蛇形输出文件为列表/表

Question

我已经在我的蛇形文件中写了这个规则

rule extractfeat:
input:
'/path/to/file/{genome}.gbk'
output:
'{genome}_{locus_tag}_{gene}_{substrate}.fasta'
shell:
'''
extractfeat {input} {output} -value {wildcards.genome}_{wildcards.locus_tag} -type CDS -describe product,locus_tag
'''

我想要得到所有的输出文件(这里的输出文件是指file=row)，它们被写在一个单独的文件中，看起来像这样:

genome  locus_tag   gene    substrate
PalbDSM11370    02121   susC    pululan
PalbDSM11370    02122   susD    pululan
PalbDSM11370    01210   susC    arabinan
PalbDSM11370    01209   susD    arabinan
PalbDSM11370    02015   susC    bglukan
PalbDSM11370    02016   susD    bglukan
PpalDSM17968    00934   susC    pululan
PpalDSM17968    00933   susD    pululan
PpalDSM17968    02229   susC    arabinan
PpalDSM17968 02228 susD arabinan
PpalDSM17968 01622 susC bglukan
PpalDSM17968 01623 susD bglukan
PREVCOP 05864 susC pululan
PREVCOP 05865 susD pululan
PREVCOP 05852 susC arabinan
PREVCOP 05851 susD arabinan
PREVCOP 05099 susC bglukan
PREVCOP 05098 susD bglukan
PREVCOP 03646 susC ksiloglukan
PREVCOP 03645 susD ksiloglukan
Psp.AGR2160 00839 susC ksiloglukan

感谢

Answer 1

您可以将其添加为另一个规则，其输入依赖于生成规则的所有输出:

rule tabulate:
input: <ALL THE FASTA FILES>
output: 'table.txt'
run:
wcs = glob_wildcards('{genome}_{locus_tag}_{gene}_{substrate}.fasta')
with open(output[0], 'w') as outfile:
outfile.write('genometlocus_tagtgenetsubstraten')  # header
for row in zip(*wcs):  # order will match order in wildcard string
outfile.write('t'.join(row) + 'n')

或者如果你已经有了这些通配符的列表，你可以直接写，而不是使用glob_wildcards。