未提供项目说明
genetable的Python项目详细描述
吉纳吉
安装
pip install genetable
或者：
^{pr2}$使用
获取功能
获取基因可用性并绘制出它（即-p）。在
lookfeatures "Alopias vulpinus"coi 47
nd2 14
hsp70 11
12s ribosomal rna 7
trna-leu 6
16s ribosomal rna 6
trna-ser 6
trna-val 5
trna-phe 4
cytb 4
默认情况下，文件名由物种名称和名称组成。如果每个物种有超过200个NCBI id，则每个物种的下载表数量由参数--cache控制。在
lookgenomes
看看基因组元数据
lookgenomes Clupeiformes
accession seq_length conting_n50 sci_name ass_level
GCA_007927625.1 812159898 1632759 Coilia nasus Chromosome
GCF_900700415.1 725670187 1151065 Clupea harengus Chromosome
GCA_900700415.1 725670187 1151065 Clupea harengus Chromosome
GCA_902175115.3 790426535 22496 Clupea harengus Scaffold
GCA_900323705.1 789621745 28410 Clupea harengus Scaffold
GCA_000966335.1 807695261 22277 Clupea harengus Scaffold
GCA_900499035.1 949617276 9398 Sardina pilchardus Scaffold
GCA_003604335.1 641491539 10878 Sardina pilchardus Scaffold
GCA_003651195.1 815647530 129889 Tenualosa ilisha Scaffold
GCA_004329175.1 710279582 1092 Tenualosa ilisha Scaffold
GCF_900700375.1 567401054 3059612 Denticeps clupeoides Chromosome
GCA_900700375.2 567401054 3059612 Denticeps clupeoides Chromosome
GCA_900700375.1 567401054 3059612 Denticeps clupeoides Chromosome
GCA_900700345.2 457704509 384267 Denticeps clupeoides Scaffold
看看吧
查看SRA元数据
looksra Argentiniformes
accession total_bases layout species_name platform is_public lib_strategy lib_source
SRR11679483 1676957378 paired Argentina silus Illumina HiSeq 4000 true WGS GENOMIC
SRR11537143 2577408128 paired Argentina sphyraena Illumina HiSeq 4000 true WGS GENOMIC
ERR3332509 26274979990 paired Opisthoproctus soleatus Illumina HiSeq X Ten true WGS GENOMIC
ERR3332508 26507370802 paired Opisthoproctus soleatus Illumina HiSeq X Ten true WGS GENOMIC
ERR3332507 32283025068 paired Opisthoproctus soleatus Illumina HiSeq X Ten true WGS GENOMIC
ERR3332506 25164048528 paired Opisthoproctus soleatus Illumina HiSeq X Ten true WGS GENOMIC
SRR5997680 4591698120 paired Argentina sp. CUR14063.G Illumina HiSeq 2000 true RNA-Seq TRANSCRIPTOMIC
获取基因组
用包含登录码和物种名称的文件获取基因组。例如，给定以下文件listacc.txt：
cat listacc.txt
GCF_001319825.1,Yersinia wautersii
GCF_000493475.1,Yersinia wautersii
我们可以使用以下方法从该文件中获取基因组：
getgenomes listAcc.txt
head Yersinia_wautersii__GCF_001319825.1/GCF_001319825.1_5139_1_1_genomic.fna
>NZ_CVMG01000001.1 Yersinia wautersii strain WP-931201, whole genome shotgun sequence
ATGGCCCACGGTGGAAAACTGGCCACAGGTTGAGTTGCCGGAACTGCCGCAATGGCTTTTGATTGAAGCGGTCAATCAGG
GTTATATTGTTCCCGACTGGCCGCCAGTCGTATAGGCCTGCCCAACAACCCCTCCAGTCGGGGTTGTTGGTTTCTCTGTT
GTGCCACCCCCCACACAATCCTCATCACCTGCCCCGCGCGCAGTAATCCGGCATCATAGCGAATGAACGCTTAACCGGAG
AAAAACGCATGTCTGCAACCGATTACCACCACGGTGTGCGCGTCATTGAAATCAGCGAAGGCACTCGCCCGATCCGCACT
GTCAGTACGGCGGTAGTCGGGATGGTCTGTACTTCCGATGATGCTGACCCCACTCTGTTCCCACTCAATACCCCGGTATT
ACTCACCGATGTGCTGGCCGCCAGCGGCAAGGCCGGTGAAACCGGCACATTAGCCCATTCACTGGATGCTATCAGCGACC
AAACCAAGCCCGTGACTATTGTTGTCCGCGTGGCTCAGGGGGAAACCGAAGCCGAAACTACCTCCAATATTATCGGCGGC
TCCACGCCAGATGGCCGTTATACCGGCATGAAAGCGCTGTTAGCGGCGCAGGGTAAGTTTGACGTCAAGCCCCGTATTTT
AGGGGTGCCCGGTCATGACACTCTGGCGGTATCCACTGAGCTACTTTCCATCGCTCAGAGCCTACGTGCCTTTGCCTACA
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