Metadata-Version: 2.1
Name: genetable
Version: 0.5
Summary: UNKNOWN
Home-page: https://github.com/Ulises-Rosas/geneTable
Author: Ulises Rosas
Author-email: ulisesfrosasp@gmail.com
License: UNKNOWN
Description: [![pypi](https://img.shields.io/pypi/v/genetable.svg)](https://pypi.python.org/pypi/genetable)
        
        # geneGet
        
        ## Installation
        
        ```shell
        pip install genetable
        ```
        
        Alternatively:
        
        ```Shell
        git clone https://github.com/Ulises-Rosas/geneTable.git
        cd geneTable
        python3 setup.py install
        ```
        
        ## Usage
        
        
        ### getFeatures
        
        Get gene availability and plot it (i.e. `-p`).
        
        ```Shell
        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
        ```
        
        <!-- ![](https://github.com/Ulises-Rosas/geneTable/blob/master/img/Alopias_vulpinus_getFeatures.png)
         -->
        Filnames are composed by using species name as well as its title by default. If there were more than 200 hundred NCBI ids per species, the number of downloaded tables per species is controled with the argument `--cache`.
        
        ### lookgenomes
        
        Look at genome metadata
        
        ```Shell
        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
        ```
        
        ### looksra
        
        Look at SRA metadata
        
        ```Shell
        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
        ```
        
        ### getgenomes
        
        Get genomes with a file containing accession codes and species names. For example, given the following file `listacc.txt` :
        
        ```
        cat listacc.txt
        ```
        ```
        GCF_001319825.1,Yersinia wautersii
        GCF_000493475.1,Yersinia wautersii
        ```
        We can get genomes from that file by using:
        
        ```
        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
        ```
        
        
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Description-Content-Type: text/markdown
