfile9', help='number__nt_bacteria_blastn_match_taxid_lineage_add_kgs_delrepeat1_out_finalout/...',required=True)


def align_output(input_hostfilter_file,docker,gsnap_aligndatabase,gsnap_aligndatabase_index,input_hostfilter_file_name,gsnap_m8_path,reference,outfile1,outfile2,outfile3,outfile4,outfile5,outfile6,outfile7,outfile8,outfile9):
    val1 = os.system("echo '复制文件进入docker进行gsnap比对' && docker cp %s %s:/ && docker exec -it %s /bin/bash -c 'gsnapl -A m8 --batch=0 --use-shared-memory=0 --gmap-mode=none --npaths=100 --ordered -t 36 --max-mismatches=40 -D %s -d %s /%s > temp_gsnap.m8' && docker cp %s:/temp_gsnap.m8 %s " % (input_hostfilter_file,docker,docker,gsnap_aligndatabase,gsnap_aligndatabase_index,input_hostfilter_file_name,docker,gsnap_m8_path ))

    val2=os.system("echo '比对文件输出' && python3 blastn_match_taxid_totaxid_lineage_add_kgs_delrepeat1_out.py -i %s -r %s -o1 %s -o2 %s -o3 %s -o4 %s -o5 %s -o6 %s -o7 %s -o8 %s -o9 %s" % (gsnap_m8_path,reference,outfile1,outfile2,outfile3,outfile4,outfile5,outfile6,outfile7,outfile8,outfile9))

if __name__ == '__main__':
    align_output()